2026-06-26T07:21:50+02:00 https://library.wur.nl/oai

oai:library.wur.nl:wurpubs/8f423e15-0e14-4216-932c-45ce9d89cb6d 2026-06-24 thesis

urn:nbn:nl:ui:32-8f423e15-0e14-4216-932c-45ce9d89cb6d 2026-06-24 urn:nbn:nl:ui:32-8f423e15-0e14-4216-932c-45ce9d89cb6d/mods Building effective patient-centred dietetic treatment for adults with obesity in primary care: from core components, perspectives and practice to co-designing a tailored treatment toolbox : an act to connect Wageningen University dgg van de Riet Annemieke 0000000530410446 aut M.A.E. de van der Schueren opn H. Jager-Wittenaar opn J.A.E. Langius opn B.S. van der Meij opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 350 10.18174/681789 en Obesity is a complex, chronic disease with major consequences for health, society, and the economy. Dietetic treatment can be effective, but outcomes vary widely and many patients discontinue treatment before reaching their goals. Understanding what works for whom is therefore essential. The aim of this thesis was to identify core components of effective dietetic treatment for patients with obesity in primary care, and to use those insights to develop a digital toolbox for dietitians. A mixed-methods approach was used, combining quantitative and qualitative research into dietetic practice.What routine practice and intervention data showTwo retrospective cohort studies showed that approximately one third of patients achieved clinically relevant weight loss (≥5%) within one year. This weight loss occurred primarily early in treatment; most patients who reached the threshold did so within the first three months. More consultations, longer treatment duration, and early engagement were associated with better outcomes.A Qualitative Comparative Analysis of published lifestyle interventions showed that no single intervention component explained weight loss results. A combination of a dietary restriction, physical activity, and behavioural change most often led to successful intervention outcomes.Perspectives of dietitians and patients and what is observed in practiceDietitians emphasised the importance of building a trusting therapeutic relationship, identifying individual patient needs, and applying counselling and behaviour change techniques. Patients valued personalised, responsive support, practical advice, and a respectful, non-judgmental attitude. Both groups emphasised that effective treatment requires more than nutritional guidance alone and must address behavioural, psychological, and contextual factors. Structured observations of dietetic consultations confirmed that while nutrition dominated, behavioural change, physical activity, and psychosocial issues were also regularly addressed. Consultations varied substantially in content and style, reflecting the need for professional judgement rather than standardised pathways. Across all qualitative studies, patient-centred care emerged as the central theme. Effective treatment was characterised by relationship building, empathy, clear communication, shared decision-making, and adaptation to individual circumstances. At the same time, limited consultation time and restricted insurance coverage were identified as important barriers.From evidence to practice through co-designing a toolboxBuilding on these findings, a digital toolbox was co-designed with dietitians and patients using a participatory design thinking approach. The toolbox contains a wide range of practical materials and enables dietitians to select tools tailored to individual patient needs. A feasibility study showed that dietitians rated usability positively and patient-centred care scores were high. However, toolbox use varied considerably and declined over the 18-week study period. Barriers included limited time, lack of routine integration, and fragmented workflows. Sustained use will require strong governance and better embedding in daily practice.ConclusionEffective dietetic treatment for patients with obesity cannot be reduced to fixed pathways or isolated components. Effectiveness depends on connecting core elements of care. The patient–dietitian relationship emerged as a central condition: it supports trust, openness, and sustained motivation. It also provides the foundation for tailoring treatment intensity, behavioural support, and nutritional expertise to individual needs. Understanding what works for whom in dietetic treatment of obesity is, ultimately, an act to connect. VLAG Global Nutrition VLAG Wereldvoeding urn:nbn:nl:ui:32-8f423e15-0e14-4216-932c-45ce9d89cb6d/obj 2026-06-24 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/e5ca6747-4262-42ef-96e8-ab76490d7a0d 2026-06-24 thesis

urn:nbn:nl:ui:32-e5ca6747-4262-42ef-96e8-ab76490d7a0d 2026-06-24 urn:nbn:nl:ui:32-e5ca6747-4262-42ef-96e8-ab76490d7a0d/mods Coldspot, hotspot or heatwave? : The ecology of triazole resistance in Aspergillus fumigatus Wageningen University dgg Kortenbosch Hylke Hessel 0000-0001-7699-6391 0000000530331975 aut B.J. Zwaan opn S.E. Schoustra opn E. Snelders opn B. Auxier opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 200 10.18174/681273 en Aspergillus fumigatus is a pathogenic fungus that everyone in the Netherlands inhales daily. Inhaling this fungus is harmless to most people, but it can cause opportunistic infections in people with a weakened immune system. These infections are treated with triazole antifungals, but A. fumigatus has become more frequently resistant to these medications over the past two decades. Triazoles are used not only in medicine but also in agriculture as fungicides to protect against or treat crops affected by fungal diseases. A. fumigatusis exposed to these fungicides in plant waste heaps where this fungus naturally grows, leading to selection for antifungal resistance. In the first research Chapter, I describe a method to spatially and quantitatively measure airborne triazole resistance for this fungus. In the second research chapter, I studied how airborne abundance and triazole resistance in A. fumigatus varied over roughly two years in Wageningen. In the third research chapter, we used the air-sampling method I developed in this thesis to measure airborne triazole resistance across the Netherlands with the help of hundreds of citizen scientists during the schimmelradar project. In the last research chapter, I brought a mixture of triazole-sensitive and triazole-resistant A. fumigatus isolates, captured during the schimmelradar project, into competition in a grass mesocosm under different fungicide conditions. Through this competition experiment, I provide evidence that even in the absence of triazole fungicides, other non-triazole fungicides can also select for triazole resistance in the environment. An extended version of this summary, one in English ánd one in Dutch, can be found in the thesis. PE&RC Genetics (GEN) PE&RC Genetics (GEN) urn:nbn:nl:ui:32-e5ca6747-4262-42ef-96e8-ab76490d7a0d/obj 2026-06-24 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/1bd9594f-c374-4c17-933e-59e9ae24e93a 2026-06-24 thesis

urn:nbn:nl:ui:32-1bd9594f-c374-4c17-933e-59e9ae24e93a 2026-06-24 urn:nbn:nl:ui:32-1bd9594f-c374-4c17-933e-59e9ae24e93a/mods From space to soil: modelling and mapping soil organic carbon dynamics using machine learning and earth observation Wageningen University dgg Tian Xuemeng 0000000530302293 aut S. de Bruin opn K.M. de Beurs opn M. Herold opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 248 10.18174/682189 en Digital soil mapping (DSM) of soil organic carbon (SOC) has advanced rapidly due to growing demand for climate-relevant soil information, expanding SOC measurements, open data, Earth Observation archives, and machine learning. Yet pan-European 3D+T SOC mapping remains constrained by fragmented data, limited harmonized databases, and computational demands. This thesis develops an operational 30 m, wall-to-wall SOC pipeline for Europe (2000–2022), integrating a cloud-optimized Landsat data cube with harmonized SOC observations. Using Random Forest, Quantile Regression Forest, and neural network approaches, it generates multi-depth SOC density time series with pixel-level uncertainty and extrapolation diagnostics. Results provide the first temporally explicit European SOC baseline at high resolution, though pixel-scale change detection remains limited due to low signal-to-noise ratios. Hybrid soil-informed neural networks improve SOC density reconstruction under sparse bulk density data. Overall, the work clarifies methodological constraints, uncertainty communication needs, and practical limits of large-scale SOC monitoring, supporting more transparent and scalable DSM frameworks. PE&RC Geo-information Science and Remote Sensing PE&RC Geo-information Science and Remote Sensing urn:nbn:nl:ui:32-1bd9594f-c374-4c17-933e-59e9ae24e93a/obj 2026-06-24 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/52057ef1-ce80-4c23-a202-c1c499dc5aa3 2026-06-23 thesis

urn:nbn:nl:ui:32-52057ef1-ce80-4c23-a202-c1c499dc5aa3 2026-06-23 urn:nbn:nl:ui:32-52057ef1-ce80-4c23-a202-c1c499dc5aa3/mods Interaction between acute illness and malnutrition in children in sub-Saharan Africa and South Asia Wageningen University dgg Mudibo Evans O. 0000000530410497 aut S. Kersten opn G.B. Gonzales opn James M. Njunge opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 293 10.18174/682118 en Undernutrition, particularly severe wasting, remains a major contributor to childhood morbidity and mortality in low- and middle-income countries, where infectious diseases such as pneumonia, diarrhoea, malaria, sepsis, tuberculosis and HIV are highly prevalent. Malnutrition and infection interact in a self-reinforcing cycle that increases vulnerability to illness, impairs recovery and contributes to poor survival. However, the biological mechanisms underlying these interactions remain incompletely understood. This thesis investigated the systemic interplay between acute illness, malnutrition and recovery using secondary analyses of two cohorts of acutely ill children from sub-Saharan Africa and South Asia. Multi-omics profiling was integrated with mixed-effects modelling, network analysis and structural equation modelling to characterise biological responses to acute illness, identify determinants of post-discharge outcomes and evaluate biomarkers of immuno-nutritional vulnerability.Using proteomic, metabolomic and lipidomic data from the Childhood Acute Illness and Nutrition (CHAIN) cohort, Chapter 2 characterised biological responses across diverse clinical syndromes, including malaria, diarrhoea, tuberculosis, sepsis, HIV, anaemia and pneumonia. Despite differences in clinical presentation, children exhibited a common response characterised by heightened inflammation, antimicrobial activity and metabolic mobilisation, alongside suppression of pathways involved in growth, bone mineralisation and tissue repair. Distinct syndrome-specific signatures were also observed. Severe wasting amplified catabolic processes, altered lipid and amino acid metabolism and modified immune responses, demonstrating that malnutrition substantially shapes host responses to illness.Chapter 3 examined whether biological disturbances persist after hospital discharge among children recovering from complicated severe malnutrition. In a nested case-control study of Kenyan children, those who subsequently died during convalescence displayed persistent inflammation, immune dysregulation, endothelial dysfunction and coagulation abnormalities at two months post-discharge. These biological patterns closely resembled acute-phase responses, indicating that clinical recovery often occurs in the absence of complete physiological restoration. The findings suggest that unresolved biological disturbances contribute to the high burden of post-discharge mortality.Chapter 4 focused on HIV as a chronic infectious condition that may further impair recovery among severely wasted children. Analysis of over 7,000 plasma proteins showed that HIV influenced post-discharge growth indirectly through reduced baseline nutritional status and alterations in pathways related to bone mineralisation, growth factor signalling and humoral immunity. These findings demonstrate that chronic infection can sustain biological vulnerability during recovery and contribute to poor growth outcomes through specific molecular mechanisms.Chapter 5 evaluated the prognostic nutritional index (PNI), derived from serum albumin and lymphocyte counts, as a biochemical marker of immuno-nutritional vulnerability. Among 2,694 acutely ill children, PNI distinguished severe malnutrition, predicted hospital length of stay and correlated with multi-omic signatures of anabolic, reparative and immune-regulatory processes. Lower PNI values were associated with inflammation, catabolic stress and metabolic disruption, suggesting that PNI captures biological dimensions of vulnerability not reflected by anthropometric measures alone.Overall, this thesis demonstrates that acute illness and malnutrition are interconnected manifestations of systemic biological dysregulation. The findings reveal shared and persistent pathways linking illness, mortality and impaired growth, supporting the development of biology-guided risk stratification and targeted interventions to improve recovery and long-term outcomes among vulnerable children in resource-limited settings. VLAG Nutrition, Metabolism and Genomics VLAG Voeding, Metabolisme en Genomica urn:nbn:nl:ui:32-52057ef1-ce80-4c23-a202-c1c499dc5aa3/obj 2026-06-23 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/29cfa295-a848-4ca2-8cc8-6c207d25a423 2026-06-23 thesis

urn:nbn:nl:ui:32-29cfa295-a848-4ca2-8cc8-6c207d25a423 2026-06-23 urn:nbn:nl:ui:32-29cfa295-a848-4ca2-8cc8-6c207d25a423/mods Going full circle : a multi-stakeholder approach to risk analysis of recycled food contact materials Wageningen University dgg van der Linden Niels 0009-0007-6741-9606 0000000530410390 aut P.A. Luning opn H. Schebesta opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 312 10.18174/681474 en Europe is transitioning to a circular economy, in which waste is (re)used as a resource for new cycles. However, the circular economy is a double-edged sword. Despite its potential environmental benefits, it can also introduce potential food risks. This thesis investigates how risk analysis of food contact materials can be improved in the context of the transition to the circular economy. The results highlight that assessing the impact of recycling on risk analysis is highly complex and mainly suffers from a lack of data, which is made worse by the unpredictable mixtures that can be formed during recycling. The networks that exist to perform risk analysis are also very complex, and have very different structures between EU Member States. Bringing together different stakeholders from these networks, potential solutions were developed, including a roundtable to discuss how different stakeholders experience different barriers to circularization. First steps in overcoming these barriers include setting up a platform to exchange risk analysis data. VLAG Food Quality and Design VLAG Food Quality and Design urn:nbn:nl:ui:32-29cfa295-a848-4ca2-8cc8-6c207d25a423/obj 2026-06-23 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/f32a4dea-4290-4e51-8bee-a6733e02c220 2026-06-22 thesis

urn:nbn:nl:ui:32-f32a4dea-4290-4e51-8bee-a6733e02c220 2026-06-22 urn:nbn:nl:ui:32-f32a4dea-4290-4e51-8bee-a6733e02c220/mods Between stomata and clouds : Unveiling vegetation-atmospheric boundary layer interactions with high resolution observations and modeling Wageningen University dgg González Armas Raquel 0000000523483591 aut J. Vila-Guerau de Arellano opn H.J. de Boer opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 206 10.18174/681656 en Vegetation and atmosphere interact by exchanging energy, water and carbon. Yet, uncertainties remain in how these exchanges are represented in Earth system models, particularly regarding their diurnal evolution, vertical variability within canopies, and sensitivity to clouds. This dissertation addresses these gaps by integrating observations and modeling, linking leaf-scale processes to canopy and atmospheric dynamics. Modeling approaches range from a conceptual atmospheric model to canopy-resolving Large Eddy Simulations. Study cases represent three contrasting ecosystems: an agricultural field, a tropical rainforest, and a temperate forest. Results show that diurnal variations in ecosystem water and CO₂ exchange are strongly controlled by radiation, temperature, and vapor pressure deficit. Within-canopy stratification can decouple lower canopy layers from the overlying atmosphere, affecting residence times. A multi-spectral canopy radiative transfer scheme is also developed, enabling analysis of spectral influences on microclimate and photosynthesis. Overall, the findings highlight the need to better represent diurnal, vertical, and cloud-related processes in land-atmosphere models and demonstrate the value of canopy-resolving approaches. WIMEK Meteorology Meteorology and Air Quality WIMEK Meteorologie Meteorologie en Luchtkwaliteit urn:nbn:nl:ui:32-f32a4dea-4290-4e51-8bee-a6733e02c220/obj 2026-06-22 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/d999f7bb-d0dc-4070-a48c-ead99b1ede20 2026-06-22 thesis

urn:nbn:nl:ui:32-d999f7bb-d0dc-4070-a48c-ead99b1ede20 2026-06-22 urn:nbn:nl:ui:32-d999f7bb-d0dc-4070-a48c-ead99b1ede20/mods Food system transitions in lower and middle-income countries : Exploring the missing middle in the cases of Vietnam Wageningen University dgg Nguyen Quoc 0000-0002-2717-4700 0000000530457789 aut P. Oosterveer opn I.D. Brouwer opn R. Vignola opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 234 10.18174/680985 en Food systems in low- and middle-income countries (LMICs) face complex, interconnected challenges as they transition towards more sustainable futures. Despite notable progress, persistent and emerging problems remain: food safety risks, the triple burden of malnutrition, socio-economic inequities, environmental degradation, and climate change impacts. Overcoming these requires food systems governance to shift beyond single-sector interventions toward more holistic, coordinated approaches. Such coordination is frequently undermined by critical disconnects operating both horizontally - across production, distribution, and consumption - and vertically - between global or national agendas and local implementation. This thesis conceptualizes these disconnects as the "Missing Middle." The research is based on case studies in Vietnam, with primary empirical fieldwork conducted between 2020 and 2023 in Hưng Yên Province and Hanoi, examining pork and vegetable commodity chains that are central to Vietnamese diets and rural livelihoods yet continue to face critical food safety challenges. The thesis employs two complementary theoretical lenses: Social Practice Theory (SPT), focusing on micro-level changes in the everyday practices of food system actors, and Transition Theory, particularly the Multi-Level Perspective (MLP) and Strategic Niche Management (SNM), which investigates macro-level dynamics across landscape, regime, and niche levels. Multiple methods were deployed, including scoping reviews, semi-structured interviews, surveys, observations, and stakeholder consultations. The thesis includes four empirical chapters examining overall food system transitions, changes in small-scale vegetable and pork practices, and the development and diffusion of agri-food certification niches. Together, these reveal how disconnects emerge through complex interactions across levels and segments, and how they can be understood and addressed in LMIC contexts. Environmental Policy WASS Milieubeleid WASS urn:nbn:nl:ui:32-d999f7bb-d0dc-4070-a48c-ead99b1ede20/obj 2026-06-22 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/9fc7ac7b-fdf2-4bc6-8a31-416772d04b4f 2026-06-22 thesis

urn:nbn:nl:ui:32-9fc7ac7b-fdf2-4bc6-8a31-416772d04b4f 2026-06-22 urn:nbn:nl:ui:32-9fc7ac7b-fdf2-4bc6-8a31-416772d04b4f/mods Detecting the undetectable : DIY sample preparation and infrared spectroscopy for portable mycotoxin analysis Wageningen University dgg Bosman Anouk Julia 0000000530457834 aut M.W.F. Nielen opn J.G.M. Janssen opn G.Ij. Salentijn opn F.S. Ruggeri opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 199 10.18174/681613 en Access to safe and sufficient food is a basic human right. However, ensuring that everyone has access to safe food is still a major global challenge. This is not only due to limitations in food testing methods, but also because of many interconnected factors such as population changes, climate change, transport and storage systems, and economic stability. Food safety testing plays a crucial role in this system. It acts as the “eyes and ears” of the food chain by providing information about the quality and safety of food. This information helps governments, companies, and regulators make decisions that protect public health and maintain trust in food markets. In this thesis, I focus on improving how we detect mycotoxins, which are harmful substances produced by fungi. These toxins commonly contaminate crops and food products and are very difficult to completely prevent. Because of this, reliable detection methods are essential. Traditionally, food safety testing is done in laboratories using advanced analytical methods. While these methods are accurate, they are often time-consuming, expensive, and require specialized equipment and trained personnel. Recently, there has been a growing interest in making food testing more portable and accessible, so that it can be done directly in the field, during production, or at storage sites. For such portable testing to work well, it is important that the methods are simple, fast, and easy to use. One promising technology for this is infrared (IR) spectroscopy, which uses light to measure the chemical composition of materials. IR spectroscopy is already widely used to assess food quality and can be applied in real time during production. However, detecting mycotoxins with IR spectroscopy is challenging. These toxins are often present in very low concentrations, making them difficult to measure directly in foods with sufficient accuracy. This is why the thesis is called “Detecting the Undetectable”. In this work, IR spectroscopy is explored in depth to see how it can be improved or adapted to directly detect mycotoxins in food. In addition, 3D-printing technologies are explored to provide a complete sample-to-result workflow that allows for user-friendly sample preparation. The ultimate goal is to contribute to portable, easier, and more widely available food safety testing methods, helping to better protect consumers around the world. VLAG Organic Chemistry VLAG Organische Chemie urn:nbn:nl:ui:32-9fc7ac7b-fdf2-4bc6-8a31-416772d04b4f/obj 2026-06-22 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/e1522162-d04e-4c3e-8adf-397681c6f822 2026-06-22 thesis

urn:nbn:nl:ui:32-e1522162-d04e-4c3e-8adf-397681c6f822 2026-06-22 urn:nbn:nl:ui:32-e1522162-d04e-4c3e-8adf-397681c6f822/mods Standardizing chepa shutki - a traditional fermented fish product from Bangladesh Wageningen University dgg Farhana Jasmin Ara 0000000530457869 aut S.E. Schoustra opn B. Zwaan opn O. van Mastrigt opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 186 10.18174/681839 en Chepa shutki is a widely consumed traditional fermented fish product of Bangladesh. It plays an important role in local diets and economies. The unique production process of chepa shutki involves spontaneous fermentation of fish with no additives. Despite its cultural and nutritional importance, chepa shutki production remains unstandardized due to insufficient information on the production process and the impact of processing variations on the flavour, safety and microbial communities of chepa shutki. Firstly, this thesis documents current processing methods of chepa shutki and identifies the vital process parameters such as types of fish, types of fermentation container (old/new) and fermentation time. Chepa shutki is produced from different small fish (Puntius, Setipinna and Otolithoides) referred to as punti, phaisha and puma type, respectively. Among these, the punti type is produced the most and puma type the least. The fermentation duration varies from three to twelve months. Secondly, locally collected chepa shutki samples were analysed for the physicochemical properties, aroma and bacterial community. Tetragenococcus and Staphylococcus were identified and key genera in the communities, wich are selected by the combination of anaerobic conditions and relatively low water activity. Most processing parameters were associated with one or more aroma groups, with fish type showing the strongest effect. Fish type and district significantly influenced bacterial communities. However, limited correlation between bacterial communities and aroma suggests functional redundancy among bacterial species. These findings highlight key processing parameters shaping functional properties of chepa shutki. Thirdly, the impact of the fish soaking time, fermentation time and endogenous starter culture on Puntius fermentation were examined. Bacterial growth was affected by different water soaking times, but the starter culture had limited effect on the fermentation outcome. Both fermentation time and water soaking time significantly influenced aroma production suggesting high quality chepa shutki can be consistently produced by standardizing the production method, particularly fermentation time and water soaking time. Lastly, this thesis examines the impact of the processing method on the safety of chepa shutki, in particular on the histamine content. Histamine contents in collected chepa shutki samples were highly variable and sometimes exceeded regulatory limits. High histamine contents were associated with punti chepa sthuki, the district Kishoregonj and a high pH. In conclusion, this thesis provides comprehensive insights into the current processing method of chepa shutki. By identifying how key processing parameters such as fermentation time and water activity shape the flavour and safety of chepa shutki, this research paves the way to standardize traditional chepa shutki production, enhancing the quality of this fermented fish product for local producers and consumers. PE&RC Genetics (GEN) PE&RC Genetics (GEN) urn:nbn:nl:ui:32-e1522162-d04e-4c3e-8adf-397681c6f822/obj 2026-06-22 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/d11a6a1d-e0b2-4e43-a6d7-741c50f5e313 2026-06-22 thesis

urn:nbn:nl:ui:32-d11a6a1d-e0b2-4e43-a6d7-741c50f5e313 2026-06-22 urn:nbn:nl:ui:32-d11a6a1d-e0b2-4e43-a6d7-741c50f5e313/mods Carbon against PFAS : Adsorption at low concentration Wageningen University dgg Pranić Marko 0000000530457738 aut A. van der Wal opn J.E. Dykstra opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 283 10.18174/681560 en The removal of per- and polyfluoroalkyl substances (PFAS) by activated carbon under drinking-water treatment conditions was investigated in this PhD Thesis. The work was motivated by increasingly stringent PFAS regulations, the growing relevance of short-chain PFAS, and the limited performance of granular activated carbon (GAC) filters at environmentally relevant concentrations. Through batch and column experiments combined with mechanistic modelling, this Thesis provides a framework to understand the factors limiting PFAS adsorption and identifies strategies to improve treatment performance. A central finding is that PFAS adsorption behaves fundamentally differently at environmentally relevant concentrations than at the elevated concentrations commonly studied in the literature. Adsorption isotherm parameters were strongly dependent on the initial PFAS concentration. Isotherms derived at µg/L–mg/L concentrations substantially overestimate adsorption capacity at ng/L levels because high concentrations promote cooperative adsorption phenomena such as aggregation and multilayer formation. Consequently, adsorption data obtained at elevated concentrations cannot be directly extrapolated to drinking-water applications. PFAS adsorption kinetics were inherently slow under drinking-water conditions. Intraparticle transport was governed primarily by surface diffusion rather than pore diffusion. PFAS transport decreased at lower concentrations, when more adsorption sites were available, and in carbons with larger mesopore volumes. As a result, long equilibration times in batch systems and long empty bed contact times in column systems are required for effective PFAS removal. Competitive adsorption between PFAS was identified as a key mechanism controlling removal performance. Long-chain PFAS consistently outcompete short-chain PFAS due to stronger hydrophobic interactions, often resulting in desorption of previously adsorbed short-chain compounds. The influence of GAC properties was clarified by separating the effects of pore structure, surface chemistry, and transport limitations. A higher micropore surface area did not improve PFAS adsorption because slow intraparticle transport limits micropore utilization. Instead, mesopores dominated adsorption performance. Surface chemistry also influenced adsorption, with carbons containing fewer acidic surface groups or exhibiting a net positive surface charge showing enhanced PFAS adsorption. Natural organic matter (NOM) was identified as the dominant factor limiting PFAS adsorption. NOM reduced adsorption capacity by at least an order of magnitude, with low-molecular-weight fractions exerting the strongest competitive effects. These findings explain rapid PFAS breakthrough in GAC filters and demonstrate the importance of controlling NOM. Increasing temperature reduced adsorption of short-chain PFAS, whereas long-chain PFAS adsorption was largely unaffected, suggesting that short-chain PFAS removal may vary seasonally. To improve PFAS removal, the results indicate that GACs with high mesopore volume and favorable surface charge should be selected, while competing NOM should be removed through biological treatment or combined ozonation–biological processes. Electroregeneration was shown to preferentially desorb and concentrate short-chain PFAS, demonstrating its potential as a more sustainable alternative to frequent thermal reactivation. Overall, this Thesis demonstrates that PFAS removal by GAC at drinking-water concentrations is constrained by low influent concentrations, slow intraparticle transport, competition from NOM and co-occurring PFAS, and temperature effects. By linking these limitations to measurable material properties and operating conditions, this work provides a mechanistic basis for improving PFAS treatment and regeneration strategies. WIMEK Environmental Technology WIMEK Milieutechnologie urn:nbn:nl:ui:32-d11a6a1d-e0b2-4e43-a6d7-741c50f5e313/obj 2026-06-22 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/12c2728e-d84d-4f6f-a06f-c8c4638e7c04 2026-06-19 thesis

urn:nbn:nl:ui:32-12c2728e-d84d-4f6f-a06f-c8c4638e7c04 2026-06-19 urn:nbn:nl:ui:32-12c2728e-d84d-4f6f-a06f-c8c4638e7c04/mods Nutritional strategies to modulate gut health and improve well-being : Insights from randomized controlled intervention studies Wageningen University dgg van den Belt Maartje 0000000530457850 aut B.J.M. Witteman opn N.M. de Roos opn Nicole J.W. de Wit opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 243 10.18174/682065 en Optimal gastrointestinal functioning, including a healthy stool pattern, is essential for overall health and well-being. Disruptions in stool patterns are common in the general population and especially prevalent in people with gastrointestinal disorders such as irritable bowel syndrome (IBS). These disturbances negatively affect quality of life, increase the risk of chronic disease, and create significant socioeconomic burden. Specific diets and nutritional supplements are promising strategies to modulate gut health by their impact on gut microbiota, immune function, and gastrointestinal symptoms. However, better mechanistic insight from well-designed randomized controlled trials (RCTs) is needed. This thesis investigated diet–gut health interactions through four RCTs across different populations. Chapters 2–4 focused on targeted dietary supplements in IBS patients, while Chapters 5–6 examined whole-diet interventions in healthy adults. Chapter 2 reported on an RCT involving 180 IBS patients with predominant constipation (IBS-C). Participants received either acacia fibre (AF), the probiotic Bifidobacterium animalis subsp. lactis (BLa80), or placebo for four weeks. Both AF and the probiotic increased stool frequency, while the probiotic also reduced overall IBS symptom severity. Stool consistency, stool mass, and quality of life measures did not differ between groups. Chapter 3 examined whether four supplements with expected bifidogenic effects could increase Bifidobacterium abundance in 70 IBS patients over four weeks. No significant increases were observed compared with placebo, nor were there notable changes in overall microbiota composition, short-chain fatty acids, or IBS symptoms. The lack of effect may relate to high baseline Bifidobacterium levels, substantial inter-individual variability, and the relatively small sample size. Chapter 4 used a crossover design to test whether three-day turmeric supplementation affected fasting and postprandial levels of LPS, Apo-B48, and triglycerides in 18 IBS-D or IBS-M patients following a high-fat challenge. Turmeric reduced postprandial Apo-B48 and triglycerides, suggesting a potential to attenuate lipid-mediated inflammatory responses. Although postprandial LPS was unchanged, a trend toward lower fasting LPS suggests a potential anti-inflammatory effect. Chapters 5 and 6 explored an 8-week high-fibre or high-fermented-food diet, combined with targeted supplements, in healthy adults. Citizen science elements were used to stimulate behaviour change. Both groups increased intake of fibre or fermented foods during the intervention, with partial retention at 3 months. Each diet produced distinct changes in gut microbiota composition. Fermented foods did not alter microbiota alpha-diversity, while the high-fibre diet slightly reduced it. The high-fibre diet improved sleep quality and increased transit time, and the fermented-food diet modulated immune responses. Across studies, strong placebo effects were seen in IBS patients, especially for subjective outcomes, highlighting the need for placebo-controlled designs. High inter-individual variability in biomarkers, microbiota, and transit time suggests that personalized or targeted nutritional approaches may be more effective than general dietary recommendations. Overall, this thesis demonstrates both the promise and complexity of using dietary strategies to improve gut health. Future research should prioritize rigorous trial designs, mechanistic insights, and personalized approaches using innovative, non-invasive tools. VLAG Nutrition and Disease Food, Health & Consumer Research VLAG Voeding en Ziekte Food, Health & Consumer Research urn:nbn:nl:ui:32-12c2728e-d84d-4f6f-a06f-c8c4638e7c04/obj 2026-06-19 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/c252f170-f43b-4f71-9474-8b7c77ae94c0 2026-06-26 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-c252f170-f43b-4f71-9474-8b7c77ae94c0 2026-06-26 urn:nbn:nl:ui:32-c252f170-f43b-4f71-9474-8b7c77ae94c0/mods Root microbiomes under stress: from assembly to function Wageningen University dgg Carracedo Lorenzo Zulema 000000053039487X aut M. Dicke opn C. Testerink opn K.J. Kloth opn R.B. Karlova opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 268 10.18174/681289 en During their lifetime, plants are continuously challenged by a range of abiotic and biotic stresses. Although chemical fertilizers and pesticides have traditionally been used to improve crop performance, there is growing interest in environmentally friendly alternatives. Root-associated microorganisms have been recognized for their capacity to enhance plant growth and stress resilience and are increasingly considered promising biostimulants for sustainable agriculture. This thesis investigated how the root microbiome responds to (a)biotic stress and explores the mechanisms through which beneficial microbes alleviate stress. In Chapter 2, I took the first step towards understanding how drought stress shapes root-associated microbial communities. Using Arabidopsis thaliana and Solanum lycopersicum, exposed to different drought intensities, changes in both the endosphere and rhizosphere microbiomes were characterized. Microbiome composition was strongly influenced by host identity, root compartment, and drought severity. Although both plant species showed broadly similar patterns under drought, species-specific responses were also observed. These findings are consistent with previous reports of shared drought-induced microbiome shifts, suggesting conserved mechanisms of microbial recruitment across plant families. Chapter 3 focused on uncovering the mechanisms by which beneficial microorganisms alleviate drought stress. Arabidopsis thaliana and Brassica oleracea were exposed to volatile organic compounds (VOCs) emitted by three Pseudomonas strains, including the well-characterized plant-growth-promoting strain P. simiae WCS417. In all systems, Pseudomonas VOCs enhanced plant growth under drought. Transcriptomic analyses revealed substantial changes in plant gene expression, and root microbiome profiling showed shifts toward communities more similar to those of well-watered plants. GC-MS analyses further identified candidate bacterial volatiles that may underlie these beneficial effects. These results highlight the importance of microbial VOCs in cross-kingdom communication and their potential use as plant stimulants. To explore how plant defences influence root microbiome assembly, Chapter 4 examined the rhizosphere microbiome composition of 22 wild and domesticated Brassicaceae species in response to aboveground phytohormone-induced biotic stress. Because plants activate distinct hormonal pathways, involving salicylic acid (SA) or jasmonic acid (JA), depending on the type of herbivorous insect, we investigated the effects of aboveground SA- and JA-pathway activation on the rhizosphere microbiome composition. Each phytohormone triggered distinct shifts in both bacterial and fungal communities, with most responsive taxa being pathway-specific. Moreover, the SA-induced microbiome exhibited a phylogenetic signal, suggesting evolutionarily conserved mechanisms of microbiome assembly under biotic stress in the Brassicaceae family. Finally, in Chapter 5, I tested whether stress-enriched bacteria are beneficial under stress conditions. A stress-enriched synthetic community (SE-SynCom), composed of strains enriched under drought stress and/or SA treatment in Brassicaceae plants, was evaluated under drought, aphid infestation, and their combination. The SE-SynCom did not improve plant resilience to any stress, but instead increased leaf surface area and C content in control conditions and plant susceptibility to aphids under drought. Microbiome analyses showed that although all SE-SynCom members persisted in soil, only a subset colonized the plant roots, and their abundances varied depending on the stress condition. These findings suggest that stress-enriched microbes are not necessarily beneficial for stress resilience and highlight the complexity of designing SynComs that can enhance multi-stress tolerance. EPS Entomology (ENT) Plant Physiology (PPH) EPS Entomology (ENT) Plant Physiology (PPH) urn:nbn:nl:ui:32-c252f170-f43b-4f71-9474-8b7c77ae94c0/obj 2026-06-26 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/601bf9ea-a518-4a19-8993-1c133a69ff71 2026-06-26 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-601bf9ea-a518-4a19-8993-1c133a69ff71 2026-06-26 urn:nbn:nl:ui:32-601bf9ea-a518-4a19-8993-1c133a69ff71/mods Subsurface water reuse: insights into the occurrence, fate, and transformation of organic micropollutants Wageningen University dgg Ore Alessia aut N.B. Sutton opn A.P. van Wezel opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 263 10.18174/681675 en Freshwater scarcity increasingly challenges the stability and reliability of water supply systems. This situation is expected to worsen due to climate change and population growth. Water reuse is therefore essential to reduce the gap between demand and supply, but improved water management strategies are necessary. The subsurface has great potential for water reuse, providing natural storage for surplus water during wet seasons and improving water quality through soil passage. Managed aquifer recharge (MAR) technologies ensure a more stable quantity and a higher quality of water for drinking water production compared to direct use of surface water. Different water sources can be infiltrated in MAR, such as treated wastewater and surface water. However, these sources often contain organic micropollutants (OMPs) that may compromise the groundwater quality. OMPs are a wide range of chemicals, including pharmaceuticals, pesticides, industrial chemicals, and their transformation products (TPs), which can be detected in the environment at concentrations ranging from ng/L to µg/L. Although some are included in water quality monitoring programs, regulatory frameworks target only a limited subset of OMPs, overlooking numerous potentially hazardous compounds, particularly TPs. A more complete characterization of reused water sources is needed to establish safe and sustainable water reuse. Moreover, the fate of OMPs entering the subsurface remains uncertain. Many factors play a role in determining whether OMPs are transported unchanged with the water flow, retained in soil and aquifers, or (further) transformed into TPs. These factors include molecular properties (e.g., charge state) and environmental conditions (e.g., subsurface redox conditions). The extent of their influence on OMP fate and transformation needs further investigation, especially under anaerobic conditions typical of the subsurface. This thesis aimed to provide new insights into the occurrence and fate of OMPs and their TPs in reused water and in the subsurface. To achieve this, we combined field investigations and laboratory experiments to better understand the range of OMPs present in reused water, their transport and transformation processes in the subsurface, and the environmental factors influencing OMP transformation. This integrated approach relied on advanced methods, including target and non-target analytical techniques and in-silico prediction methods. Throughout our study, TPs emerged as widespread yet overlooked in water reuse systems. Although our assessment showed that generally TPs produced are less toxic, more biodegradable, and more mobile than the respective parent compounds, some exceptions were observed, highlighting the need for a better representation of TPs in monitoring programs, regulatory frameworks, and standardized persistence assessment. Likewise, in situ environmental conditions should be better considered in the standardized tests. This thesis demonstrated how microbial community characteristics and redox conditions influence the fate of OMPs in the subsurface, dictating their persistence or biodegradation potential. As the subsurface is mainly an anaerobic environment, with redox-shifting layers and consequently different microbial communities, it is important to further unravel OMP biodegradation and TP formation dynamics in such environments. These insights will provide a more realistic understanding of OMP fate in water (re)cycle, supporting a safer and more sustainable water reuse to meet the increasing freshwater demands. WIMEK Environmental Technology WIMEK Milieutechnologie urn:nbn:nl:ui:32-601bf9ea-a518-4a19-8993-1c133a69ff71/obj 2026-06-26 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/a7a24a79-db61-42d4-8b1e-bed845f3260c 2026-06-25 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-a7a24a79-db61-42d4-8b1e-bed845f3260c 2026-06-25 urn:nbn:nl:ui:32-a7a24a79-db61-42d4-8b1e-bed845f3260c/mods Improving North Sea biodiversity monitoring using novel molecular approaches : A strategy based on Nanopore sequencing Wageningen University dgg Doorenspleet Karlijn aut A.J. Murk opn R. Nijland opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 337 10.18174/681198 en The North Sea is a highly productive, yet heavily used sea, with industry putting substantial pressure on its ecosystems. In response, various conservation, restoration, and nature-inclusive industry measures have been implemented, requiring robust and transparent monitoring. eDNA metabarcoding is highly promising for assessing marine biodiversity, and long-read sequencing platforms like Oxford Nanopore could improve marine monitoring. In this thesis, new molecular platforms and methods were validated and applied to explore biodiversity in natural and artificial habitats of the North Sea. Chapter 2 presents metabarcoding results for benthic biodiversity in the Belgian North Sea, comparing Oxford Nanopore sequencing with Illumina MiSeq and NovaSeq metagenomics. Using a COI primer, Nanopore and MiSeq showed similar alpha and beta diversity levels and consistent community structures. But mismatches with morphological findings remain. In contrast, NovaSeq metagenomics showed differences and had a weak correlation with morphological abundance data. Overall, nanopore metabarcoding is a viable alternative to Illumina MiSeq for macrobenthos biodiversity. Chapter 3 describes a long-read eDNA metabarcoding method using a 2kb fish mitochondrial primer and presents the DECONA pipeline to manage nanopore errors. Results from this primer were compared with the universal 150 bp MiFish primer. Mock communities and aquarium eDNA showed better species resolution with the 2kb fragment. However, North Sea reef samples yielded more detections with MiFish, likely due to the rapid degradation of longer fragments, highlighting long-read metabarcoding's potential to provide more temporally accurate signals. In chapter 4, short-read eDNA, long-read eDNA, and short-read eRNA were evaluated to assess how nucleic acid type and length represent the vertebrate community of a natural Modiolus modiolus reef. 2 kb fragments had the lowest detectability, and short-read metabarcoding detected the highest diversity and was the only method to distinguish high- and low-reef-density communities. eRNA was similar to short-read eDNA but missed many large vertebrates, such as sharks and rays, indicating that it may reflect the active benthic community. Chapter 5 reviews tools for monitoring North Sea biodiversity, focusing on molecular methods like species-specific assays, eDNA metabarcoding, and metagenomics. It covers improvements, new DNA/RNA techniques, database challenges, and integrating these methods into long-term monitoring. Chapter 6 applies metabarcoding to study marine vertebrate diversity in a mixed shellfish reef in the Dutch Voordelta and an M. modiolus reef in Scotland, to evaluate their role as essential fish habitats. Stations inside and outside the reef were compared using eDNA and baited remote underwater video (BRUVs). This chapter shows that vertebrate diversity was consistently highest inside the reef and included reef-associated species such as gobies, gunnels, and clingfish, as well as commercially important species. eDNA detected more species overall, but BRUVs captured different life stages, demonstrating the importance of using complementary methods for monitoring. Chapter 7 summarizes the thesis outcomes, showing that nanopore metabarcoding matches Illumina for macrobenthos assessment, while long-read and eRNA metabarcoding improve species detection and active community analysis. eDNA reveals biodiversity patterns related to reef density and natural reefs. Overall, it underscores the value of these methods for standardized, non-invasive North Sea monitoring. Marine Animal Ecology WIMEK Mariene Dierecologie WIMEK urn:nbn:nl:ui:32-a7a24a79-db61-42d4-8b1e-bed845f3260c/obj 2026-06-25 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/267ffe39-4c52-485c-bd43-aea17aae6f25 2026-06-19 thesis

urn:nbn:nl:ui:32-267ffe39-4c52-485c-bd43-aea17aae6f25 2026-06-19 urn:nbn:nl:ui:32-267ffe39-4c52-485c-bd43-aea17aae6f25/mods What the fish leave behind : Diet-driven loops in recirculating aquaculture systems Wageningen University dgg Syropoulou Elisavet 0000000530410374 aut D. Sipkema opn J.W. Schrama opn F. Kokou opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 183 10.18174/681316 en Aquaculture is growing rapidly, but the availability of traditional feed ingredients like fish meal is limited. To meet demand, aquafeeds increasingly include alternative ingredients such as insect meal, seaweeds, and byproducts. These ingredients often contain more carbohydrates, which can be challenging to digest for carnivorous fish like European seabass and gilthead seabream. As a result, higher dietary carbohydrate levels can reduce fish growth and increase faecal waste production. While the effects on growth are well documented, the consequences for solid waste are often overlooked. This is particularly relevant in water-reuse systems such as recirculating aquaculture systems (RAS), where waste accumulation promotes microbial growth and deteriorates water quality, potentially compromising fish welfare. This PhD project took a holistic approach to investigate how different carbohydrate sources influence faecal production, waste buildup, and microbial communities in both the fish and the aquaculture environment. The results provide guidance for selecting feed ingredients that not only support fish growth but also improve solid waste management and RAS functioning. WIAS Aquaculture biology and Fisheries ecology Microbiology WIAS Aquaculture biology and Fisheries ecology Microbiology urn:nbn:nl:ui:32-267ffe39-4c52-485c-bd43-aea17aae6f25/obj 2026-06-19 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/c8c0d419-a74f-417a-aa54-5591dbf166b2 2026-06-22 thesis

urn:nbn:nl:ui:32-c8c0d419-a74f-417a-aa54-5591dbf166b2 2026-06-22 urn:nbn:nl:ui:32-c8c0d419-a74f-417a-aa54-5591dbf166b2/mods A Portrait Under Ultraviolet : Physiological and Biochemical Responses in Medicinal Cannabis Wageningen University dgg Contreras Avilés C.W. 0000000530410470 aut L.F.M. Marcelis opn E. Heuvelink opn I.F. Kappers opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 188 10.18174/682037 en Cannabis sativa L. is a plant producing health-affecting specialized metabolites including terpenoids, cannabinoids, and flavonoids. Terpenoids and cannabinoids are abundantly produced in cannabis flowers, whereas flavonoids accumulate in both flowers and leaves. Light is of paramount relevance because it is the major driver of photosynthesis and thus influences growth, morphology, and specialized metabolism. Light spectrum has been used to modulate specialized metabolism via photoreceptor signaling involved in the regulation of the biosynthesis of specialized metabolites. In medicinal cannabis cultivation, UV is used to potentially enhance the production of terpenoids, cannabinoids, and flavonoids in leaves and inflorescences, though underlying mechanism are poorly understood. Therefore, this thesis evaluates the effect of different UV spectra and doses in medicinal cannabis growth, morphology, physiology, and specialized metabolism. It is concluded that UVB strongly stimulates pigments, sesquiterpenoids, and flavonoids accumulation and profiles. UVB application in medicinal cannabis cultivation poses a useful horticultural strategy to increase floral quality by enhancing the production of glycosylated flavonoids. Horticulture and Product Physiology (HPP) PE&RC Plant Physiology (PPH) Horticulture and Product Physiology (HPP) PE&RC Plant Physiology (PPH) urn:nbn:nl:ui:32-c8c0d419-a74f-417a-aa54-5591dbf166b2/obj 2026-06-22 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/54e8b1a3-6b23-428a-a366-03b9e87f89c6 2026-06-19 thesis

urn:nbn:nl:ui:32-54e8b1a3-6b23-428a-a366-03b9e87f89c6 2026-06-19 urn:nbn:nl:ui:32-54e8b1a3-6b23-428a-a366-03b9e87f89c6/mods The two sides of the same coin: introduction of technology in SMEs Wageningen University dgg Silva de Mattos Camila 0000000530332003 aut W. Dolfsma opn G. Hagelaar opn G. Pellegrini opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 187 10.18174/681113 en The rapidly evolving global business environment, shaped by technological advances, regulatory changes, increasing competition, and disruptions such as COVID-19 and the Fourth Industrial Revolution, has intensified the pressure on small and medium-sized enterprises (SMEs) to innovate and adapt. In this context, technological transformation has become essential for SMEs seeking to remain competitive and survive. Despite its growing relevance, there remains a limited understanding of how SMEs can effectively manage this process in an integrated manner. This thesis addresses the overarching research question: How can an integrative framework for the technological transformation process be developed to support and guide the organizational transformation that SMEs undergo when introducing new technologies? To answer this question, the research is structured around three core studies. Chapter 2 investigates the state of the art of technological transformation in SMEs through a systematic literature review of 165 peer-reviewed articles. The chapter reveals that the field remains fragmented and multidisciplinary, with studies often examining isolated aspects of the transformation process. The review identifies key elements influencing technological transformation, including drivers, barriers, enablers, controls, processes, and outcomes. It also highlights the interconnectedness between technology assimilation and business model innovation (BMI), emphasizing that these processes should not be treated independently. Based on these findings, the chapter proposes a visual, sequential framework and identifies five research avenues to guide the thesis's subsequent empirical and conceptual investigations. Chapter 3 examines the transformation of EU agri-food SMEs through a multiple-case study of 39 SMEs. The findings reveal distinct technological transformation trajectories across 10 SME groups and demonstrate how companies assimilate technologies, modify their business models, and perceive performance outcomes. The study identifies the technological, organizational, and environmental conditions shaping these processes and outcomes. The chapter shows that successful transformation depends not only on technology adoption but also on the alignment among technology assimilation, BMI, and the broader organizational context. Building on the insights from the previous chapters, Chapter 4 develops a conceptual framework designed to support SMEs in understanding and managing technological transformation. The framework was developed through an exploratory conceptual development approach that combined systematic, iterative literature analysis with qualitative empirical validation. Its application to three pilot agri-food SME cases demonstrates its logical coherence and practical relevance, while uncovering additional insights into the conditions that influence transformation processes and outcomes. Finally, Chapter 5 synthesizes the findings and discusses their implications for theory and practice. The thesis emphasizes the importance of context in shaping technological transformation and argues for an integrative perspective that jointly considers technology assimilation, BMI, and organizational, environmental, and technological conditions. Overall, the thesis contributes to the literature by providing a structured, holistic understanding of technological transformation in SMEs and by proposing a framework that supports both researchers and practitioners in managing this complex process. Business Management and Organisation WASS Bedrijfsvoering en Organisatie WASS urn:nbn:nl:ui:32-54e8b1a3-6b23-428a-a366-03b9e87f89c6/obj 2026-06-19 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/505c5982-9f8e-4f3d-8a60-8926b1ea8592 2026-06-19 thesis

urn:nbn:nl:ui:32-505c5982-9f8e-4f3d-8a60-8926b1ea8592 2026-06-19 urn:nbn:nl:ui:32-505c5982-9f8e-4f3d-8a60-8926b1ea8592/mods Unraveling acclimation mechanisms in plants to fluctuating light Wageningen University dgg Shrestha Samikshya 0000000530410438 aut L.F.M. Marcelis opn S.R.M. Vialet-Chabrand opn E. Kaiser opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 172 10.18174/681737 en Fluctuations in light intensity are ubiquitous for plants growing in the field and in greenhouses. Long-term exposure to fluctuating light induces acclimatory adjustments of morphology, anatomy and/or biochemistry to optimize photosynthetic efficiency and productivity. This thesis explores two aspects of fluctuating light acclimation: 1) interaction between environmental factors such as CO2 concentration and temperature with fluctuating light and 2) natural genetic variation in acclimation to fluctuating light. The results show that fluctuating light negatively impacts plant growth and this is partially mitigated under elevated CO2 by adjustments in plant morphology and anatomy. When light fluctuations were accompanied by fluctuations of leaf temperature, leaf photosynthesis and stomatal responses were stronger than when only light fluctuated. Substantial genetic variation was demonstrated in the magnitude of acclimation to fluctuating light. Overall, this research advances our understanding of acclimation mechanisms employed by plants to fluctuating light. This might hold the potential for identification of novel targets for crop improvement, and therefore increasing food production. Horticulture and Product Physiology (HPP) PE&RC Horticulture and Product Physiology (HPP) PE&RC urn:nbn:nl:ui:32-505c5982-9f8e-4f3d-8a60-8926b1ea8592/obj 2026-06-19 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/587b49cb-1111-46a0-ad79-0310636e77a0 2026-06-24 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-587b49cb-1111-46a0-ad79-0310636e77a0 2026-06-24 urn:nbn:nl:ui:32-587b49cb-1111-46a0-ad79-0310636e77a0/mods Towards a meaningful functioning of food systems: performance, resilience and scaling of underutilized crops in Europe Wageningen University dgg Brémaud Nguyen Marie-Fleur 0000000530302189 aut Miranda P.M. Meuwissen opn Yann de Mey opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 233 10.18174/681754 en This thesis examines the functioning of European food systems using underutilized crops (UCs)—genetically diverse, locally adaptable crops that may enhance sustainability and resilience. Because research on UCs, especially their economic aspects, is scarce and fragmented, this thesis investigates their role at farm, value chain, and policy levels. Findings show that UC farms are generally profitable, operating with low input costs, moderate but stable yields, and diversified income through direct sales and short supply chains. Farmers are often motivated by local food autonomy, environmental stewardship, and community well-being, rather than profit maximization. UC value chains rely on collaboration, long-term partnerships, and diversity in crops, products, and markets, contributing to resilience despite challenges such as limited seed access and unsuitable regulations. Scaling UCs requires policy adjustments, increased societal awareness, and support for diversifying farms and enhancing local food businesses, alongside initiatives for education, seed access, and stronger networks to unlock UC potential in sustainable and resilient European food systems. WASS Business Economics WASS Bedrijfseconomie urn:nbn:nl:ui:32-587b49cb-1111-46a0-ad79-0310636e77a0/obj 2026-06-24 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/c4e8c1ec-0a45-4403-833e-2894562cab4a 2026-06-19 thesis

urn:nbn:nl:ui:32-c4e8c1ec-0a45-4403-833e-2894562cab4a 2026-06-19 urn:nbn:nl:ui:32-c4e8c1ec-0a45-4403-833e-2894562cab4a/mods Soil organic carbon: pools and predictors in nordic agricultural soils, and insights into SOM fractionation methodology Wageningen University dgg Salonen Anna-Reetta 0000000530402331 aut R.E. Creamer opn R. de Goede opn H. Soinne opn J. Heinonsalo opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 205 10.18174/681381 en Soil organic carbon (SOC) underpins key processes in agricultural soils, including nutrient cycling, aggregation, and water regulation, and constitutes one of the largest actively cycling carbon pools. Understanding how SOC is distributed among pools with contrasting persistence and functional roles is therefore central to interpreting soil functioning and management-relevant carbon dynamics. A widely used framework partitions soil organic matter into particulate organic matter (POM), which cycles relatively rapidly, and mineral-associated organic matter (MAOM), which is stabilised on mineral surfaces and persists over longer timescales. POM is generally considered a more labile pool supporting biological activity and nutrient cycling, whereas MAOM is viewed as a more persistent, mineral-protected pool. This study tests two key assumptions underpinning this framework: (1) that MAOM accumulation is constrained by reactive soil mineral surfaces (SOC saturation concepts, typically approximated using clay and silt content), and (2) that operationally defined POM and MAOM fractions correspond to these conceptual pools. These assumptions are evaluated in Finnish agricultural soils and across a wider set of European soils using different fractionation approaches. Across a 24-year field experiment and a survey of 93 farms in southern Finland, MAOM dominated SOC (83–97%) throughout the soil profile. MAOM showed weak relationships with clay content, whereas reactive aluminium and iron oxides were more strongly associated, although substantial variation remained unexplained. Soil texture-based saturation metrics were inconsistent across sites. Comparison of fractionation methods with Rock–Eval thermal analysis showed that density fractionation produced thermally distinct POM and MAOM pools, whereas size fractionation yielded a POM fraction containing substantial mineral-associated carbon. This was linked to incomplete dispersion of soil aggregates, leading to systematic overestimation of POM and underestimation of MAOM, particularly in soils rich in carbon and metal oxides. Overall, SOC saturation concepts based on texture were not consistently applicable in these soils, and density fractionation better separated conceptually distinct POM/MAOM pools than size fractionation. More broadly, the study highlights the need to critically evaluate conceptual frameworks and analytical methods when transferring SOC understanding across soil systems. PE&RC Soil Biology Soil Biology Operations Manager PE&RC Bodembiologie Soil Biology Operations Manager urn:nbn:nl:ui:32-c4e8c1ec-0a45-4403-833e-2894562cab4a/obj 2026-06-19 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/d888ff36-d27c-40fa-b3c5-91462852849c 2026-06-22 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-d888ff36-d27c-40fa-b3c5-91462852849c 2026-06-22 urn:nbn:nl:ui:32-d888ff36-d27c-40fa-b3c5-91462852849c/mods Making cells feel like at home : are microfluidic systems ready for use in a Next-Generation Risk Assessments toolbox? Wageningen University dgg Nitsche Katharina S. 0000000530391580 aut P. Carmichael opn H. Bouwmeester opn I. Müller opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 10.18174/681507 en Traditional animal testing is often slow, costly, and can fail to accurately predict risks to humans. Consequently, chemical safety testing is shifting toward Next-Generation Risk Assessments, which use computer models and human cells. A key innovation in this field is the use of microfluidic system devices. These devices allow human cells to grow in 3D environments with flowing nutrients, making them "feel at home" by mimicking the natural conditions of the human body. This PhD research investigated whether these systems are ready for future routine safety testing. The research suggests a major challenge: many chemicals are lost through evaporation or binding to the system’s materials before reaching the cells. However, when applied to the study of liver conditions such as impaired bile flow (cholestasis), the results showed great promise. Overall, this work highlights that with further optimisation, microfluidic systems can become powerful, more accurate tools for predicting human safety, thereby reducing or replacing animal testing. VLAG Toxicology VLAG Toxicologie urn:nbn:nl:ui:32-d888ff36-d27c-40fa-b3c5-91462852849c/obj 2026-06-22 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/9ac5c383-bd94-4a2c-b3b0-8b71e87e28a9 2026-06-19 thesis

urn:nbn:nl:ui:32-9ac5c383-bd94-4a2c-b3b0-8b71e87e28a9 2026-06-19 urn:nbn:nl:ui:32-9ac5c383-bd94-4a2c-b3b0-8b71e87e28a9/mods Antibiotics and nutrients in an Indonesian multifunctional reservoir : analysis, source identification, impact assessment, and management options Wageningen University dgg Ariyani Miranti 0000000530285489 aut N. Hofstra opn P. van Oel opn M. van de Schans opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 255 10.18174/681770 en This research provides the first comprehensive assessment of antibiotics and nutrients in Cirata reservoir, a multifunctional tropical reservoir in Indonesia, linking pollution sources to ecological risks and management strategies. The research develops a framework to evaluate the occurrence, prioritization, sources, fate, transport, and impacts of antibiotics and nutrients, and to predict their future state and proposed management strategies under different climate change and socio-economic scenarios. Twelve antibiotics were prioritized for monitoring, with livestock farming identified as the dominant source, and point sources exceeding diffuse sources. Under an economy-driven scenario with strong climate change, Cirata reservoir may face combined pressures from nutrient enrichment and antibiotic mixtures by 2050, threatening hydropower generation, aquaculture, and irrigation. Integrated management strategies addressing both nutrients and antibiotics are most effective for mitigating these risks, although nutrient-focused strategies alone can also reduce antibiotic loads. The findings provide a scientific basis for designing targeted interventions to protect reservoir ecosystem services and contribute to achieving multiple Sustainable Development Goals (SDGs). WIMEK Earth Systems and Global Change Team Animal Drugs 1 Water Resources Management WIMEK Earth Systems and Global Change Team Animal Drugs 1 Water Resources Management urn:nbn:nl:ui:32-9ac5c383-bd94-4a2c-b3b0-8b71e87e28a9/obj 2026-06-19 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/8fbfed28-2af6-4cb4-933f-f6a2fcba18c9 2026-06-22 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-8fbfed28-2af6-4cb4-933f-f6a2fcba18c9 2026-06-22 urn:nbn:nl:ui:32-8fbfed28-2af6-4cb4-933f-f6a2fcba18c9/mods Multiscale modeling of molybdenum and tungsten carbide catalysts for sustainable biomass conversion Wageningen University dgg Meena Raghavendra 0000-0002-2019-8806 0000000530394888 aut J.H. Bitter opn J. Zuilhof opn G. Li opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 174 10.18174/681305 en With limited fossil fuels as our primary energy source, it is crucial that we find cheaper and sustainable alternatives for meeting increasing energy demand. Biomass is identified as a renewable alternative to fossil fuels. However, converting biomass into useful chemicals is challenging. Transition metal carbides (TMCs) are promising catalysts to replace traditionally used precious metals like Platinum and Palladium for biomass conversion via hydrodeoxygenation (HDO) reaction. This thesis provides a unified, multiscale modeling of TMCs in HDO catalysis and provides rational TMC catalysts design strategies. The integration of theory, kinetics, and data science demonstrated here exemplifies how computational chemistry can guide the development of catalysts for renewable chemical transformations. Finally, this work also contributes towards realizing two crucial Sustainable Development Goals as set forward by the UN, linking abstract science to real-life societal goals that affect the lives of billions of people. VLAG Organic Chemistry Biobased Chemistry and Technology VLAG Organische Chemie Biobased Chemistry and Technology urn:nbn:nl:ui:32-8fbfed28-2af6-4cb4-933f-f6a2fcba18c9/obj 2026-06-22 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/d157a399-1086-46c0-9b4a-61e946fa65c8 2026-06-19 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-d157a399-1086-46c0-9b4a-61e946fa65c8 2026-06-19 urn:nbn:nl:ui:32-d157a399-1086-46c0-9b4a-61e946fa65c8/mods Artificial intelligence and computer vision for quantitative assessment of eating behavior and urban food landscapes Wageningen University dgg Tufano Michele 0000000530394896 aut E.J.M. Fesken opn G. Camps opn M. Lasschuijt opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 165 10.18174/681714 en Eating behavior and food environment accessibility are key determinants of nutrition and health, yet traditional assessment methods—manual video annotation and observational food environment audits—are labor-intensive, time-consuming, and difficult to scale. This thesis investigated how artificial intelligence can automate the assessment of eating behavior and urban food environments to support nutrition research at both individual and population levels. At the population level, a data-driven framework was developed to assess urban food environments using restaurant menu data from online delivery platforms in Boston, London, and Dubai (Chapter 2). Machine learning matched menu items to the U.S. FoodData Central database, enabling neighborhood-level nutritional profiling. Coverage differed substantially across cities—Boston (71%), London (56%), and Dubai (42%)—highlighting regional limitations in nutritional databases. Higher dietary fiber availability was significantly associated with lower obesity prevalence in London (p=0.001) and Boston (p=0.004), while higher socioeconomic neighborhoods consistently had better access to nutrient-rich foods. This scalable methodology enables policymakers to identify neighborhoods at risk for poor nutritional access. At the individual level, a PRISMA-based systematic review identified five approaches for automated eating behavior detection from video: facial landmarks, deep learning, optical flow, active appearance models, and video fluoroscopy (Chapter 3). Facial landmarks emerged as the most promising method for detecting bites and chews. Building on this, a computationally efficient rule-based system using 468 3D facial keypoints was developed for automated bite counting, achieving 79% accuracy with annotations and 71.4% without annotations across 164 videos from 15 participants, with stable performance across food textures (Chapter 4). To further improve accuracy, transformer-based architectures were developed using 103 annotated videos from 36 participants consuming standardized meals (Chapter 5). A Vision Transformer achieved 98.45% frame accuracy and 86.2% counting accuracy for bite detection by effectively modeling global spatial relationships. For chew detection, a CNN-LSTM outperformed the Vision Transformer (85.56% vs. 69.21%), as sequential architectures better captured chewing dynamics. Sip detection using pretrained VideoMAE reached 61% accuracy, limited by sparse training data and annotation challenges. These models were integrated into the Automated Meal Video Analysis (AMVA) Toolkit, an open-source, cloud-native platform deployed on AWS serverless infrastructure with GDPR-compliant data handling and privacy-preserving facial masking (Chapter 6). The system reduced annotation time 40-fold—from six weeks to six hours for 118 videos—while maintaining linear scalability with video duration. Overall, this thesis demonstrates that artificial intelligence can automate the assessment of eating behavior and urban food environments, transforming labor-intensive manual methods into scalable, objective systems. Current limitations include incomplete nutritional databases, cultural bias toward Western dietary patterns, and limited training data for drinking behaviors (Chapter 7). Future work should focus on improving cultural representation, model generalizability across eating contexts, and integrated multimodal AI systems for comprehensive behavioral assessment. By linking food environments, eating behavior, and health outcomes, this thesis establishes AI as a foundational methodology for scalable, data-driven nutrition science. VLAG Global Nutrition Sensory Science and Eating Behaviour VLAG Wereldvoeding Sensoriek en eetgedrag urn:nbn:nl:ui:32-d157a399-1086-46c0-9b4a-61e946fa65c8/obj 2026-06-19 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/1cdbdbe9-383d-428a-9c68-8127510f0876 2026-06-18 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-1cdbdbe9-383d-428a-9c68-8127510f0876 2026-06-18 urn:nbn:nl:ui:32-1cdbdbe9-383d-428a-9c68-8127510f0876/mods Agroecological practices to improve smallholder farmers’ resilience to climatic variability: insights from the North Sudanian agroecological zone of Burkina Faso Wageningen University dgg Bagagnan Abdoul-Rasmane 0000000530367978 aut K. Descheemaeker opn D. Berre opn H. Webber opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 224 10.18174/681230 en This thesis investigates how agroecological (AE) practices and agroecological intensification (AEI) can improve the resilience, productivity, and food self-sufficiency of smallholder farming systems in the Sudano-Sahelian zone of Burkina Faso. Agriculture in the region is predominantly rainfed and constrained by climate variability, declining soil fertility, and limited access to fertilizers, all of which contribute to large yield gaps and food insecurity. Although agroecology is increasingly promoted as a sustainable solution, empirical evidence of its effectiveness remains limited. To address this gap, the study combined farm characterization, participatory assessments, agronomic experiments, and crop simulation modelling across four chapters. The research first explored farm diversity, implementation of AE practices, and farmers’ criteria for adopting these practices. Farmers valued AE practices primarily for their potential to improve yields, conserve soil fertility, and fit existing farming conditions. Practices such as crop rotation, intercropping, and zai pits were commonly used. However, the implementation levels and adoption criteria differed little among farm types, suggesting that shared environmental and socio-economic constraints such as climate variability, limited access to inputs, and weak market opportunities influence farmers’ decisions more strongly than differences in resource endowment. The thesis also examined farmers’ perceptions of risk, resilience capacities, and responses to hazards. Risk perception was highly context-specific, with Striga infestation and climate-related hazards identified as major threats. Farmers considered dry spells particularly difficult to manage and often expected substantial yield losses during severe years. Most farmers relied on robustness and adaptability strategies, including soil and water conservation techniques, early-maturing varieties, livelihood diversification, and social support networks. Nevertheless, many farmers reported having no responses to severe dry spells. A participatory co-design process was then used to evaluate and redesign AE practices over a three-year period. Farmers and researchers jointly assessed farmers’ usual systems, researcher-proposed systems, and farmer-redesigned systems. Results showed that researcher-designed systems did not consistently outperform farmers’ traditional practices, emphasizing the importance of incorporating farmers’ knowledge and experience. In contrast, farmer-redesigned systems developed through iterative collaboration achieved significant yield improvements, demonstrating the value of participatory innovation. Farmers’ evaluations of cropping systems were influenced not only by yield performance but also by labor requirements, labor costs, and pest and disease management. Finally, the thesis used crop simulation modelling to assess the long-term performance of AEI practices under climate hazards over a ten-year period. Simulations revealed strong year-to-year variability in sorghum yields, with hazards such as late rainfall onset and early rainfall cessation causing severe yield reductions. Improved cropping systems enhanced yields in favorable years but were less effective under severe hazard conditions. Household food self-sufficiency also fluctuated considerably with climate variability. Overall, the thesis demonstrates that agroecological practices can contribute to improved productivity and resilience, but their success depends strongly on local environmental, socio-economic, and institutional conditions. Strengthening agroecological transitions therefore requires not only technical innovation, but also improved risk management, access to resources, and supportive institutional environments. PE&RC Plant Production Systems (PPS) PE&RC Plant Production Systems (PPS) urn:nbn:nl:ui:32-1cdbdbe9-383d-428a-9c68-8127510f0876/obj 2026-06-18 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/94c30a32-f1b6-43cf-8364-34cc34568e8e 2026-06-12 thesis

urn:nbn:nl:ui:32-94c30a32-f1b6-43cf-8364-34cc34568e8e 2026-06-12 urn:nbn:nl:ui:32-94c30a32-f1b6-43cf-8364-34cc34568e8e/mods Minds, meals and motivations : Understanding lifestyle change for cognitive health: insights from research and everyday practice Wageningen University dgg Terlouw-Otte Rebecca 0000000530394909 aut M.A.E. de van der Schueren opn J.Th.C.M. de Kruif opn E. Naumann opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 267 10.18174/681715 en This dissertation examines how older adults engage with and experience lifestyle interventions aimed at maintaining cognitive functioning and reducing dementia risk, with the Dutch FINGER-NL study as a central case. A longitudinal mixed-methods design was used, combining repeated qualitative interviews with cross-sectional questionnaire data to examine why people participate in lifestyle interventions, how motivation develops over time, and how lifestyle changes are implemented and maintained in everyday life. The dissertation consists of two complementary research tracks. The first track focused on older adults participating in the FINGER-NL multidomain lifestyle intervention and explored motivation, engagement, adherence, and the feasibility of implementing lifestyle changes in daily life. Longitudinal qualitative interviews conducted at different timepoints captured how participants’ experiences and engagement developed over time. In addition, quantitative questionnaire data were used to examine how beliefs and motivation regarding dementia risk reduction related to modifiable lifestyle-related dementia risk factors. The second track extended these insights beyond the research setting by examining lifestyle change and obesity treatment in routine dietetic care through interviews, focus groups, and configurational analyses of intervention components using a Qualitative Comparative Analysis. The findings show that many participants were motivated to participate because of personal concerns about memory problems and dementia, often shaped by experiences within their family or social environment. Knowledge regarding dementia risk reduction was generally limited. Although participants often enrolled in the intervention with strong intentions to change, motivation alone was insufficient to sustain long-term behavior change. Participants encountered practical, emotional, and social barriers, and engagement developed differently across individuals and over time. While some participants gradually integrated new habits into their daily routines and became more motivated after experiencing positive effects, others experienced declining motivation or interruptions due to major life events. Some participants in the low-intensity control group, despite receiving only minimal information and no active guidance, nevertheless initiated lifestyle changes independently, often motivated by participation in the study itself and concerns about cognitive decline. In addition, participants in the qualitative substudy were generally aware of their group allocation, raising questions about the feasibility of maintaining blinding within lifestyle intervention research. Across the intervention, diet and physical activity emerged as the most tangible and achievable lifestyle domains. Participants frequently made selective choices regarding which intervention components to follow, and this flexibility resulting in the feeling of autonomy within the intervention was experienced as important for sustaining engagement. Structured guidance and regular contact with lifestyle coaches supported motivation and adherence, whereas information alone was often insufficient to facilitate long-term change. Similar patterns emerged in routine dietetic care, where both dietitians and patients emphasized the importance of personalized guidance, attention to individual circumstances, and a trusting patient–professional relationship. Rather than depending on standardized advice alone, sustaining lifestyle change appeared to require support that could be adapted to people’s needs, capabilities, and everyday lives over time. VLAG Global Nutrition VLAG Wereldvoeding urn:nbn:nl:ui:32-94c30a32-f1b6-43cf-8364-34cc34568e8e/obj 2026-06-12 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/dd87f137-40e6-435c-817b-f4605dc70d90 2026-06-18 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-dd87f137-40e6-435c-817b-f4605dc70d90 2026-06-18 urn:nbn:nl:ui:32-dd87f137-40e6-435c-817b-f4605dc70d90/mods Photons for food intake : measuring macronutrients with hyperspectral imaging and machine learning Wageningen University dgg Kok Esther 0000000530367847 aut E.J.M. Feskens opn G. Camps opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 295 10.18174/681725 en What if a device could determine the nutritional content of a meal simply by imaging it? That is the vision behind this research. Measuring what people actually eat is surprisingly difficult. Current methods rely on individuals remembering and reporting their own food intake, which is often inaccurate and time-consuming. This thesis explores a more objective alternative: hyperspectral imaging, a camera technology that captures detailed chemical information from food, far beyond what the human eye can see. Combined with machine learning, the technology behind many modern pattern recognition systems, these cameras can predict the fat and protein content of foods such as closed sandwiches and cheeses with toppings, without any physical contact or destruction of the sample. This research demonstrates that this combination is effective, and lays the groundwork for a future automated system: point a device at a plate, and instantly obtain its nutritional composition. A meaningful step toward more accurate and objective measurement of dietary intake. VLAG Global Nutrition VLAG Wereldvoeding urn:nbn:nl:ui:32-dd87f137-40e6-435c-817b-f4605dc70d90/obj 2026-06-18 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/0903542b-16a5-4f21-add5-eb6f4f1a243c 2026-06-12 thesis

urn:nbn:nl:ui:32-0903542b-16a5-4f21-add5-eb6f4f1a243c 2026-06-12 urn:nbn:nl:ui:32-0903542b-16a5-4f21-add5-eb6f4f1a243c/mods Optimization-based meal planning for sustainable diets Wageningen University dgg van Rooijen Maike Anna 0000000530367556 aut S.L.J.M. de Leeuw opn J.C. van Lemmen-Gerdessen opn G.D.H. Claassen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 118 10.18174/681917 en Designing sustainable diets within planetary boundaries requires considering not only choosing what foods we eat, but also how foods are planned, purchased, and combined into meals. This thesis examines how optimization-based meal planning can contribute to sustainable diets by reducing food waste and increasing the consumption of locally in-season foods. Key drivers of household food waste are poor meal planning and discrete package sizes. A meal planning model is developed to generate meal plans and shopping lists that account for retail package sizes. Results show that healthy meal plans with negligible food waste are feasible, but that reducing waste by weight alone does not necessarily lower dietary carbon footprints. By incorporating uncertainty in household food needs, the analysis highlights how optimal planning horizons and shopping frequencies vary across household situations. The thesis further examines the implications of shifting towards more local and seasonal diets, given that food miles account for approximately 20% of global food-related greenhouse gas emissions. The results show that meal plans can increase the use of locally in-season foods at lower cost and carbon footprint while maintaining nutritional adequacy throughout the year. Finally, computational challenges arising from mutually exclusive choices in meal planning models are addressed through improved branching strategies. Overall, this research demonstrates that optimization-based meal planning can contribute to the development of more sustainable diets by revealing key trade-offs across nutritional, environmental, and economic dimensions. The findings reinforce existing evidence on the need to shift towards more plant-based diets, while showing how different planning and shopping strategies influence sustainability outcomes. Operations Research and Logistics WASS Operationele Research en Logistiek WASS urn:nbn:nl:ui:32-0903542b-16a5-4f21-add5-eb6f4f1a243c/obj 2026-06-12 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/00f88e2f-b874-4987-9868-7631b64359e0 2026-06-12 thesis

urn:nbn:nl:ui:32-00f88e2f-b874-4987-9868-7631b64359e0 2026-06-12 urn:nbn:nl:ui:32-00f88e2f-b874-4987-9868-7631b64359e0/mods Understanding and improving the gelation of commercial plant protein isolates: the role of structure, processing, and composition Wageningen University dgg Janssen Senna W.P.M. 0000000530427416 aut R.J. de Vries opn L. Pouvreau opn E. Scholten opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 274 10.18174/681684 en Plant-based food products often contain several additives, resulting in longer ingredient lists than the animal-based products they aim to replace. These additives are required to compensate for the lower functional quality of plant proteins in structuring food products. However, consumers perceive these ingredients negatively due to their unfamiliarity or highly processed nature. As a result, there is a growing interest in developing clean-label strategies that enhance plant protein functionality and reduce the need for additives. The overall aim of this thesis was to understand and improve the gelation properties of commercial plant protein isolates. To achieve this, we investigated physical processing, explored potential synergistic effects between plant proteins from different sources, assessed the impact of fibre addition, and evaluated the role of enzymes on the gelation properties of various commercial legume protein isolates. Our findings demonstrated that physical processing via high-pressure homogenization improves protein dispersibility and strengthens heat-set gel structures by reducing insoluble particles that otherwise act as weak points within the network. Combining proteins from different plant sources did not result in synergistic improvements but rather showed anti-synergistic or linear mixing behaviour, indicating that blending proteins alone is not a straightforward route to enhance heat-set gel properties. In contrast, the addition of oat beta-glucan fibres increased the hardness and stiffness of heat-set gels, which was more pronounced with the addition of higher purity oat beta-glucan. These effects were linked to microstructural phase separation and to water distribution between phases, thereby promoting the formation of a denser protein network. Enzymatic modification offered another promising strategy: the crosslinking enzyme transglutaminase substantially enhanced the properties of cold-set gels. These properties were further enhanced when combined with physical processing (homogenization and heat), which increased protein dispersibility and substrate accessibility. Meanwhile, protein glutaminase showed potential to increase protein dispersibility and reduce syneresis, but offered limited benefits for the mechanical properties. Overall, the findings demonstrate that the gel properties of complex and heterogeneous commercial plant protein isolates can be modified and enhanced through physical and enzymatic processing, by varying the gel composition or combinations thereof. These outcomes provide valuable insights to contribute to the development of clean-label solutions for structuring plant-based foods. Physical Chemistry and Soft Matter VLAG Physical Chemistry and Soft Matter F Food Technology Physics and Physical Chemistry of Foods Fysische Chemie en Zachte Materie VLAG Physical Chemistry and Soft Matter F Food Technology Physics and Physical Chemistry of Foods urn:nbn:nl:ui:32-00f88e2f-b874-4987-9868-7631b64359e0/obj 2026-06-12 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/56fdb4aa-37e2-4769-a158-3305a24bba7c 2026-06-17 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-56fdb4aa-37e2-4769-a158-3305a24bba7c 2026-06-17 urn:nbn:nl:ui:32-56fdb4aa-37e2-4769-a158-3305a24bba7c/mods Microbial stabilization and protein functionality of plant-based liquids using pulsed electric fields Wageningen University dgg de Gol Cora 0000000530302242 aut M.H. Zwietering opn H.M.W. den Besten opn M. Beyrer opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 200 10.18174/681940 en Plant-based food products are rapidly gaining market share as consumers shift toward more sustainable and healthy diets. Compared to animal-based products, their production requires less land and water, and generates a substantially lower carbon footprint. Among them, meat substitutes have become particularly popular for their ease of use. They are typically produced by extrusion, where plant-based protein isolate powders are hydrated and texturized into meat-like products. The functionality of the protein, primarily its gelling properties, is therefore crucial for the process. Conventional protein extraction from the raw material and drying steps involve high temperatures and chemical use, which not only consume large amounts of energy, but also impair the gelling properties of the proteins. Additionally, most commercial meat substitutes are soy-based, raising concerns about deforestation, large-scale monoculture and global transport dependence. This thesis aims to combine local sourcing, minimal processing, and mild preservation technologies to produce protein-rich ingredients for plant-based food products. Specifically, it proposes eliminating drying steps, and instead, using protein-rich liquid ingredients obtained under mild aqueous conditions. Two such ingredients were investigated: a suspension of Chlorella vulgaris, and a yellow pea protein extract (PPE). The latter was obtained from air-classified pea protein concentrate under mild, aqueous and room temperature conditions. The feasibility of incorporating these liquid ingredients directly into extrusion processes was demonstrated without compromising the final product’s texture. Additionally, a life cycle assessment revealed substantial environmental benefits when replacing soy with pea protein and avoiding drying steps. A major challenge with handling liquids is their microbial instability. While extrusion (high temperature, pressure and residence time) ensures the microbial safety of the final product, quality deterioration of the liquid during refrigerated storage and prior to extrusion limits processing flexibility. To address this, pulsed electric field (PEF) treatment combined with cold storage was investigated as a mild preservation strategy. PEF treatment is based on the application of high-voltage short pulses to liquids, inactivating bacteria with minimal temperature increase and reduced damage to heat-sensitive protein compounds, predominantly present in liquid foods. The results showed that PEF achieved significant microbial reductions (around 4 log cycles) in both Chlorella suspension and PPE, effectively extending their shelf life by several days. The viability of PEF as a preservation method depends on its ability to maintain protein functionality. Hence, the impact of PEF on pea protein’s structure and functionality was investigated and compared with conventional heat pasteurization. Results revealed partial protein unfolding following PEF, promoting intermolecular interaction and even enhanced (> 50%) gelling properties. In contrast, heat pasteurization caused protein aggregation and 60% reduction in gelling properties for equivalent microbial inactivation levels. These functional improvements were confirmed during lab-scale extrusion trials, where incorporating PEF-treated PPE into pea protein isolate did not negatively affect the texture of the meat substitutes in contrast to thermally treated counterparts. To conclude, the proposed approach significantly reduces carbon footprint and enhances protein functionality for meat substitute production. Overall, this thesis advanced the development of plant-based protein ingredients, bridging sustainability and functionality through innovative use of PEF technology. VLAG Food Microbiology VLAG Levensmiddelenmicrobiologie urn:nbn:nl:ui:32-56fdb4aa-37e2-4769-a158-3305a24bba7c/obj 2026-06-17 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/7bc957e0-4ea5-4b71-b0d4-d486e95fdafb 2026-06-15 thesis

urn:nbn:nl:ui:32-7bc957e0-4ea5-4b71-b0d4-d486e95fdafb 2026-06-15 urn:nbn:nl:ui:32-7bc957e0-4ea5-4b71-b0d4-d486e95fdafb/mods Dual nitrogen and phosphorus control for mitigating eutrophication and cyanobacterial blooms Wageningen University dgg Shi Yuxin 0000000530367919 aut M. Lürling opn M. Mucci opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 186 10.18174/681330 en Eutrophication driven by excessive nutrient loading remains a major challenge for freshwater ecosystems. This thesis evaluated the feasibility of geo-engineering materials to mitigate eutrophication and cyanobacterial blooms by controlling internal nitrogen (N) and phosphorus (P) loads. Batch adsorption experiments assessed phosphate and ammonium binding capacities of different materials, while up-scaled sediment core experiments showed that natural zeolite (NZ) combined with lanthanum-modified bentonite, aluminium-modified zeolite, and NZ with poly-aluminium chloride effectively reduced P and N in the water column and limited their release from sediment. Reducing N availability suppressed Microcystis aeruginosa biomass more effectively than P limitation once blooms were established. Long-term field evaluation of a “Floc & Lock” intervention confirmed sustained P control but highlighted the need to address internal N release and external nutrient inputs. This thesis provided potential materials for controlling internal N loading as tools for lake restoration if internal N control is required. WIMEK Aquatic Ecology and Water Quality Management WIMEK Aquatische Ecologie en Waterkwaliteitsbeheer urn:nbn:nl:ui:32-7bc957e0-4ea5-4b71-b0d4-d486e95fdafb/obj 2026-06-15 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/c2e84956-4a42-4402-b067-b7d638e9c21e 2026-06-17 thesis

urn:nbn:nl:ui:32-c2e84956-4a42-4402-b067-b7d638e9c21e 2026-06-17 urn:nbn:nl:ui:32-c2e84956-4a42-4402-b067-b7d638e9c21e/mods Understanding drivers of vegetable agro-biodiversity in smallholder farming in northern Vietnam Wageningen University dgg Nguyen Thi Phuong 0000000530394853 aut T.J. Stomph opn P.C. Struik opn C.P.M. Swaans opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 330 10.18174/681070 en Vegetables play essential roles in smallholder farming households by contributing to food, nutrition, income, feed, and resilience. Yet, compared to staple crops, vegetable diversity and its link to seed systems remain understudied. This thesis explores how vegetable agro-biodiversity is shaped, maintained, or lost through farmers’ crop and seed management practices in northern Vietnam. Using mixed methods, including household surveys, interviews, focus groups, and participatory experiments, the research shows that vegetable diversity was strongly linked to farmers’ use of multiple seed sources, especially self-saved seed and local markets. Diversity accumulates across spatial levels, with rare vegetables maintained through household preferences and seed saving. Focusing on pumpkin varieties, the thesis further demonstrates that farmers’ seed and variety choices were adaptive and shaped by market opportunities, labor, and changing livelihood strategies rather than simple adoption processes. The thesis highlights the central role of informal and intermediate seed systems in sustaining vegetable agro-biodiversity over time. PE&RC Centre for Crop Systems Analysis (CSA) PE&RC Centre for Crop Systems Analysis (CSA) urn:nbn:nl:ui:32-c2e84956-4a42-4402-b067-b7d638e9c21e/obj 2026-06-17 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/4a738653-ccd7-45cd-bc03-a048fd842166 2026-06-15 thesis

urn:nbn:nl:ui:32-4a738653-ccd7-45cd-bc03-a048fd842166 2026-06-15 urn:nbn:nl:ui:32-4a738653-ccd7-45cd-bc03-a048fd842166/mods Optimizing food supply for nutrition and environmental sustainability : the potential of plant-based foods to improve nutrient supply and reduce environmental externalities in China Wageningen University dgg Li Yijun 0000000530367521 aut S.L.J.M. de Leeuw opn W. van der Werf opn J.C. van Lemmen-Gerdessen opn A. Kuijsten opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 285 10.18174/682016 en The overall goal of food systems is to sustainably provide nutritious and healthy food for everyone at any time. Exploring strategies to achieve this goal and providing guidance on how these strategies can be implemented requires accounting for local conditions (e.g., land, yields, and water availability). This thesis, which mainly focuses on China, explores potential strategies for enhancing nutrient supply in a sustainable and diverse way. It focused on plant-based foods because partially substituting animal-based foods with plant-based foods has the potential to achieve better health and environmental outcomes, and traditional Chinese diets are largely plant-based. Chapter 2 explores strategies from food production, storage, distribution, and processing, to food environments, and consumption in Asia to balance productivity with sustainability, reduce food loss and waste, enhance food quality, and promote a healthy food environment through aligned actions among stakeholders, policy intervention, and investment. Chapter 3 assesses the current role and potential of plant-based foods in China to meet the population's needs for dietary energy and 17 nutrients. Chapter 4 explores how shifting some rice and wheat areas to underutilized cereals and beans, combined with greater use of whole-grain rice and wheat, can improve nutrient supply and reduce environmental impact. Finally, Chapter 5 evaluates whether utilizable protein supply can be increased through reallocating areas among cereals and beans and expanding maize/soybean intercropped area without compromising other nutritional and environmental outcomes. In this thesis, I integrate evidence from nutrient supply, nutrient intake, and nutrient status to identify nutrient gaps resulting from food system limitations, and I use supply chain modeling and optimization to explore possible solutions that contribute to narrowing these gaps. The modeling results show that area reallocation, intercropping, reducing food loss and waste, reducing red meat intake, and repurposing crop uses have the potential to increase micronutrient and utilizable protein supply and reduce environmental impact in China. The results show to what extent expanding the cultivation of underutilized cereals and beans can simultaneously improve nutrient supply and environmental sustainability. Furthermore, the results show the importance of incorporating protein quality in assessments of protein adequacy and when exploring shifts from animal-based protein to more plant-based protein. Overall, supply-side strategies will require corresponding dietary shifts and vice versa. Integrated analyses that link production, trade, processing, and consumption can guide food system transformations towards better nutrition and environmental outcomes. Operations Research and Logistics WASS Operationele Research en Logistiek WASS urn:nbn:nl:ui:32-4a738653-ccd7-45cd-bc03-a048fd842166/obj 2026-06-15 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/71025123-ae83-40e6-8843-ed2a783944ce 2026-06-15 thesis

urn:nbn:nl:ui:32-71025123-ae83-40e6-8843-ed2a783944ce 2026-06-15 urn:nbn:nl:ui:32-71025123-ae83-40e6-8843-ed2a783944ce/mods Between light and shade, from young to old: unraveling the dynamics of leaf photosynthesis in the crop canopy Wageningen University dgg Shao Bingjie 0000000530367900 aut L.F.M. Marcelis opn E. Kaiser opn T. Li opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 180 10.18174/681464 en Dynamic photosynthesis is an important yet often overlooked component of carbon assimilation under fluctuating light, a condition frequently experienced in both natural and greenhouse environments. Within crop canopies, leaves experience strong vertical gradients in light intensity, light spectrum, and leaf age, which may alter photosynthetic performance. This thesis aimed to characterise how photosynthesis, particularly dynamic photosynthesis, varies within crop canopies and to identify the roles of light intensity, red-to-far-red (R:FR) ratio, and leaf age in driving this variation. Experiments were conducted in tomato, cucumber, and sweet pepper. Chapter 1 introduces the physiological basis of photosynthesis and the mechanisms underlying dynamic photosynthesis, including diffusional, biochemical, and photoprotective limitations. The chapter highlights current knowledge gaps regarding within-canopy variation in photosynthetic responses under fluctuating light and presents the objectives of the thesis. Chapter 2 investigated vertical variation in photosynthesis within a mature greenhouse tomato canopy. Upper canopy leaves exhibited higher steady-state photosynthesis and slightly faster photosynthetic induction than lower leaves. These differences were associated with greater stomatal conductance and faster activation of carboxylation and electron transport. Despite variation in transient responses, steady-state photosynthesis contributed more strongly than dynamic photosynthesis to carbon gain under fluctuating light. Chapter 3 examined how acclimation to growth light intensity influences photosynthesis in cucumber, tomato, and sweet pepper. Increasing growth light intensity enhanced steady-state photosynthetic capacity and accelerated NPQ induction. However, it had limited effects on photosynthetic induction, except in cucumber, where high growth light slowed induction through reduced stomatal opening speed and stronger biochemical limitation. These results indicate that light intensity primarily affects steady-state photosynthesis rather than dynamic photosynthetic performance. Chapter 4 explored the effects of acclimation to different R:FR ratios in tomato. Low R:FR induced typical shade-avoidance responses, including increased leaf area and plant height. However, R:FR had little influence on leaf photosynthetic traits, including steady-state and dynamic photosynthesis. The results suggest that far-red light mainly promotes growth through changes in plant architecture rather than intrinsic leaf photosynthetic performance. Chapter 5 investigated the effects of leaf age on photosynthesis using cucumber plants grown horizontally under uniform light conditions. While steady-state photosynthesis remained relatively stable across leaves of different ages, photosynthetic induction slowed significantly with increasing leaf age, mainly due to reduced stomatal kinetics and increased diffusional and biochemical limitations. NPQ relaxation also accelerated in older leaves. Chapter 6 synthesises these findings and evaluates the relative importance of light intensity, R:FR ratio, and leaf age in shaping dynamic photosynthesis within crop canopies. Overall, this thesis demonstrates that leaf age exerts the strongest influence on dynamic photosynthesis, whereas light intensity mainly affects steady-state photosynthesis and R:FR primarily alters plant morphology. These findings improve our understanding of canopy photosynthesis under fluctuating light and provide a physiological basis for improving crop management and canopy photosynthesis modelling in controlled-environment agriculture. Horticulture and Product Physiology (HPP) PE&RC Horticulture and Product Physiology (HPP) PE&RC urn:nbn:nl:ui:32-71025123-ae83-40e6-8843-ed2a783944ce/obj 2026-06-15 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/f6152cbc-198c-4c0f-8c02-2a64c8d5e743 2026-06-12 thesis

urn:nbn:nl:ui:32-f6152cbc-198c-4c0f-8c02-2a64c8d5e743 2026-06-12 urn:nbn:nl:ui:32-f6152cbc-198c-4c0f-8c02-2a64c8d5e743/mods Deciphering virulence dynamics in potato cyst nematodes to detect and counteract resistance breakdown Wageningen University dgg Schaveling Arno S. 000000053036753X aut G. Smant opn M.G. Sterken opn A. Goverse opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 249 10.18174/681930 en Plant-parasitic nematodes cause substantial crop losses around the world every year. Among the most damaging plant-parasitic nematodes are the potato cyst nematodes (PCN) G. pallida and G. rostochiensis. Symptoms of infected plants include stunting and leave yellowing, resulting in a reduced yield. Worldwide yield losses caused by PCN have not recently been quantified, but in the past, it has been estimated to be responsible for the loss of roughly 9% of the potato production worldwide. Effective PCN management is challenging, complicated by both nematode and potato biology. This thesis aimed to decipher virulence dynamics in G. pallida in response to resistance in potato and to identify and counteract mechanisms of resistance breakdown. Through refined effector-mediated manipulation of the host, sedentary juveniles withdraw nutrients from the roots, while constantly suppressing host immune responses (Chapter 1). Depending on the infective success and the nutrient availability in the roots, juveniles develop into males or females, a process known as environmental sex determination (Chapter 2). Under nutrient-poor conditions, juveniles are more likely to develop into males, whereas nutrient-rich conditions enable development into females. Our data suggested a model in which juveniles follow a default pathway towards male development under nutrient-poor conditions, whereas nutrient-rich conditions can override this pathway, enabling development into females (Chapter 2). Since potato resistances predominantly inhibit female development, avirulent juveniles can contribute to the next generation as males and virulent juveniles as males and females. Thereby, maintaining the genetic diversity that is crucial to quickly adapt to potato resistances. This adaptability causes major challenges in G. pallida management. The cultivation of resistant potato varieties plays a crucial role in G. pallida management. However, the widespread and repeated use of the same resistance, GpaVvrn from S. vernei, led to the emergence of virulent G. pallida populations capable of overcoming this resistance (Chapter 3). Globodera pallida populations from Germany, the Netherlands, the United Kingdom, and France have shown the ability to overcome GpaVvrn, either under field conditions or through experimental evolution (Chapter 3). The moment resistance breakdown becomes visible in a crop in the field, countless virulent juveniles are already present in the soil. The early identification of virulence requires a genetic marker for virulence. Selection experiments with two G. pallida populations allowed for associating virulence on GpaVvrn to a single genomic G. pallida locus (Chapter 3). Within this locus, a single gene was identified, named Gp-pat-1, that contributes to the breakdown of GpaVvrn resistance (Chapter 3). This gene contained a single nucleotide polymorphism (SNP) that was consistently selected by GpaVvrn in 13 Dutch, British and French G. pallida populations (Chapter 4), indicating that the genetic basis for virulence is likely conserved across Western Europe. Moreover, its allele frequency showed to be a reliable genetic marker for virulence on GpaVvrn resistant potato plants. Management of GpaVvrn-breaking G. pallida populations requires the identification and introgression of novel resistances. Nematode infection assays with a GpaVvrn-breaking G. pallida population on the S. sparsipilum-derived GpaVspl resistance showed that GpaVspl can control GpaVvrn-breaking G. pallida populations (Chapter 5). EPS Nematology (NEM) EPS Nematology (NEM) urn:nbn:nl:ui:32-f6152cbc-198c-4c0f-8c02-2a64c8d5e743/obj 2026-06-12 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/1280a472-0d60-4e15-b677-0bc6fbc59e4d 2026-06-12 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-1280a472-0d60-4e15-b677-0bc6fbc59e4d 2026-06-12 urn:nbn:nl:ui:32-1280a472-0d60-4e15-b677-0bc6fbc59e4d/mods Breaking cells while keeping the value: mild cell disruption for microalgae biorefineries Wageningen University dgg Günerken Emre 000000053023557X aut R.H. Wijffels opn M.H.M. Eppink opn K. Elst opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 162 10.18174/701661 en Microalgae biorefineries present a promising pathway for the sustainable production of fuels, food, and high-value biochemicals. However, their commercial viability is currently constrained by energy-intensive downstream processing, particularly the cell disruption step required to recover intracellular target products from robust microalgal cells. This thesis systematically evaluates and optimizes cell disruption, framing it not as an isolated unit operation, but as a deeply integrated component of the broader biorefinery system. The research begins with a comprehensive review of conventional and emerging cell disruption technologies, identifying high energy consumption, product degradation due to harsh shear forces & temperature differences, and a lack of standardized evaluation frameworks as critical bottlenecks. Mechanical methods are subsequently evaluated as a state-of-the-art mechanical method. To demonstrate the crucial link between upstream cultivation and downstream processing, the study investigates the disruption of Neochloris oleoabundans under nitrogen-depleted and repleted conditions. The findings reveal that nitrogen depletion significantly enhances both the overall disruption efficiency and the selective release of intracellular lipids during bead milling, fundamentally challenging the assumption that mechanical disruption is inherently non-selective. To overcome the analytical limitations of conventional disruption assessment, a rapid and high-throughput flow cytometry method was developed. By correlating long-pass filter fluorescence data with gravimetric biomass release in Chlorella sp., this technique reduces measurement time from days to minutes, enabling real-time process monitoring and optimization. Finally, the thesis applies process intensification principles to develop and patent a novel continuous explosive decompression device. By optimizing CO2-liquid mass transfer and reactor design, this mild disruption method successfully addresses the limitations of traditional mechanical techniques. The continuous explosive decompression system achieves substantial energy savings—consuming significantly less energy than bead milling—while enhancing biomass release efficiency, lowering CO2 requirements, and preserving product quality. Ultimately, this work demonstrates that achieving economically feasible and sustainable microalgae biorefineries requires a holistic, systems-level design where cultivation strategies, disruption mechanisms, and analytical methodologies are jointly optimized. Bio Process Engineering VLAG Bio Process Engineering VLAG urn:nbn:nl:ui:32-1280a472-0d60-4e15-b677-0bc6fbc59e4d/obj 2026-06-12 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/666c4b8c-5864-4cf0-b35b-3eaa4a657cdf 2026-06-12 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-666c4b8c-5864-4cf0-b35b-3eaa4a657cdf 2026-06-12 urn:nbn:nl:ui:32-666c4b8c-5864-4cf0-b35b-3eaa4a657cdf/mods Molecular insights into the role of VRS5 in tillering and lateral spikelet development in barley Wageningen University dgg Winkelmolen Antonius Johannes Gerardus 0009-0001-1178-3501 0000000530276523 aut R.G.H. Immink opn G.W. Esse opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 206 10.18174/681744 en In barley, the transcription factor VRS5, regulates both tiller development and lateral spikelet development. Both of these processes are important yield related traits and their genetic connection makes it difficult to manipulate these traits independently. The main objective in this thesis was to provide molecular insights that can help untangle these traits, with the focus on VRS5. As a transcription factor, VRS5 can directly bind to DNA and regulate the expression of downstream targets. Understanding what these targets are, can help to better understand how VRS5 exactly functions and regulates these different processes. In Chapter 2, we identified these direct targets in barley by combining two techniques. Using DNA-affinity purification followed by sequencing (DAP-seq), we identified the genome-wide binding sites of VRS5. Next to that, we compared gene expression in vrs5 mutants to wild-type at four developmental stages using RNA sequencing. By combining the genes that are differentially expressed in vrs5 and the loci where VRS5 binds, we obtained a set of direct VRS5 targets that are thus bound by and regulated by VRS5. Next, we looked in more detail at VRS5 as a protein in Chapter 3. We found that in barley two different protein isoforms of VRS5 are formed; VRS5alpha and VRS5beta. We wanted to know if these isoforms function differently, and by CRISPR mutagenesis we made mutations causing only one of the protein isoforms to be formed. After investigating these lines, we found that it is possible to uncouple the tillering from the row-type function. While complete knock-out lines of vrs5 have both an increased number of tillers and six-rowed to intermediate spike phenotype, the vrs5alpha mutants only show increased tillering, but a two-rowed spike. We showed that these phenotypical differences are likely caused by differences in DNA binding of the isoforms in complex with another transcription factor, TB2. One of the direct targets of VRS5 identified in Chapter 2, VRS1 was already known as thus far the most downstream regulator of lateral spikelet development. Despite this role in such an agronomically important trait, little is known of the molecular function of VRS1. In Chapter 4, we identified the consensus DNA binding motif of VRS1, using DAP-seq. In combination with an already available RNA-seq dataset of a VRS1 allele, we also identified some potential direct downstream targets of VRS1. One of these targets was SOC1-like, of which we made CRISPR mutants. These mutants showed significantly smaller lateral spikelets compared to WT. Many of the experiments performed in this thesis would be impossible without having an efficient CRISPR based mutagenesis protocol. In Chapter 5, we showed how we greatly improved the editing efficiency of Cas9 in barley by combining several methods shown to improve editing efficiency. With this improved system we were able to generate multiple knock-out lines and even double knock-outs in primary transformants already. In conclusion, with the molecular insights provided in this thesis, I showed several potential ways to help untangle yield-related traits in barley, specifically via VRS5. EPS Molecular Biology (MOB) EPS Molecular Biology (MOB) urn:nbn:nl:ui:32-666c4b8c-5864-4cf0-b35b-3eaa4a657cdf/obj 2026-06-12 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/7ac078e3-e99c-4505-b5ff-0be85a8868ae 2026-06-10 thesis

urn:nbn:nl:ui:32-7ac078e3-e99c-4505-b5ff-0be85a8868ae 2026-06-10 urn:nbn:nl:ui:32-7ac078e3-e99c-4505-b5ff-0be85a8868ae/mods Tunable kafirin nanoparticles at oil-water interfaces: interfacial assembly and emulsion stabilization Wageningen University dgg Ye Ziyang 0000000530367580 aut L.M.C. Sagis opn J. Landman opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 206 10.18174/681875 en Pickering emulsions are stabilized by particles adsorbed at oil–water interfaces and are increasingly explored as alternatives to conventional surfactants in food systems. Kafirin, a major prolamin of sorghum that shares high homology with the well-studied maize protein zein, can self-assemble into nanoparticles and act as a Pickering stabilizer. However, the interfacial assembly and emulsion stabilization properties of these prolamin nanoparticles remain poorly understood, which limits their broader application. Due to their high surface hydrophobicity, the interfacial behavior of kafirin nanoparticles largely depends on their physicochemical properties, particle-oil interactions, and in-plane particle-particle interactions. A clear understanding of how these factors affect interfacial assembly and emulsifying properties is still lacking. This thesis answers questions regarding the effects of wettability, bioactive distribution, and oil polarity on the interfacial mechanical properties and emulsion stabilization properties of kafirin-based nanoparticles. The results provide guidance for the rational design of plant-protein-based Pickering stabilizers for bioactive encapsulation and colloidal delivery applications. VLAG Physics and Physical Chemistry of Foods VLAG Physics and Physical Chemistry of Foods urn:nbn:nl:ui:32-7ac078e3-e99c-4505-b5ff-0be85a8868ae/obj 2026-06-10 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/f0a6d472-a3a1-416c-b9b2-878653c36a67 2026-06-11 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-f0a6d472-a3a1-416c-b9b2-878653c36a67 2026-06-11 urn:nbn:nl:ui:32-f0a6d472-a3a1-416c-b9b2-878653c36a67/mods Phyllosticta on citrus: exploring pathogenicity, genomics, and taxonomy Wageningen University dgg van Ingen-Buijs Valerie A. 0000000530353664 aut P. W. Crous opn J.Z. Groenewald opn M.F. Seidl opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 191 10.18174/680968 en Citrus Black Spot (CBS), caused by the fungus Phyllosticta citricarpa, is a devastating disease that leads to significant economic losses in citrus production worldwide. In this thesis, I investigate key aspects of CBS and its closely related species to better understand fungal pathogenicity on citrus. First, I examine the fungi’s ability to grow on different substrates and explore whether these nutritional traits correlate with their capacity to cause disease. Next, I analyze genomic differences between pathogenic and non-pathogenic species to identify potential genetic determinants of virulence. To enable future functional genomics studies, I also develop and present a proof-of-principle CRISPR/Cas9-based genome editing system for one of these species. Finally, I resolve the ongoing taxonomic debate surrounding P. citricarpa and its sister species P. paracitricarpa. This work advances our understanding of pathogenicity in Phyllosticta species and provides new tools and insights that can support the development of improved disease management strategies for citrus crops. EPS Phytopathology (PHP) EPS Phytopathology (PHP) urn:nbn:nl:ui:32-f0a6d472-a3a1-416c-b9b2-878653c36a67/obj 2026-06-11 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/aa41bc4a-3733-4700-a847-958cb4d0baa5 2026-06-10 thesis

urn:nbn:nl:ui:32-aa41bc4a-3733-4700-a847-958cb4d0baa5 2026-06-10 urn:nbn:nl:ui:32-aa41bc4a-3733-4700-a847-958cb4d0baa5/mods Competencies in food technology education : a framework for the identification, selection, and implementation of competencies in a university curriculum Wageningen University dgg van Berkum Melanie 0000000530314358 aut P. den Brok opn R.M. Boom opn J. Diederen opn C.A.P. Buijsse opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 191 10.18174/681142 en Students should develop competencies during their studies, to ensure that they are prepared for their future career. In this thesis, it was studied which competencies should be developed and how these competencies can be implemented in a university curriculum. Through surveys and interviews, the most important competencies were identified that students should develop better in the bachelor programme Food Technology. Next, the presence of these competencies was mapped to identify opportunities for improvement in this bachelor. To stimulate higher-order thinking competencies, a blueprint was developed to implement collaborative learning. Furthermore, a blueprint was developed for defining and designing learning trajectories with activities to implement competencies. This thesis resulted in a framework that other study programmes can use to identify, select, and implement competencies, by providing methods to identify and select competencies, and by providing frameworks to implement competencies in learning trajectories. Food Process Engineering VLAG Education and Learning Sciences Food Chemistry Food Process Engineering VLAG Onderwijs- en leerwetenschappen Levensmiddelenchemie urn:nbn:nl:ui:32-aa41bc4a-3733-4700-a847-958cb4d0baa5/obj 2026-06-10 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/61528661-f93a-4595-85a2-f8f132f051c3 2026-06-10 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-61528661-f93a-4595-85a2-f8f132f051c3 2026-06-10 urn:nbn:nl:ui:32-61528661-f93a-4595-85a2-f8f132f051c3/mods Inverse modeling of carbonyl sulfide to constrain photosynthesis across scales Wageningen University dgg Cho Ara 0000000530302066 aut M.C. Krol opn L.M.J. Kooijmans-de Vries opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 159 10.18174/681148 en This dissertation evaluated the potential of carbonyl sulfide (COS) as a tracer for gross primary productivity (GPP) by combining experiments, modeling, and inverse analyses from leaf to global scales. The central finding is that COS provides valuable complementary information on plant carbon uptake, but its quantitative use as a global proxy for GPP remains constrained by both physiological and methodological uncertainties. A key contribution of this work is to show that COS does not simply scale linearly with CO2 uptake. Leaf-level experiments revealed conditions under which COS uptake responded differently from photosynthesis, including high-temperature emission potentials and amplified sensitivities to stomatal closure. At larger scales, these physiological characteristics necessitated refinements in model parameterizations of stomatal and mesophyll conductance. Although such improvements enhanced agreement with site-level flux observations after parameter optimization, the global inversions continued to reveal structural limitations—most notably a strong dependence on prior COS vegetation fluxes, incomplete representation of COS-specific processes, and the absence of diurnal variability in the inversion framework. This dissertation further demonstrates that COS can provide information on photosynthesis that is not accessible from CO2 alone. At the leaf scale, COS uptake offered additional constraints on stomatal conductance, complementing the traditional reliance on H2O and CO2 observations. At the canopy scale, COS fluxes revealed additional insights into stomatal dynamics during autumn and at night, and suggested improvements in the treatment of humidity stress as well as an original stomatal conductance model in SiB4. At the global scale, COS provided limited additional constraints on CO2, primarily due to the sparse observational coverage of COS and the resulting weak constraints, compounded by structural limitations in current model. Nevertheless, the inversion results showing a persistent underestimation of the COS vegetation sink at high latitudes may point to biases in current GPP representations. Taken together, these results show that COS contributes independent and complementary information across scales, underscoring its potential as a tracer of photosynthesis. At the same time, they emphasize that further progress depends on (i) refining the mechanistic understanding of COS exchange across species and environments, (ii) improving the representation of nocturnal and stress-related processes in land surface models, (iii) strengthening coupled CO2–COS inversion frameworks, and (iv) expanding observational networks globally through coordinated campaigns and satellite missions. These advances will determine the extent to which COS vegetation fluxes can be integrated into robust global monitoring of GPP. WIMEK Meteorology and Air Quality WIMEK Meteorologie en Luchtkwaliteit urn:nbn:nl:ui:32-61528661-f93a-4595-85a2-f8f132f051c3/obj 2026-06-10 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/d4f6a6e8-2f92-436f-a038-b3fad015313a 2026-06-09 thesis

urn:nbn:nl:ui:32-d4f6a6e8-2f92-436f-a038-b3fad015313a 2026-06-09 urn:nbn:nl:ui:32-d4f6a6e8-2f92-436f-a038-b3fad015313a/mods Antarctic tourism diversification : Governance, place-making, and values in the Antarctic Treaty System Wageningen University dgg Makanse Yousra 0000-0003-3095-326X 0000000530331967 aut E.H. Huijbens opn K. Bastmeijer opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 343 10.18174/681561 en This dissertation examines the diversification of Antarctic tourism and its implications for tourism practices, Antarctic places, governance, and the values and principles of the Antarctic Treaty System (ATS). While Antarctic tourism has expanded significantly in recent decades, diversification has often been discussed primarily in relation to individual activities or emerging risks rather than as an ongoing process shaping how tourism develops and is governed over time. Drawing on interdisciplinary insights from tourism studies, cultural geography, policy, and legal scholarship, this dissertation investigates how diversification unfolds in practice, how it is framed and addressed within ATS policy debates, how it contributes to Antarctic place-making, and how ATS values and principles are interpreted and enacted in tourism governance. The overarching research question guiding this dissertation is: How does Antarctic tourism diversification shape tourism practices, Antarctic places, and governance, and how are Antarctic Treaty System values and principles reflected in this? This dissertation shows that Antarctic tourism diversification involves the gradual normalization of new forms of access, presence, and engagement with Antarctica, reshaping how tourism is practiced and how the continent is experienced. These changes also contribute to Antarctic place-making by reinforcing imaginaries of Antarctica as exploratory, exceptional, consumable, or spectacular, thereby shaping expectations about appropriate forms of human presence on the continent. At the governance level, responses have often been reactive and fragmented, allowing tourism developments to become established through continued practice rather than explicit collective decisions. In this sense, governance inaction functions as an enabling condition for diversification. Finally, while ATS values and principles remain central to Antarctic governance, their influence depends on how consistently they are translated into concrete governance arrangements and decision-making practices. In light of these dynamics, Antarctic tourism governance requires a shift away from reactive responses toward more comprehensive and anticipatory approaches that strengthen collective capacity to guide tourism development in advance and align it more closely with ATS values and principles. By conceptualizing Antarctic tourism diversification as a process with material, spatial, institutional, and normative implications, this dissertation contributes empirically and conceptually to Antarctic tourism scholarship and offers policy-relevant insights to support more proactive, coordinated, and value-informed approaches to Antarctic tourism governance. WASS Cultural Geography WASS Cultural Geography urn:nbn:nl:ui:32-d4f6a6e8-2f92-436f-a038-b3fad015313a/obj 2026-06-09 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/5170fb16-82fb-4037-b9a9-f72943430527 2026-06-10 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-5170fb16-82fb-4037-b9a9-f72943430527 2026-06-10 urn:nbn:nl:ui:32-5170fb16-82fb-4037-b9a9-f72943430527/mods Mammal density estimation using camera traps: new perspectives Wageningen University dgg He Shuiqing 0000000530331940 aut F. van Langevelde opn P.A. Jansen opn J.M. Rowcliffe opn C. Carbone opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 118 10.18174/681912 en Reliable estimates of wildlife abundance are fundamental to ecological research and conservation. Over the past decades, camera traps have become a central tool for wildlife monitoring because they provide non-invasive observations across broad spatial and temporal scales. However, camera-trap data do not directly reflect animal density. As a result, variation in detectability represents a key limitation for inference from camera-trap data and can therefore be seen as “the Achilles’ heel” of camera trapping. This thesis addresses how wildlife density estimation from camera-trap data can be improved by explicitly accounting for detection processes and detectability, with a focus on unmarked terrestrial mammals that cannot be individually identified. Using the Random Encounter Model (REM) as a analytical framework, the thesis examines how deployment decisions, detection geometry, and data structure jointly shape what can be inferred from camera-trap encounters. Rather than treating camera deployment as a fixed design choice, the work views deployment orientation and detectability as integral components of density inference. At the site level, this thesis extends the REM to vertically oriented camera traps. Vertical deployments can substantially reduce camera damage, theft, and data loss in high-risk field conditions, but they alter detection geometry relative to conventional horizontal setups. By reformulating detection-zone geometry and associated parameters, this work demonstrates that density estimation for unmarked species can be maintained under vertical deployment when changes in detectability are explicitly incorporated. Empirical comparisons between vertical and horizontal deployments show that protection and detectability are linked through a measurable trade-off, governed primarily by the relationship between mounting height and species-specific effective detection distance. Beyond site-level estimation, this thesis addresses the challenge that most existing camera-trap datasets consist capture-rate information only and lack the additional parameters or specific study design required for full density estimation designed for unmarked species these years. To improve the interpretability of such data, the thesis develops a mass-relative abundance index (mRAI) that accounts for systematic differences in detectability among species. By incorporating scaling relationships between body mass, movement behaviour, and detection processes, mRAI improves correspondence between capture rates and independently estimated density across species. Taken together, the chapters demonstrate that variation in detection processes underlies both methodological and practical limitations of camera-trap–based inference. By adapting detection geometry to alternative deployments and correcting capture-rate indices for detectability, this thesis extends the conditions under which camera-trap data can be used to reflect animal abundance in a more robust way. These contributions do not eliminate all sources of bias in camera-trap data, nor do they resolve all camera-trap–based limitations. Rather, they provide concrete and tested approaches that reduce data and equipment loss, improve inferential robustness, and enable more effective use of the exisiting camera-trap datasets. More broadly, this work highlights that future progress in camera-trap ecology depends on recognising the detection process as the link between animal density and observed data. By linking deployment design, detection geometry, and scalable inference, this thesis contributes a coherent framework for improving wildlife density estimation from camera-trap data across local, regional, and macroecological scales. PE&RC Wildlife Ecology and Conservation PE&RC Natuurecologie en natuurbehoud urn:nbn:nl:ui:32-5170fb16-82fb-4037-b9a9-f72943430527/obj 2026-06-10 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/bfcbeeb4-d116-4b56-9f34-b2f7c9c8ff34 2026-06-09 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-bfcbeeb4-d116-4b56-9f34-b2f7c9c8ff34 2026-06-09 urn:nbn:nl:ui:32-bfcbeeb4-d116-4b56-9f34-b2f7c9c8ff34/mods Seeding water : Unravelling the sociohydrology of small-scale managed aquifer recharge and drought mitigation: insights from Mexico, Ethiopia, and India Wageningen University dgg Basel Britt 0000000530367871 aut P.J.G.J. Hellegers opn J.D. Hoogesteger van Dijk opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 252 10.18174/681471 en Groundwater sustains life and livelihoods across much of the world. Shallow aquifers can buffer drought, storing precipitation during wetter periods that later sustains people and ecosystems. These reserves are being depleted, while groundwater recharge is increasingly limited by environmental degradation, urbanized landscapes, and shifting patterns of precipitation and temperature. Such trends are not only 'environmental.' They are shaped by decisions about land, infrastructure, and water allocations, and by what 'needs,' and whose 'needs,' are prioritized. Human responses to depleted aquifers are hydrological and technical. They are also unavoidably social, political, and rooted in how people value and understand both water and each other. Small-scale managed aquifer recharge (s-MAR), the replenishment of unconfined aquifers through low-cost, ecologically regenerative structures including check dams and gully restoration, is one response. Whether s-MAR addresses water scarcity, who benefits, and what it sets in motion depends on more than hydrology. Drawing on the social and hydrological sciences, this research asks: Why and how do people act to implement and maintain s-MAR, and how does s-MAR (re)shape social and hydrological systems? I developed a sociohydrological framework sharpened by political ecology to conceptualize what drives s-MAR implementation, how multi-scalar political and economic dynamics enable or undermine local action, and resulting feedback loops and consequences. Contrary to previous sociohydrological theory, experiencing drought was not a primary driver for action; it was people knowing they could act and experiencing benefit. Sustained s-MAR was rooted in increased hydrological fluency through direct participation; values of reciprocity and mutual accountability; participatory decision-making; local institutions organizing collective action; and a strengthened relationship between people and place. These dynamics enhanced capacity to respond to, cope with, or transform amid water scarcity and other hazards. Unintended consequences common in water interventions, for example, greater water availability resulting in increased use and renewed scarcity, were largely absent. This research argues that such consequences are not universal but reflect how water is understood and valued within a given context. These findings inform the Sociohydrology of Interventions Framework (SHIF), which provides a structure for understanding complex dynamics when implementing interventions intended to address water-related hazards. By integrating social norms, power relations, and institutions within linked human-water-climate systems, SHIF advances sociohydrology toward a more ontologically aware and context-based science of praxis. WASS Water Resources Management WASS Water Resources Management urn:nbn:nl:ui:32-bfcbeeb4-d116-4b56-9f34-b2f7c9c8ff34/obj 2026-06-09 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/ee985821-aae0-4f61-9694-622a9426a094 2026-06-08 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-ee985821-aae0-4f61-9694-622a9426a094 2026-06-08 urn:nbn:nl:ui:32-ee985821-aae0-4f61-9694-622a9426a094/mods Multispecies swards and multiple soil functions: evidence from agricultural grasslands Wageningen University dgg Obasoro Omotola 000000053033202X aut E. Hoffland opn R.G.M. de Goede opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 184 10.18174/681125 en Growing global population, increasing income, and dietary shifts toward animal-based food have intensified livestock production, increasing resource use and environmental footprint. Transitioning to a more sustainable livestock production system is therefore a priority in many countries in the European Union. However, conventional agricultural grasslands are typically dominated by perennial ryegrass (Lolium perenne) monoculture, which require high levels of mineral nitrogen (N) fertilizer with associated environmental impact. Increasing plant species diversity through the inclusion of legumes and forbs has shown to enhance the delivery of soil-based ecosystem services in semi-natural experimental grassland but the direct extrapolation of these findings to agricultural grasslands is limited. Moreover, there is limited evidence on the effect of sward diversification and management practices on the simultaneous delivery of multiple soil-based ecosystem functions. Therefore, the main aim of this research is to examine how different sward types, managed with different N fertilizer forms, influence multiple soil-based ecosystem functions in agricultural grasslands.To achieve this, I conducted greenhouse and field experiments using four sward types: perennial ryegrass monoculture, permanent pasture and two multispecies swards and three N fertilizer treatments: mineral N fertilizer (protected urea), organic fertilizer (cattle slurry), and a combination of both mineral and organic fertilizers. Multispecies swards outperformed perennial ryegrass monocultures in terms of biomass production, N yield and N use efficiency (NUE) despite receiving lower N fertilizer amount primarily due to the presence of legumes. However, the high NUE in the multispecies swards was accompanied by a more negative partial N balance – an indication of soil N depletion, suggesting a trade-off. Swards managed using a combination of mineral and organic N fertilizer did not consistently achieve the highest herbage N yield or NUE. Zn and Se uptake increased with increasing species richness with multispecies swards achieving greater Zn and Se uptake than perennial ryegrass monoculture. The results further indicated that legumes, rather than grasses facilitated Zn and Se uptake for the neighbouring species. There was also an indication of asymmetric facilitation in which some legumes increased Zn and Se uptake for the neighbouring species at their own expense. Multispecies swards supported lower abundance of plant-parasitic nematodes than perennial ryegrass monoculture. This suggests that diverse swards may be less favourable to plant-parasitic nematodes, potentially due to the inclusion of legumes and forbs that are considered less suitable hosts. However, the sustenance of this benefit may be dependent on maintaining the species composition of the multispecies sward, which may require frequent reseeding and the associated costs. The limited effect of organic N fertilizer observed may reflect the short timeframe of this study, as benefits associated with organic N inputs often emerge over longer periods. In conclusion, the results showed that increasing plant diversity through the inclusion of legumes and forbs can deliver multiple ecosystem functions simultaneously in agricultural grasslands, although trade-offs exist and this require careful consideration. While mineral N fertilization supported greater biomass production and NUE compared to organic or combined fertilizer treatments, this should be interpreted with care as they reflect short-term responses. PE&RC Soil Biology Soil Biology Operations Manager PE&RC Bodembiologie Soil Biology Operations Manager urn:nbn:nl:ui:32-ee985821-aae0-4f61-9694-622a9426a094/obj 2026-06-08 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/268316e3-b433-480a-8dbd-f926ae147058 2026-06-08 thesis

urn:nbn:nl:ui:32-268316e3-b433-480a-8dbd-f926ae147058 2026-06-08 urn:nbn:nl:ui:32-268316e3-b433-480a-8dbd-f926ae147058/mods Health at steak : dairy and meat consumption and the risk of cancer recurrence and mortality in subgroups of individuals with colorectal cancer Wageningen University dgg van Lanen Anne-Sophie 0000000530302082 aut E. Kampman opn F.J.B. van Duijnhoven opn D.E. Kok opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 204 10.18174/681456 en Colorectal cancer (CRC) accounts for around 10% of all cancer cases globally. There is strong evidence that dairy consumption reduces the risk of developing CRC, while processed meat and unprocessed red meat intake increase the risk of CRC. It is unclear whether dairy and meat intake also influence the risk of cancer recurrence and mortality after a CRC diagnosis, and whether associations are similar for different types of products and for different subgroups of individuals with CRC. The aim of this thesis was twofold: 1) to investigate whether dairy and meat intake are associated with the risk of recurrence and mortality after a stage I-III CRC diagnosis, and 2) to study whether this applies equally to different subgroups of individuals. In doing so, this thesis aimed to support the development of more personalised dietary guidelines for individuals with CRC.A higher pre-diagnostic low-fat dairy intake was associated with a reduced risk of recurrence in individuals with stage I-III CRC in Chapter 2. Higher pre-diagnostic intakes of low-fat dairy and yoghurt were associated with a reduced risk of all-cause mortality, while a higher intake of high-fat dairy tended to be associated with an increased all-cause mortality risk. Milk and cheese were not associated with disease prognosis. Building on Chapter 2, Chapter 3 focused on low- and high-fat dairy and recurrence risk in subgroups. Especially in men, a higher pre-diagnostic low-fat dairy intake was associated with a reduced risk of recurrence. High-fat dairy was associated with an increased risk of recurrence in individuals with colon cancer, but not in those with rectal cancer. Observed associations were not different by stage. Pre- and post-diagnostic intakes of processed meat and unprocessed red meat were not associated with risk of recurrence or all-cause mortality in Chapter 4. However, results should be interpreted with caution until we can biologically explain why processed meat and unprocessed red meat are associated with CRC development, but do not seem associated with disease prognosis. Pre- and post-diagnostic unprocessed poultry intakes were associated with a reduced all-cause mortality risk. Observed associations were not different by sex, tumour location, or stage. Studying dairy and meat intake in relation to the risk of recurrence in subgroups based on molecular tumour characteristics in Chapter 5, a higher pre-diagnostic intake of processed meat was associated with a decreased risk of recurrence in microsatellite stable KRAS-mutated colon cancer, but not in microsatellite stable KRAS-wildtype CC. However, the number of participants was limited for some analyses, and results need to be confirmed in larger studies. Future observational and intervention studies should confirm these findings, investigate the potential effect of substitution of high-fat dairy with low-fat dairy, and aim to establish causality. In subgroup analyses, they should further study associations in subgroups of sex and molecular tumour characteristics, study proximal and distal colon cancer separately, and clarify underlying biological mechanisms to contribute to more tailored and CRC-specific dietary recommendations. Ultimately, CRC-specific dietary guidelines may serve as a useful tool for individuals with CRC to improve their disease prognosis. VLAG Nutrition and Disease VLAG Voeding en Ziekte urn:nbn:nl:ui:32-268316e3-b433-480a-8dbd-f926ae147058/obj 2026-06-08 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/516c305d-c6cc-4ef4-a5bf-c7a781dfc33b 2026-06-04 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-516c305d-c6cc-4ef4-a5bf-c7a781dfc33b 2026-06-04 urn:nbn:nl:ui:32-516c305d-c6cc-4ef4-a5bf-c7a781dfc33b/mods From soil to tuber: cadmium uptake by potato plants and remediation mechanisms Wageningen University dgg Qin Yuwei 0000000530314366 aut R.N.J. Comans opn J.E. Groenenberg opn S. Alves opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 220 10.18174/681242 en High levels of geogenic soil cadmium (Cd) concentration have been reported in certain regions of the world, potentially increasing the risk of Cd concentrations in edible parts of agronomic crops, such as potatoes, exceeding their maximum allowable level of 0.1 mg Cd kg (fresh weight, FW)-1 set by various jurisdictions globally. Ireland has strong historical and cultural ties to potato cultivation, and potato-based foods are a significant dietary preference for its population. Consequently, the elevated Cd concentrations in Irish soils pose a substantial risk of excessive Cd exposure through potato consumption. Due to the geogenic origin of Ireland’s Cd problem, rather than anthropogenic inputs, nationwide research in Ireland has focused on soil amendments and breeding low-Cd potato cultivars. In previous field trials conducted by Teagasc, the agriculture and food development authority of Ireland, various soil organic amendments were selected and tested for their efficacy in reducing Cd content in potatoes and carrots. Results showed that, when applied at their highest rates, spent mushroom compost (SMC), poultry manure, and farmyard manure reduced tuber Cd concentrations by up to 40% relative to tubers grown in unamended soil. However, no single amendment consistently and significantly reduced tuber Cd across all tested soils. Therefore, a systematic understanding of the factors influencing Cd transfer from soil to potato tubers, as well as the mechanisms underlying the ameliorative effects of soil amendments, is essential. In this thesis, I traced the transfer of Cd from soil to potato tubers to study its uptake mechanisms and to evaluate the effectiveness of several soil amendments in reducing tuber Cd concentration, with a primary focus on soil geochemical processes. This thesis consists of four main chapters (Chapters 2-5) and a general discussion (Chapter 6). WIMEK Soil Chemistry WIMEK Soil Chemistry urn:nbn:nl:ui:32-516c305d-c6cc-4ef4-a5bf-c7a781dfc33b/obj 2026-06-04 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/aebf190b-b606-4405-a16e-f308c2aadfec 2026-05-29 thesis

urn:nbn:nl:ui:32-aebf190b-b606-4405-a16e-f308c2aadfec 2026-05-29 urn:nbn:nl:ui:32-aebf190b-b606-4405-a16e-f308c2aadfec/mods UAV-Based maize disease monitoring: Integrating physical models and machine learning Wageningen University dgg Bai Yali 0000000530314374 aut B. Tekinerdogan opn X. Jin opn Q. Liu opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 196 10.18174/682139 en This PhD research uses drone technology to better protect corn crops from devastating diseases. Finding disease plants early is traditionally difficult. To solve this, we equipped drones with advanced cameras that capture light beyond human vision, allowing us to monitor maize health from the sky. The core innovation combines artificial intelligence (AI) with computer simulations of how plants reflect light. This approach led to two major breakthroughs: a new tool for spotting diseases much earlier than human observation, and a predictive model that acts like a "weather forecast" for crop infections, anticipating exactly where and when disease will spread across a field. For agriculture, these early-warning systems are game-changing. They empower farmers to intervene before crops are severely damaged. Ultimately, this research drives smarter precision farming, helping secure global food production and minimize losses. Information Technology WASS Toegepaste Informatiekunde WASS urn:nbn:nl:ui:32-aebf190b-b606-4405-a16e-f308c2aadfec/obj 2026-05-29 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/37a90ae9-ff8b-4876-bc61-a3a7105b0685 2026-06-04 thesis

urn:nbn:nl:ui:32-37a90ae9-ff8b-4876-bc61-a3a7105b0685 2026-06-04 urn:nbn:nl:ui:32-37a90ae9-ff8b-4876-bc61-a3a7105b0685/mods Ion-Selective electrodialysis for water treatment applications : Transport phenomena in polyelectrolyte multilayer membranes Wageningen University dgg Elozeiri Alaaeldin A.E. 0000000530302138 aut H.H.M. Rijnaarts opn J.E. Dykstra opn R. Lammertink opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 369 10.18174/681713 en Ion-selective separations can address important societal challenges, for example, by recovering valuable nutrients from wastewater, making brine streams usable, and removing unwanted minerals from irrigation water. Electrodialysis is a water technology that can be applied for ion-selective separations. In electrodialysis, an electric potential difference is applied across special membranes to transport dissolved salts (ions) from one aqueous stream to another. We explored how inorganic ions, like sodium, phosphate, and calcium, move across different types of membranes during electrodialysis. The membrane surface was coated with several layers of charged polymers (polyelectrolyte multilayers) in order to enhance the transport selectivity of monovalent ions over multivalent ones, for example, K+/Mg2+. Furthermore, we explored the application potential of electrodialysis for brine management as well as the production of acids and bases from untreated brine or seawater. The acid and base products of electrodialysis can be used in various water treatment processes, for example, to regenerate ion-exchange columns used for ultrapure water production. Lastly, we characterized the regeneration wastewater of industrial ion-exchange columns and presented strategies to reduce the water and chemical footprint of the regeneration process. WIMEK Environmental Technology WIMEK Milieutechnologie urn:nbn:nl:ui:32-37a90ae9-ff8b-4876-bc61-a3a7105b0685/obj 2026-06-04 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/b7c23573-ab9b-43e8-ba5a-557fed059263 2026-06-05 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-b7c23573-ab9b-43e8-ba5a-557fed059263 2026-06-05 urn:nbn:nl:ui:32-b7c23573-ab9b-43e8-ba5a-557fed059263/mods Improving solar-induced fluorescence retrieval from GOME-2 and TROPOMI for long-term vegetation monitoring Wageningen University dgg Anema Juliëtte C.S. 000000053027654X aut K.F. Boersma opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 198 10.18174/681681 en The biosphere plays a key role in the carbon cycle by acting as a major carbon sink. During photosynthesis, vegetation takes up carbon dioxide (CO2) and mitigates climate change by damping atmospheric CO2 buildup. As such, land-based mitigation techniques (LMTs), like reforestation, are central in climate strategies. LMTs are deliberate human actions aimed at enhancing the land’s capacity to sequester carbon. Despite their crucial role in achieving the Paris Agreement targets, the magnitude and variability of the global land carbon sink remain highly uncertain. This study uses satellite remote sensing to observe faint optical light emitted by plants during photosynthesis. This light signal (650—850 nm), referred to as solar-induced fluorescence (SIF), is directly linked to photosynthesis, and thus carbon uptake. Therefore, space-based SIF observations have high potential to enhance understanding of vegetation activity at a global scale. This thesis has two goals: (1) assess the fitness-for-purpose of space-based SIF data as a monitoring tool for LMTs and (2) building a consistent satellite climate data record of SIF. First, we evaluated the applicability of SIF for vegetation monitoring within the European Union Horizon 2020 LANDMARC project. The analysis used SIF observations from TROPOMI and GOME-2A to assess two distinct cases of land-use change: a 2019 eucalyptus wildfire in Australia and large-scale reforestation in China. This work demonstrates that SIF captures both abrupt disruptions and gradual vegetation change. When combined with complementary data, such as land cover data, the response of vegetation can be linked to the land-use change. The second goal was to construct a consistent long-term SIF record. Specifically, we focused on retrieving SIF from the Global Ozone Monitoring Experiment-2 (GOME-2) series. This series consists of three sensors (GOME-2A, GOME-2B, and GOME-2C) with identical design, which were launched in sequence. Together, GOME-2 provides a continuous record since October 2006, spanning over 18 years. However, instrument degradation introduces artificial trends within each record, limiting their robustness and across-sensor harmonisation. To correct for these artificial trends, an advanced in-flight degradation correction was implemented in the improved Solar-Induced Fluorescence of Terrestrial Ecosystems Retrieval (SIFTER) retrieval algorithm: SIFTER v3. SIFTER v3 improved the GOME-2 SIF retrieval by correcting time, wavelength, and scan-angle dependencies of instrument degradation. Thereby, SIFTER v3 enabled retrieval of stable SIF records from GOME-2A (2007 to 2017), GOME-2B (2012 to 2023), and GOME-2C (2019 to 2024), showing high consistency with independent GPP data from FluxSat and FLUXCOM-X. SIFTER v3 also allowed harmonisation of SIF across the different GOME-2 sensors. When accounting for viewing-angle differences, GOME-2A and GOME-2B can be merged to obtain a coherent long-term time series of SIF products. SIFTER v3 was also successfully applied to TROPOMI, contributing to inter-sensor comparability. Finally, we show that SIF depends on viewing geometry, driven by factors such as canopy structure and hotspot effects, with higher values at off-nadir viewing angles. Consistent sampling of viewing angles is required for robust comparison. Overall, this work contributed to the creation of long-term satellite-based SIF records, which show high potential to enhance understanding of vegetation dynamics worldwide. WIMEK Air Quality Meteorology and Air Quality WIMEK Luchtkwaliteit Meteorologie en Luchtkwaliteit urn:nbn:nl:ui:32-b7c23573-ab9b-43e8-ba5a-557fed059263/obj 2026-06-05 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/6410cce6-54b5-4c84-9cfa-cc807ebc894b 2026-06-05 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-6410cce6-54b5-4c84-9cfa-cc807ebc894b 2026-06-05 urn:nbn:nl:ui:32-6410cce6-54b5-4c84-9cfa-cc807ebc894b/mods Decoding nodules : The spatiotemporal hormonal regulation of tissue-specific nodule initiation in Medicago truncatula Wageningen University dgg Müller Sophia 0000000530228513 aut V. Willemsen opn W. Kohlen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 233 10.18174/681603 en This thesis explores how certain plants, such as Medicago truncatula (Medicago), form a close partnership with soil bacteria collectively called rhizobia. These rhizobia have the unique ability to convert atmospheric dinitrogen (N2) into a form that plants can use for growth. In return, the plant provides the bacteria with sugars and a protected space inside small structures on its roots known as nodules. This interaction is especially important because nitrogen is an essential nutrient for plant growth. However, plants cannot access it directly from the atmosphere, but require a reduced form, such as ammonium (NH4+), which rhizobia provide. This research focuses on how these nodules begin to form, particularly during the earliest stages. A key question is how specific root cells know when and where to change their identity and start forming a root nodule. Unsurprisingly, plant hormones play a central role in guiding this process. One of these hormones, auxin, is known to regulate plant growth. Part of this work demonstrates that auxin accumulates very early in specific root cells in the pericycle after bacterial infection, prior to the first cell divisions. From here, it is relocated towards the root cortex. This process is tightly controlled through both local production and polar transport within the root and is essential for initiating cell divisions and nodule formation. In contrast, the hormone ethylene acts as a repressor of nodulation. The detected ethylene readout clearly shifts from the inside to the outside root tissue, preventing excessive nodule initiation. Additionally, ethylene acts in positioning nodules towards the xylem of the plant. Although the role of ethylene in nodule positioning was known, our results show that the mechanism by which this occurs is more complex than was previously assumed. This demonstrates that the function of ethylene is probably more than just an inhibitor of nodulation. The examples of auxin and ethylene emphasized how important the regulation of hormones and gene expression is in time and space during nodulation. Therefore, the next step in this thesis was to generate a near cell-type specific resolution atlas of gene expression during nodule initiation and development. This was reached by developing single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq) for Medicago. Using this dataset, transcription factors were identified, that showed expression in the pericycle, which was validated in planta. Although the expression of these genes correlated with nodule initiation, their direct involvement in regulating nodulation could not reproducibly be validated. This either indicates limitations of our genetic tools, more complex regulatory mechanisms, or the need for stringent candidate selection. Together, this thesis provides insights into how Medicago controls nodule formation, both in space and time. Furthermore, it contains the first, robust, single-cell atlas of the root susceptible zone during nodule initiation, and describes how to generate such high-resolution atlases, which can be applied in other, legume, species. EPS Cell Biology (CBL) EPS Cell Biology (CBL) urn:nbn:nl:ui:32-6410cce6-54b5-4c84-9cfa-cc807ebc894b/obj 2026-06-05 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/b9721924-d842-43d8-bb3f-eae4cc719191 2026-06-04 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-b9721924-d842-43d8-bb3f-eae4cc719191 2026-06-04 urn:nbn:nl:ui:32-b9721924-d842-43d8-bb3f-eae4cc719191/mods Between Boundaries and Bridges : Friction, translation, and mutual learning in mangrove swamp rice farming in Guinea-Bissau Wageningen University dgg Sandoval Joseph Daniel 0000000530253284 aut C.J. Ritsema opn J. Vos opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 172 10.18174/681403 en This thesis examines friction as the messy and uneven quality of knowledge encounters, or moments in which different knowledge systems meet across domains such as research, development, and conservation. While friction has often been used to describe tensions, misalignments, and power relations, it is frequently treated as background rather than analysed in its own right. This thesis instead places friction at the centre of analysis and treats it as an entry point for generating insight into the possibilities, limits, and conditions of mutual learning and collaboration within knowledge encounters. To do so, it develops a theoretical–methodological framework—translating along friction—that approaches friction as something to work through rather than resolve. Translation here refers to making sense of knowledge in each other’s frames while remaining grounded in context. It is understood as contextual, multi-directional, and situated: knowledge is rooted in socio-ecological settings, reshaped through reciprocal interaction, and performed by actors who must remain reflexive about their own assumptions and positionalities. The framework is applied to the water management of mangrove swamp rice farming in Guinea-Bissau, where farmers’ livelihoods depend on reading and adapting to tides and mangrove ecosystems, as well as managing dikes and drainage. These practices are increasingly shaped by interventions from researchers, NGOs, and government actors, bringing endogenous and exogenous knowledge systems into contact and, often, into friction. The thesis follows four interrelated empirical cases—tides, dikes, pipes, and mangroves—each highlighting a distinct form of friction: between farmers’ and scientific knowledge, among farmer groups, between local practices and exogenously introduced technologies, and between global environmental agendas and local livelihood needs. Across these cases, translating along friction reveals translation, mutual learning, and collaboration as situated, partial, and recursive processes shaped by diversity, Overall, the thesis illustrates that mutual learning and collaboration are not smooth or complete processes, but are partial, situated, and shaped by power and difference. By engaging with friction rather than avoiding it or keeping it in the background, the thesis offers a way to better understand how diverse knowledge systems can work together without erasing their differences.assumptions, and hierarchies. WIMEK Soil Physics and Land Management Water Resources Management WIMEK Bodemfysica en Landbeheer Water Resources Management urn:nbn:nl:ui:32-b9721924-d842-43d8-bb3f-eae4cc719191/obj 2026-06-04 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/77d5c164-b123-4d56-bd4e-9aeb709774f9 2026-06-04 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-77d5c164-b123-4d56-bd4e-9aeb709774f9 2026-06-04 urn:nbn:nl:ui:32-77d5c164-b123-4d56-bd4e-9aeb709774f9/mods Spodoptera frugiperda management using local resources in the maize smallholder farming system in Zambia Wageningen University dgg Durocher-Granger Léna 000000053027646X aut M. Dicke opn C. Leeuwis opn D. Ludwig opn M. Kenis opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 212 10.18174/680979 en Fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), an insect pest originating from the Americas, has become one of the main invasive alien species (IAS) worldwide since it was first detected in 2016 in Africa, where it causes considerable losses on cereals such as maize, sorghum, rice and sugarcane. The majority of African governments reacted to FAW outbreaks by purchasing and providing, for free, massive amounts of synthetic pesticides to smallholder farmers in the hope to mitigate crop losses, raising great concerns for health and environmental risks. When applied individually on a field-by-field basis, synthetic pesticides have little impact on highly mobile insect pests such as FAW, which can travel hundreds of kilometres to find a suitable maize field to oviposit. Over the past few decades, scientists investigated the role of collective action for invasive species management and found that the principles can be applied and adapted to reduce the damage caused by IAS across a landscape. However, its application is still poorly studied in low- and middle-income countries where national plant health systems in place to prevent and manage biological invasions, are limited. “Collective pest management” can provide benefits over individual field-by-field management, especially for highly mobile pests when consistent and coordinated actions are implemented. The geographic focus of my thesis was located in the maize belt of Central and Lusaka provinces of Zambia where FAW is a major pest problem. In chapter 2, I surveyed the local native parasitoid species successfully attacking FAW and evaluated the factors affecting their occurrence. Chapter 3 studies the feasibility of creating a collective action to promote biological control of FAW among maize smallholder farmers in rural Zambia, and the social and institutional conditions needed for it to be successful and sustainable. Chapter 4 reports preliminary effects of planting date and maize growth stages on FAW density and on its local parasitoids from a field study. Chapter 5 explores the influence of intercropping maize on FAW density and parasitoids occurrence. In this chapter, I focused on investigating the natural resources available for smallholder farmers to maximize pest control by intercropping maize with commonly grown crops. Chapter 6 consolidates the entomology and social sciences by assessing the experiences of smallholder farmers with intercropping maize with local companion crops. Specifically, I assessed their experiences in terms of ecological knowledge, willingness and preferences to operationalize collective action principles, long-term pest management and evaluated their limiting factors. Considering all the findings from the five empirical chapters, I consolidated and synthesized in Chapter 7 the new insights and perspectives created during this interdisciplinary research, integrating the viewpoints of farmers who participated in the co-design, implementation and testing of intercropping practices. I further discussed the implications and influence of my research on national policies and challenge the current agricultural extension system, which focuses on reactive and individual pest management approaches. I also discussed the limitations of my research and concluded by emphasizing the need for new collective pest management approaches to uplift biocontrol programmes. PE&RC Entomology (ENT) Knowledge Technology and Innovation PE&RC Entomology (ENT) Kennis, Technologie and Innovatie urn:nbn:nl:ui:32-77d5c164-b123-4d56-bd4e-9aeb709774f9/obj 2026-06-04 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/0cb86539-48c2-48e4-99fb-49908c0d6fcf 2026-05-28 thesis

urn:nbn:nl:ui:32-0cb86539-48c2-48e4-99fb-49908c0d6fcf 2026-05-28 urn:nbn:nl:ui:32-0cb86539-48c2-48e4-99fb-49908c0d6fcf/mods The role of service plants in promoting biological pest control and pollination in Xinjiang pear Wageningen University dgg Sun Mengxiao 000000053030204X aut W. van der Werf opn F.J.J.A. Bianchi opn Y. Lu opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 190 10.18174/681120 en Enhancing ecosystem services such as biological pest control and pollination through the use of service plants is an important strategy for sustainable agriculture. However, the effectiveness of service plants depends on their traits, the resources provided to target insects, and integration into crop management. This thesis examined which traits of flowering plant species attract natural enemies and pollinators, and how alfalfa (Medicago sativa), a commonly used fodder plant, influences beneficial insects and ecosystem services in pear orchards in Xinjiang, China. Associations between plant traits, aphid prey, and natural enemy communities were assessed for 39 plant species, and between plant traits and pollinator communities for 38 species, using visual counts and sweep netting. Natural enemy abundance was primarily driven by aphid availability, with ladybeetles, predatory bugs, parasitoids, and aphid mummies responding positively to higher aphid densities. Certain plant traits influenced specific insect groups: ladybeetle adults were more abundant on plants with open corollas and extrafloral nectar, particularly when aphid densities declined, while plants with shallow corollas and longer flowering periods supported higher abundances of hoverflies, honeybees, and wild bees. Several species, including fennel, dill, arugula, and sweet alyssum, attracted both natural enemies and pollinators. Alfalfa supported diverse beneficial insect communities within orchard ground cover but had limited effects on pest control and pollination in pear trees. This was likely due to insecticide use and phenological mismatch, as alfalfa developed and flowered after pear bloom. Overall, the results show that service plant effectiveness is shaped by interactions among plant traits, prey availability, and management practices, highlighting the need for insect-friendly management and phenological alignment to enhance ecosystem services at the orchard scale. Crop and Weed Ecology PE&RC Farming Systems Ecology (FSE) Centre for Crop Systems Analysis (CSA) Crop and Weed Ecology PE&RC Farming Systems Ecology (FSE) Centre for Crop Systems Analysis (CSA) urn:nbn:nl:ui:32-0cb86539-48c2-48e4-99fb-49908c0d6fcf/obj 2026-05-28 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/58970bfb-a8f6-4baf-aba9-99b0bfe1c93e 2026-06-03 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-58970bfb-a8f6-4baf-aba9-99b0bfe1c93e 2026-06-03 urn:nbn:nl:ui:32-58970bfb-a8f6-4baf-aba9-99b0bfe1c93e/mods Smallholder seed choices under risk and uncertainty : Reflective and automatic processes shaping adoption of improved maize varieties in Uganda Wageningen University dgg Mastenbroek Astrid 392055503 0000000452588635 aut R.A. Sparrow opn E.H. Bulte opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 317 10.18174/681091 en This thesis examines why adoption of improved maize varieties remains limited in Uganda, despite their high yield potential and sustained investments in breeding, dissemination, and extension. It analyzes how smallholder farmers make seed choices under conditions of risk, uncertainty, and weak market credibility. Rather than explaining adoption through information, prices, or profitability alone, the thesis focuses on farmer behavior within these contextual constraints. Empirically, it combines participatory qualitative research with incentive-compatible framed field experiments. Chapter 2 begins by diagnosing the behavioral and institutional constraints that shape demand for drought-tolerant maize varieties. Seed choices are influenced by factors beyond awareness, availability, accessibility, or affordability. Trust in seed sources, familiarity with varieties, uncertainty regarding seed quality, and social norms all affect whether improved seed is considered a realistic option. Chapter 3 evaluates whether certification and seed-quality information increase farmers’ willingness to pay for certified open-pollinated maize seed. While the information treatment improves farmers’ knowledge of certification procedures and seed quality standards, it does not raise the average willingness to pay, suggesting that information alone is not enough in markets where seed quality is hard to verify. Chapter 4 investigates whether farmers’ valuations of hybrid maize seed are shaped by reference points. Incentive-compatible field experiments reveal a strong endowment effect: farmers demand substantially more compensation to give up hybrid seed once they possess it than they are willing to pay to obtain it. In contrast, price and ownership expectations exert only a modest influence. Chapter 5 explores gendered risk perceptions in the adoption of drought-tolerant maize. Although men and women identify similar agricultural risks, they prioritize them differently. Women emphasize production and health risks, whereas men assign greater importance to financial concerns. These differences reflect gendered responsibilities, household decision-making processes, and social norms, rather than inherent differences in risk preferences. Chapter 6 examines hybrid maize seed investment under production and background risk conditions. Farmers decrease investment in hybrid seed as the likelihood of bad weather increases, indicating responsiveness to objective production risk. An actuarially neutral background risk has minimal average effect. However, narrative framing matters selectively: when background risk is presented as a potential health shock, women reduce investment while men do not. These results suggest that socially salient cues can influence seed investment decisions even when probabilities and payoffs are unchanged. Overall, the thesis demonstrates that limited adoption of improved maize varieties does not reflect a simple absence of demand. Adoption outcomes reflect interactions between objective incentives, experience-based responses, and socially shaped norms. The findings show that while farmers adjust investment in response to explicit production risk in ways consistent with expected-value logic, decision-making can shift when affect-rich narratives or habitual defaults become salient. In low-credibility seed markets, habits, peer advice, and socially legitimate choices may partly substitute for formal quality signals that are difficult to verify. Gendered social norms and household roles further act as behavioral filters, shaping which seed investments are considered credible, appropriate, and feasible. WASS Development Economics WASS Ontwikkelingseconomie urn:nbn:nl:ui:32-58970bfb-a8f6-4baf-aba9-99b0bfe1c93e/obj 2026-06-03 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/a00326b1-71b4-4f5a-be13-bb9a119868f2 2026-06-01 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-a00326b1-71b4-4f5a-be13-bb9a119868f2 2026-06-01 urn:nbn:nl:ui:32-a00326b1-71b4-4f5a-be13-bb9a119868f2/mods The irony of industry fortification : Aligning industry-led fortified dairy-based food products with population nutritional needs in Côte d’Ivoire and Nigeria Wageningen University dgg Ayling Katie L. 0000000530287644 aut A. Melse-Boonstra opn E.F. Talsma opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 10.18174/681605 en Sub-Saharan Africa faces a triple burden of malnutrition, the coexistence of undernutrition, micronutrient deficiencies, and overweight or obesity, within rapidly urbanising populations. Market-driven food fortification, whereby manufacturers voluntarily add micronutrients to commercial products, has been proposed as a complementary strategy to address micronutrient deficiencies in low- and middle-income countries. However, its public health value depends critically on alignment with population-specific nutritional needs. This thesis developed and applied a structured framework to evaluate the feasibility and effectiveness of industry-led fortification of dairy-based food products for school-aged children and women of reproductive age in Côte d'Ivoire and Nigeria, in collaboration with FrieslandCampina. The thesis was organised around three research themes. The first characterised population nutritional needs in urban Côte d'Ivoire through a cross-sectional dietary intake survey (n = 884). Calcium, riboflavin, and zinc were the most prevalent inadequacies among both school-aged children and women of reproductive age, while iron intake was adequate for the majority. Most women (>50%) were overweight or obese, consistent with early-stage nutrition transition. Dietary patterns were city-specific, with fish-, vegetable-, and dairy-based patterns associated with higher diet quality and lower non-communicable disease risk. A methodological comparison demonstrated that the nutriR modelling tool produced inadequacy estimates comparable to traditional methods when high-quality usual intake data were available, though it does not reduce the need for rigorous primary dietary assessment. The second theme assessed the technological and commercial feasibility of improving iron bioavailability in fortified flavoured dairy powder products by substituting ferric pyrophosphate with more bioavailable iron compounds. Bench-scale trials found that encapsulated ferric pyrophosphate was the only substitute with acceptable sensory and technological properties, but its cost was five times higher than the reference, rendering reformulation economically infeasible. Ferrous fumarate was identified as a viable alternative in non-flavoured or cereal-based formats, and a commercially available multi-nutrient fortified milk-based maize porridge containing this compound was selected for evaluation in Nigeria. The third theme evaluated the effectiveness of this porridge, delivered through a School Feeding Programme, in a randomised, double-blind controlled trial in Ibadan, Nigeria (n = 945). Despite high baseline anaemia prevalence (74%), the intervention did not improve haemoglobin concentrations or iron status. Inflammation-adjusted iron deficiency affected only 9.5% of participants, and body iron stores were adequate in 99.8%, indicating that anaemia in this population was predominantly driven by inflammation, vitamin A deficiency, and malaria rather than iron-responsive deficiency. Modest improvements were observed in vitamin D status in the high-dose group, and vitamin A status improved across all groups. Together, these findings underscore a central irony of industry-led fortification: a nutrient-dense, carefully reformulated product may produce limited public health impact when the underlying aetiology of the target condition has not been thoroughly characterised. Effective market-driven fortification requires diagnostic-driven product design, grounded in high-quality population data, before evaluation. VLAG Global Nutrition VLAG Wereldvoeding urn:nbn:nl:ui:32-a00326b1-71b4-4f5a-be13-bb9a119868f2/obj 2026-06-01 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/21aaaca3-7a05-4069-ab02-eb986709c2ad 2026-06-01 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-21aaaca3-7a05-4069-ab02-eb986709c2ad 2026-06-01 urn:nbn:nl:ui:32-21aaaca3-7a05-4069-ab02-eb986709c2ad/mods Integrated modeling of nutrient emissions to air and water : Synergetic solutions for the European future Wageningen University dgg Ural-Janssen Aslıhan 0000-0001-7936-6774 aut M. Strokal opn E. Meers opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 267 10.18174/681307 en Nutrients, mainly nitrogen and phosphorus, are essential for growing food and to support all life. On the other hand, human activities have largely influenced natural nutrient cycling. Intensive agriculture and urbanization are important sources of nutrient emissions to the air and surface waters in Europe. Elevated levels of nitrogen and phosphorus emissions can negatively impact the quality of air and water, and human health. Air quality often suffers from nitrogen emissions that can be deposited on land and then reach rivers and coastal waters. Moreover, phosphorus from human activities on the land can cause eutrophication in surface waters. Thus, integrated assessments of both air and water pollution associated with nutrients are needed to understand the potential of nutrient management strategies to reduce both air and water pollution simultaneously. However, these assessments are, so far, limited, hindering a better understanding of future trends in this pollution. This research, therefore, contributes understanding of basin-specific nutrient emissions to the air and surface waters, and explore the role of bio-based fertilizers and other nutrient management strategies to reduce future nutrient pollution under global change across Europe. We find that using bio-based fertilizers in combination with increased nutrient use efficiencies and improved wastewater treatment systems could reduce nutrient emissions to air and water simultaneously in the future. WIMEK Earth Systems and Global Change WIMEK Earth Systems and Global Change urn:nbn:nl:ui:32-21aaaca3-7a05-4069-ab02-eb986709c2ad/obj 2026-06-01 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/460c5683-d705-4b4e-a522-5d05b95b8d55 2026-05-28 thesis

urn:nbn:nl:ui:32-460c5683-d705-4b4e-a522-5d05b95b8d55 2026-05-28 urn:nbn:nl:ui:32-460c5683-d705-4b4e-a522-5d05b95b8d55/mods Wild meat in the city, health risks and implications Wageningen University dgg Masudi Phyllis Sherril 0000000530260011 aut Frank van Langevelde opn Pim van Hooft opn Ralph Buij opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 239 10.18174/681968 en Consumption of and trade in wild meat could result in infectious pathogen spillover into human populations. A better understanding of how urban wild meat value chains operate, the health hazards present and their risk assessment could assist in mitigating potential spillovers and outbreak events. We used key informant interviews, priority pathogen surveillance, risk assessments and literature reviews to understand the structure and operations, actors, the health hazards and risk of human exposure to these hazards along a wild meat value chain supplying a rapidly urbanizing city in Africa, the Nairobi Metropolitan Area (NMA). The value chain operates via three main nodes: harvester, trader, and consumer nodes. We found wild meat to be harvested from peri-urban areas of the NMA, consumed or sold locally, or supplied to distant urban markets. The value chain operated informally, creating a ‘rules in use’ framework focusing on sanction avoidance, while ignoring food safety concerns. Consequently, respondents reported slaughtering wild animals on the bare ground, handling wild meat without wearing personal protective equipment, with unwashed bare hands, and uncleaned utensils. In the city, wild meat was at times sold disguised as livestock meat, meat vendors engaged in similar unsafe practices. Actors had limited awareness of the specific health hazards from wild meat. Wild meat along the value chain were contaminated with select pathogens. The prevalence of E. coli ranged from 3.7%-40.7% with EHEC-stx2 (Shiga toxin producing E. coli-2 (STEC-2)) at 40.7% (95% CI: 24.5-59.3%) and EHEC-stx1(Shiga toxin producing E. coli-1 (STEC-1)) at 29.6% (95% CI: 15.9-48.5%). Enteroaggregative E. coli had a prevalence of 3.7% (95% CI: 0.7-18.3%) while ETEC-elt, ETEC-stl and C. burnetii had a prevalence of 7.4% (95% CI: 2.1-23.4 %). I estimated the probability of hunters and traders’ exposure to STEC (both 1 and 2) above the minimum infectious dose at 0.43 (mean= 0.43; 95% CI= 0.24-0.63) and 0.27 (mean= 0.31; 95% CI= 0.08-0.60) respectively, while the probability of consumer exposure to STEC above the infectious dose was 0.03 (mean= 0.04; 95% CI= 0.009-0.08). Finally, we present data on outbreak response along wild meat value chains in the Sub-Saharan Africa from 2004-2024. During this period, there were 84 suspected wild meat-borne disease outbreak events caused by four zoonotic viruses: Ebola (n=32), Marburg (n=11), Lassa (n=19), Mpox (n=20) and one bacterium: Bacillus anthracis (n=2). At the national level, responses involved human surveillance via contact tracing, case management and mitigation of the disease spread through vaccinations, public education on infection prevention and control, and bans on wild meat use, amongst others. National response was supported by the international community. At personal level, communities either adopted, or not, the proposed infection prevention and control measures. They either stopped, reduced or continued harvesting, sale and consumption of wild meat depending on their knowledge of the outbreak, and the directives issued by the health authorities. We proposed a framework for socially responsive response measures tailored to the needs and nature of wild meat value chains in Sub-Saharan Africa. WIAS Animal Ecology Wildlife Ecology and Conservation WIAS Dierecologie Natuurecologie en natuurbehoud urn:nbn:nl:ui:32-460c5683-d705-4b4e-a522-5d05b95b8d55/obj 2026-05-28 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/503acca3-5d48-4609-a62e-8ba981579e4c 2026-05-29 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-503acca3-5d48-4609-a62e-8ba981579e4c 2026-05-29 urn:nbn:nl:ui:32-503acca3-5d48-4609-a62e-8ba981579e4c/mods Picture this: visual framing dynamics of discourse coalitions in Twitter on CRISPR-Cas technology Wageningen University dgg Rojas Padilla Eduardo 000000053028761X aut T.A.P. Metze opn C.J.A.M. Termeer opn A.R.P.J. Dewulf opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 273 10.18174/681039 en In our hyperconnected, mediatized societies, social media and online tools have transformed democratic participation, politics, and policy-making. Visualizations—memes, infographics, diagrams—play a pivotal but understudied role in these dynamics, particularly in shaping policy controversies. This dissertation explores how visualizations on social media influenced the online debate about regulatory decisions surrounding CRISPR-Cas genome editing technology in the EU, USA, and Mercosur, each of which adopted distinct frameworks. While existing literature on visualizations spans communication, political science, and sociology, it often focuses on individual cognition, news effects, or offline media, neglecting the large-scale, dynamic role of visuals in online policy controversies. This research addresses that gap by investigating how visual framing dynamics catalyze policy debates, constitute actor coalitions, and impact policy processes, especially for emerging technologies like CRISPR-Cas. The study centers on the question: What is the influence of visual framing dynamics on the online policy controversy over CRISPR-Cas in three regulatory contexts? It breaks this down into four sub-questions, examining how visualizations shape policy and politics, the nature of Multimodal Online Discourse Coalitions (MODCs), their emergence and traction, and how actors in the science–policy–society nexus can use visualizations strategically. Methodologically, the research combines quantitative social network analysis of Twitter data (2015–2019, in English, Spanish, and French) with qualitative multimodal framing analysis of highly retweeted visuals and texts. Retweet networks are clustered to identify MODCs, comparing their dominant frames, sentiment, and storylines. A longitudinal analysis of the French case traces the evolution of one of these discourse coalitions over five years. The dissertation yields four main findings. First, it identifies five roles visualizations play in public debates: as sense-making devices, emotional triggers, discursive objects, cultural icons, and representations of norms and values. Second, a comparative Twitter study introduces MODCs, showing how technocratic discourses dominate in English and Spanish, framing CRISPR as precise and novel, while French-language MODCs emphasize the emergence of a normative discourse addressing mostly ethical concerns, linking CRISPR to GMO technology and shaping a debate that mirrored the EU’s restrictive regulatory approach. Third, a longitudinal study proposes a five-stage model for MODC development—emergence, growth, adaptation, influence, and legacy—demonstrating how shifting visual framings and opinion leader actions transcends online discourse into offline traction in policy processes. Finally, it offers a heuristic for practitioners to use visualizations strategically, emphasizing their dual cognitive-normative role and potential to engage or contest online coalitions. Ultimately, the dissertation argues that visuals are not mere illustrations but central to multimodal discourse, shaping how actors construct futures for novel biotechnologies, include or marginalize voices, and influence regulatory paths. It concludes that recognizing and engaging with the visual dimension of policy controversies is crucial for democratic, reflexive governance of emerging technologies, warning that overlooking visualizations risks entrenching power structures and marginalizing societal concerns. WASS Public Administration and Policy WASS Bestuurskunde urn:nbn:nl:ui:32-503acca3-5d48-4609-a62e-8ba981579e4c/obj 2026-05-29 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/54cb7cfe-41c3-4842-acf2-739533fa201a 2026-05-29 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-54cb7cfe-41c3-4842-acf2-739533fa201a 2026-05-29 urn:nbn:nl:ui:32-54cb7cfe-41c3-4842-acf2-739533fa201a/mods Managing water excess and deficit in agriculture : Subsurface drainage and irrigation systems Wageningen University dgg (Janine), de Wit J.A. 0000000530285462 aut R.P. Bartholomeus opn C.J. Ritsema opn J.C. van Dam opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 212 10.18174/681446 en Water is essential in our daily lives: for nature, agriculture, drinking water and industry. However, the demand for freshwater is increasing while the availability is declining. In addition, climate change is increasingly causing extreme weather conditions, such as droughts and heavy rainfall. To anticipate both dry and wet conditions in agriculture is therefore becoming increasingly important. One measure is to convert existing subsurface drainage systems into controlled drainage with subirrigation (CDSI). CDSI aims to drain groundwater when necessary, retain water when possible, and supply water where feasible. In my PhD research, I investigated the hydrological opportunities of CDSI in the Dutch Pleistocene uplands. Four CDSI field pilots at the Dutch Pleistocene uplands (America, Haaksbergen, Lieshout and Stegeren) were set up. The field measurements showed that CDSI can raise groundwater levels and thereby increase crop yields. A simulation study with the Soil- Water-Atmosphere-Plant model (SWAP) shows that a minor part of the supplied water contributes to increased plant transpiration. Most of the supplied water leaves the system as ditch drainage and as downward seepage to the deeper groundwater. The distribution between these components largely depends on the adjacent surface water level and geohydrological characteristics.The required water supply (subirrigation) was high in the field experiments, because a fixed and relatively high groundwater level was maintained throughout the growing season. Water supply can be reduced by applying smarter control, whereby the CDSI system contains a dynamic crest level and dynamic pump management. The water level in the control pit is then calculated via an algorithm based on actual soil moisture conditions and weather forecasts. Water can also be saved in areas with a higher resistance to downward seepage (location characteristics), maintaining a higher ditch water level around agricultural fields (management) or cultivating crop with deeper roots (crop specific). Although water supply can be reduced through smarter applications, a CDSI system still requires water, meaning this local measure influences the regional water system. It is therefore important that stakeholders agree to the extent to which CDSI should be implemented. To support this, a system dynamics model (SDM) was developed. The results show that CDSI upscaling propagates non-linearities in hydrological fluxes with three critical phases. From phase 1 with sufficient regional water availability, through phase 2, a critical zone where water demand begins to limit regional water availability to phase 3, where high water demand significantly impacts the regional water system and CDSI is no longer beneficial for crops. All in all, CDSI could be a valuable measure for a climate robust soil-water system. However, because the local measure CDSI may increase pressure on surface water availability during dry periods, it should be carefully embedded into regional water management strategies. In the short term, it is relatively easy to convert existing drainage systems into CDSI. In the long term, CDSI can serve as a technical measure in areas where soil and water were leading in spatial planning, to mitigate both too wet and too dry circumstances. WIMEK Soil Physics and Land Management WIMEK Bodemfysica en Landbeheer urn:nbn:nl:ui:32-54cb7cfe-41c3-4842-acf2-739533fa201a/obj 2026-05-29 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/00430d10-9856-47f0-a941-9f6db3db8a4b 2026-05-29 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-00430d10-9856-47f0-a941-9f6db3db8a4b 2026-05-29 urn:nbn:nl:ui:32-00430d10-9856-47f0-a941-9f6db3db8a4b/mods Sphere of influence: insect herbivory and plant defense signaling shaping rhizosphere microbiomes in Brassicaceae Wageningen University dgg Aragón Gómez Marcela S. 0000-0001-8785-1753 0000000530284953 aut M. Dicke opn K.J. Kloth opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 315 10.18174/681363 en Plants are constantly challenged by insect herbivores and have evolved sophisticated defense mechanisms governed by phytohormonal signaling pathways. The jasmonic acid (JA) and salicylic acid (SA) defense pathways mediate responses against chewing insects such as caterpillars and phloem-feeding insects such as aphids, respectively. Activation of these pathways in aboveground tissues triggers systemic changes in root exudate composition, reshaping the rhizosphere microbiome, the diverse microbial community surrounding plant roots. The "cry-for-help" hypothesis proposes that stressed plants actively recruit beneficial soil microbes to enhance their defenses. However, whether such recruitment is stress-specific, conserved across plant species, and functionally beneficial remains largely unresolved. This thesis investigated how JA- and SA-mediated defense activation aboveground shapes root-associated microbial communities in plants from the Brassicaceae family, and whether defense-induced microbiome shifts translate into enhanced resistance to insect herbivory. All experiments were conducted using a common agricultural soil (MiCROp soil), with Brassica oleracea as the primary model crop. Plant defenses were induced via exogenous phytohormone application or by infestation with caterpillars or aphids. Microbial communities were characterized by amplicon sequencing of the bacterial 16S rRNA gene and fungal ITS region. Chapter 2 demonstrated that JA activation, via methyl jasmonate (MeJA) application at two concentrations or oral secretion from Pieris brassicae caterpillars, caused consistent, yet subtle, shifts in root-associated bacterial communities of A. thaliana and B. oleracea, with the endosphere responding more strongly than the rhizosphere. Members of the Comamonadaceae, Oxalobacteriaceae, and Rhizobiales were identified as shared JA-responsive taxa across both species, while species-specific differences in the direction of microbial responses were also observed. Chapter 3 used a plant-soil feedback design to assess whether defense-shaped rhizosphere communities conferred resistance to subsequent herbivore attack in B. oleracea. The JA and SA pathways were activated either by foliar application of MeJA or SA solutions, or by herbivory with Mamestra brassicae caterpillars and Myzus persicae aphids, respectively. Both pathways led to distinct microbial shifts, with bacterial and fungal composition varying by pathway identity and induction method. In the feedback phase, SA-conditioned soil reduced phloem feeding and aphid population development, but only under low aphid pressure, suggesting that microbiome-mediated benefits are contingent on pest pressure intensity. Chapter 4 expanded the analysis to 22 wild and cultivated Brassicaceae species treated with MeJA or SA. SA-induced rhizosphere communities showed a phylogenetically conserved signal across the family, whereas JA-induced communities varied more in a species-specific manner, indicating that the degree of conservation depends on the defense pathway activated.Chapter 5 tested whether bacteria enriched under SA treatment and drought could be assembled into a synthetic community (SynCom) to improve plant resilience. An 11-member bacterial SynCom inoculated into B. oleracea showed stress-dependent establishment in the rhizosphere, but did not enhance plant performance. Unexpectedly, aphid populations increased under combined drought and aphid herbivory stress. Together, this thesis reveals that defense phytohormonal signaling shapes belowground microbiomes in a stress-, species-, and compartment-specific manner. The context-dependency of microbiome-mediated resistance highlights the complexity of harnessing the rhizosphere for sustainable crop protection EPS Entomology (ENT) EPS Entomology (ENT) urn:nbn:nl:ui:32-00430d10-9856-47f0-a941-9f6db3db8a4b/obj 2026-05-29 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/58ea8e7e-215c-45f4-8aab-64bd795d941b 2026-05-29 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-58ea8e7e-215c-45f4-8aab-64bd795d941b 2026-05-29 urn:nbn:nl:ui:32-58ea8e7e-215c-45f4-8aab-64bd795d941b/mods Solving water conflicts : Game theoretic approaches to water allocation in Peru Wageningen University dgg Gómez Gamarra Zoila Del Rosario 000000006116275X aut H.P. Weikard opn F.R. Alpizar opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 173 10.18174/680891 en Water scarcity is a global challenge which threatens economic development, environmental stability and social cohesion. Additionally, rising pollution affects water scarcity, limiting freshwater for competing users. The overarching objective of the thesis is to contribute analyses and solutions to real-world water conflicts. It investigates (i) how scarce water can be allocated based on rules, particularly when water sources are interdependent, (ii) how joint infrastructure investments can mitigate scarcity and conflicts, (iii) how water pollution can be mitigated using side payments, and (iv) how water quality can be improved through stringent environmental policies. The study focuses on Peru, where water stress, water pollution and related conflicts are intensifying under conditions of weak governance. This thesis integrates game theory and institutional economics. The models developed demonstrate that credible institutions and enforcement are critical to align incentives leading to efficient water allocation and controlling water pollution. Effective enforcement can facilitate the achievement of economic, social and environmental policy goals by mitigating conflicts and enhancing cooperation. Environmental Economics and Natural Resources WASS Milieueconomie en Natuurlijke Hulpbronnen WASS urn:nbn:nl:ui:32-58ea8e7e-215c-45f4-8aab-64bd795d941b/obj 2026-05-29 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/e27d7f40-f56f-4dd2-ab49-837db82e4588 2026-05-29 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-e27d7f40-f56f-4dd2-ab49-837db82e4588 2026-05-29 urn:nbn:nl:ui:32-e27d7f40-f56f-4dd2-ab49-837db82e4588/mods Restoring biodiversity and ecosystem services on managed grasslands Wageningen University dgg de Vries J.P. Reinier 000000053028227X aut D. Kleijn opn J.G. van Paassen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 174 10.18174/681734 en Grassland ecosystems support high biodiversity levels and critical ecosystem services to humans, but experience widespread degradation. Land use intensification is often the main driver of degradation in grassland ecosystems. This thesis describes constraints and opportunities for the restoration of temperate managed grassland ecosystems. Two chapters investigate the implications of land use intensification for grassland biodiversity and ecosystem service delivery. Next, two chapters examine strategies to improve the effectiveness of grassland restoration schemes. Chapter one introduces how agricultural land use change has affected managed grassland ecosystems. It also introduces our study region in the south of the Netherlands. Chapter two investigates whether grassland ecosystem restoration contributes to or trades off with the income of farmers. Grassland productivity was found to be primarily driven by management intensity, with only minor contributions of biodiversity-based ecosystem services. Farmer income depends on productivity and therefore traded off strongly with the delivery of wider ecosystem services, which are primarily of public concern. Consequently, ecosystem restoration depends on societal support for the safeguarding of public goods. Chapter three investigates the effects of land use intensification on grassland arthropods in further depth. A novel analysis of the responses of individual species revealed that up to 85% of all species declined when land use intensified, while a small set of widespread species profited from increasing productivity. This can explain why land use intensification caused declines of arthropod species richness but not overall abundance: A low number of species may keep up total arthropod numbers in intensively used habitats. Chapter four showed that flower species richness can be used to rapidly assess the quality of grassland habitats for a wide range of arthropod groups and across multiple land use types. Flower richness can even reveal seasonal changes in habitat suitability. Therefore, scalable surveys of flower richness can complement the laborious biodiversity surveys that were presented in chapter three. Being directly relatable to local management, flower richness can be used to evaluate effects of restoration measures and to reward farmers financially for the biodiversity that their fields support. Chapter five examines whether adjusted mowing regimes can promote the flowering of grassland forbs at different land use types. Reduced mowing promoted flowers only at lower productivity levels and not at high productivity levels, whereas spring mowing enhanced reflowering in late summer. Flowering across the growing season can therefore be optimized by tailoring mowing regimes to local productivity levels and forb species composition, but mainly so at lower productivity levels. This thesis showed that there is much potential to restore managed grassland ecosystems and the public goods that they deliver, but that successful restoration requires a drastic extensification of current agricultural land use. In chapter six, it is discussed that this creates a public obligation to provide alternative income sources for farmers. Scientific research can improve our understanding of biodiversity responses to land use and develop effective restoration strategies. Ultimately, society must balance its demand of agricultural products with the need of safeguarding biodiversity and public goods, supported by the same rural landscapes. PE&RC Plant Ecology and Nature Conservation PE&RC Plantenecologie en Natuurbeheer urn:nbn:nl:ui:32-e27d7f40-f56f-4dd2-ab49-837db82e4588/obj 2026-05-29 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/46dfd240-4b1b-45ff-ae95-208f0452f918 2026-05-21 thesis

urn:nbn:nl:ui:32-46dfd240-4b1b-45ff-ae95-208f0452f918 2026-05-21 urn:nbn:nl:ui:32-46dfd240-4b1b-45ff-ae95-208f0452f918/mods Far-red in greenhouse tomato cultivation: from light perception to fruit yield improvement Wageningen University dgg Vincenzi Elena 0000000530276558 aut Leo F.M. Marcelis opn Ep Heuvelink opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 258 10.18174/681753 en Tomato is a globally important crop for both fresh consumption and processed products, and it also serves as a model species for physiological studies on fleshy fruit-bearing plants. In northern countries, tomato production takes place mostly in protected environments like greenhouses, where year-round cultivation is achieved through heating and supplementary lighting during the winter months. As the greenhouse sector aims to increase its sustainability without compromising yield, supplementary lighting is shifting toward energy-efficient LEDs, which allow precise control of both light intensity and spectral composition. Current supplementary lighting recipes for tomato are dominated by red light, with small proportions of blue and green, and typically lacking far-red (FR, 700–800 nm). The addition of FR to supplementary lighting has the potential to increase fruit yield by improving biomass accumulation and its allocation to the harvestable product: the fruit. Despite being outside of the photosynthetically active radiation (PAR, 400–700 nm) region, FR can drive photosynthesis when supplied together with shorter wavelengths (“FR as photon”). In addition, FR perception by phytochromes can trigger photomorphogenic responses, altering multiple plant processes from architecture to biomass partitioning to defense (“FR as signal”). The multifaceted nature of FR complicates the interpretation of its effects at the molecular, plant, and crop levels. This thesis aims to connect the physiological mechanisms underlying FR-mediated fruit growth promotion with optimal application strategies in a realistic horticultural setting, with the ultimate goal of maximising the effectiveness of FR supplementation for improving tomato fruit yield. Horticulture and Product Physiology (HPP) PE&RC Horticulture and Product Physiology (HPP) PE&RC urn:nbn:nl:ui:32-46dfd240-4b1b-45ff-ae95-208f0452f918/obj 2026-05-21 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/7e58c870-64c4-4e69-a5a8-58d021dfc899 2026-05-21 thesis

urn:nbn:nl:ui:32-7e58c870-64c4-4e69-a5a8-58d021dfc899 2026-05-21 urn:nbn:nl:ui:32-7e58c870-64c4-4e69-a5a8-58d021dfc899/mods Genetic and physiological basis of seed longevity in rice under dry storage Wageningen University dgg Cholanayakanahalli Thyagaraju Manjunath Prasad aut G.C. Angenent opn S.P.C. Groot opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 274 10.18174/680862 en Seeds slowly lose vigour and viability during storage, which can reduce productivity and is critical for farmers, seed companies, and genebanks. Rice seed quality can drop quickly, especially in warm regions where rice is often stored under open conditions. We developed a rapid laboratory test that exposes dry seeds to high oxygen levels at controlled temperatures. The test is accelerating oxidation-related damage, that naturally occurs slowly in real open storage, but now becomes visible within weeks. Combining this test with an advanced genetic approach, we identified a key gene (Rc) that boosts natural antioxidant accumulation in the seed pericarp (red colour), protects dry seeds against oxidative damage, and helps preserve seed quality for longer. We also showed that storing dry seeds, not moist seeds, in very low oxygen (anoxia or hypoxia) conditions can substantially slow ageing and can extend shelf-life. Overall, this research delivers a practical ageing test, supporting better storage and breeding strategies to keep dry rice seeds viable longer for farmers, seed companies, and gene banks. EPS Molecular Biology (MOB) Bioscience EPS Molecular Biology (MOB) Bioscience urn:nbn:nl:ui:32-7e58c870-64c4-4e69-a5a8-58d021dfc899/obj 2026-05-21 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/a94fbfe8-b5a3-4a92-8764-a656e5c94802 2026-05-29 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-a94fbfe8-b5a3-4a92-8764-a656e5c94802 2026-05-29 urn:nbn:nl:ui:32-a94fbfe8-b5a3-4a92-8764-a656e5c94802/mods The importance of realistic surface radiation in cloud-resolving models Wageningen University dgg Tijhuis Mirjam aut C.C. van Heerwaarden opn B.J.H. van Stratum opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 149 10.18174/681761 en Clouds, radiation, and the Earth’s surface closely interact. Properly representing these interactions is crucial for accurate predictions of weather, climate, and renewable energy production. Radiative transfer can be simulated accurately in 3D or simplified in the vertical direction only (1D) to reduce costs. In this thesis, we investigated how the differences between 1D and 3D radiative transfer impact clouds. We find that simulated clouds are bigger and wetter when using 3D radiation. However, the total amount of radiation at the surface is unchanged. We show that the differences in clouds are driven by the position of the cloud shadows and the horizontal distribution of scattered radiation. Furthermore, we show that capturing only the probability distribution of radiation is not sufficient, the spatial patterns are at least as important. Lastly, we show that the model used in this thesis captures the physics of convective clouds in line with an operational weather model. WIMEK Meteorology Meteorology and Air Quality WIMEK Meteorologie Meteorologie en Luchtkwaliteit urn:nbn:nl:ui:32-a94fbfe8-b5a3-4a92-8764-a656e5c94802/obj 2026-05-29 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/e3b0ff4f-2410-4725-9e00-094f53a92864 2026-05-27 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-e3b0ff4f-2410-4725-9e00-094f53a92864 2026-05-27 urn:nbn:nl:ui:32-e3b0ff4f-2410-4725-9e00-094f53a92864/mods Technical and economic aspects of alternaria Mycotoxin management in tomatoes in China Wageningen University dgg Zhang Yimin 0000000530228521 aut H.J. van der Fels-Klerx opn J. Yan opn C. Liu opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 240 10.18174/681768 en Tomato (Solanum lycopersicum) is a globally important crop, with China as the largest producer. However, tomato production is significantly affected by fungal infections caused by Alternaria species, leading to both yield losses and contamination with toxic secondary metabolites known as Alternaria mycotoxins, particularly alternariol (AOH), alternariol monomethyl ether (AME), and tenuazonic acid (TeA). These compounds are considered emerging food safety hazards due to their potential toxicological effects and their stability during food processing. Current control strategies rely mainly on routine fungicide applications, which often result in excessive chemical use, increased costs, and environmental burden. This highlights the need for more targeted and efficient control approaches. This thesis aimed to develop a quantitative framework to improve the management of Alternaria mycotoxin contamination in tomato production in China by integrating analytical chemistry, predictive modelling, and economic evaluation. First, a systematic review (2011–2024) was conducted to assess the occurrence, toxicity, exposure, and control of Alternaria mycotoxins in food. Tomatoes and cereal products were identified as major contamination sources, with AOH and AME posing potential genotoxic risks, while TeA was frequently detected at high concentrations. Second, a sensitive and efficient QuEChERS-based LC-MS/MS analytical method was developed and validated for simultaneous quantification of multiple Alternaria mycotoxins in tomato products using minimal sample size (100 mg). Application of the method to commercial samples confirmed widespread contamination, with all samples containing at least one mycotoxin. Dietary exposure assessment indicated that children are at higher risk than adults, and that exposure to AOH and AME may exceed toxicological thresholds under certain scenarios. Third, a predictive model based on a Random Forest algorithm was developed to forecast mycotoxin contamination by integrating weather data, agronomic practices, and fungal infection modelling. The model achieved high predictive performance (internal accuracy >97%, external accuracy >70%) and identified key influencing factors such as fungal infection index, temperature, and wind speed. The flowering stage was determined as the optimal timing for intervention. Finally, a cost-effectiveness analysis compared three control strategies: conventional fixed-schedule fungicide application, prediction-assisted control at harvest, and risk-based fungicide application guided by the predictive model at the flowering stage. Monte Carlo simulations incorporating uncertainty demonstrated that the risk-based strategy consistently achieved the highest net benefit, lowest overall costs, and substantial reductions in health burden (over 75% reduction in DALYs), while improving environmental sustainability. Overall, this thesis provides a comprehensive, data-driven framework for managing Alternaria mycotoxins in tomato production. By integrating detection, prediction, and economic evaluation, it supports the transition from routine to risk-based control strategies, contributing to improved food safety, public health, and sustainable agricultural practices. WASS Team Agrochains Business Economics WASS Team Agrochains Bedrijfseconomie urn:nbn:nl:ui:32-e3b0ff4f-2410-4725-9e00-094f53a92864/obj 2026-05-27 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/05a60374-00a3-43bc-9289-2b2459ffe71e 2026-05-20 thesis

urn:nbn:nl:ui:32-05a60374-00a3-43bc-9289-2b2459ffe71e 2026-05-20 urn:nbn:nl:ui:32-05a60374-00a3-43bc-9289-2b2459ffe71e/mods Mitochondrial and NAD+ metabolism in aging-related atrial fibrillation and cardiac dysfunction Wageningen University dgg Hu Liangyu 0000000530253276 aut J. Keijer opn D. Zhang opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 267 10.18174/681328 en The increasing prevalence of aging-related cardiovascular diseases, including atrial fibrillation (AF) and heart failure, poses a major global health challenge. Mitochondrial dysfunction and metabolic dysregulation are key features of cardiac aging, yet their precise roles in the development of arrhythmia and contractile dysfunction remain incompletely understood. A central factor in these processes is the age-related decline in NAD⁺, a coenzyme essential for mitochondrial energy production, redox balance, and metabolic signaling. Restoring NAD⁺ levels has therefore emerged as a potential therapeutic strategy, but its mechanisms, efficacy, and limitations in cardiac aging require further investigation. This thesis aimed to elucidate how mitochondrial dysfunction and metabolic dysregulation contribute to AF and left ventricular (LV) dysfunction during aging, and to evaluate NAD⁺-related nutritional interventions. In Chapters 2-4, I investigated the effects of mitochondrial function and oxidative damage on aging-related AF and LV dysfunction. Chapter 2 presents a comprehensive review describing a vicious cycle in which oxidative DNA damage depletes NAD⁺ and ATP, impairing mitochondrial antioxidant defenses and exacerbating myocardial dysfunction. In Chapter 3, I established and validated a method (TSIT) to assess mitochondrial respiratory capacity in frozen heart tissue, enabling translational studies using clinically relevant samples. In Chapter 4, I characterized a mouse model with an inactivating mutation in nicotinamide nucleotide transhydrogenase (Nnt), revealing that mitochondrial redox regulation influences AF susceptibility in an age- and sex-dependent manner. Chapters 5-7 focused on NAD⁺-based nutritional interventions and their potential mechanisms of action. In Chapter 5, NAD⁺ and beta-hydroxybutyrate improved mitochondrial and metabolic remodeling in cardiomyocytes by preventing a metabolic shift, mitochondrial dysfunction, mitophagy, oxidative stress, and activated NLRP3 inflammation. In Chapter 6, I demonstrated that the NAD⁺ precursor nicotinamide (NAM) has a dose- and duration-dependent effect: while moderate, late-life supplementation was protective, high-dose or long-term exposure impaired cardiac function and increased arrhythmia risk across models. In Chapter 7, I showed that another precursor, nicotinamide riboside (NR), improved metabolic remodeling and early LV dysfunction in old mice, associated with increased cardiac NAD⁺ levels and improved mitochondrial and lipid metabolism. In conclusion, the methodologies and models established in this thesis offer valuable insights for further investigation of mitochondrial function in aging-related cardiac disorders, while our evaluation of NAD⁺-based interventions highlighted their context-dependent therapeutic potential. A deeper understanding of the mechanisms underlying mitochondrial and metabolic remodeling will be essential to develop precise strategies for improving cardiovascular health in the elderly. VLAG Human and Animal Physiology VLAG Fysiologie van Mens en Dier urn:nbn:nl:ui:32-05a60374-00a3-43bc-9289-2b2459ffe71e/obj 2026-05-20 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/81a03e76-ea44-415d-89ec-39484bf6edcb 2026-05-20 thesis

urn:nbn:nl:ui:32-81a03e76-ea44-415d-89ec-39484bf6edcb 2026-05-20 urn:nbn:nl:ui:32-81a03e76-ea44-415d-89ec-39484bf6edcb/mods Taking plastics with a pinch of salt : Polyester-based polyelectrolyte complexes: from synthesis to decomplexation Wageningen University dgg Engelhardt Julian J. 0000000530276486 aut H. Zuilhof opn J. van der Gucht opn L.C.P.M. de Smet opn E. Maaskant opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 231 10.18174/681325 en Large amounts of plastic are polluting marine ecosystems and continue to accumulate due to the remarkable chemical and physical stability of conventional plastics. As current collection, reuse, and recycling strategies have proven insufficient to address this problem, it is essential to develop alternative approaches to prevent further accumulation of plastic in the oceans. This thesis investigates polyester-based polyelectrolyte complexes (PECs) as a potential solution, incorporating an on-demand trigger that enables the material to dissolve upon leaking into the ocean. PECs are formed by mixing aqueous solutions of oppositely charged polyelectrolytes. The ionic interactions between these polymers are reversible and can be cleaved by exposure to charged molecules, such as the salt present in seawater, which weakens the ionic crosslinks and eventually dissolves the complex. Additionally, incorporating a polyester backbone into the polyelectrolytes could further enable (bio)degradation of the dissolved PEC, providing a viable end-of-life scenario. The main aspect of this work revolves around the synthesis of polyester-based polyelectrolytes. Melt polycondensation and ring-opening polymerization strategies were employed, making predominant use of biobased monomers. First, we demonstrate a synthetic route toward polyester-based PECs via melt polycondensation. The resulting PEC exhibits reduced brittleness compared to state-of-the-art vinyl-based PECs. Furthermore, the lower charge density along the polymer backbone enables processing at reduced temperatures and without the need for plasticizers. When exposed to a seawater mimic, the polyester-based PEC dissolves within 30 minutes. Subsequently, we explore ring-opening polymerization of lactones as an alternative route towards polyester-based polyelectrolytes, allowing improved control of the polydispersity. Through systematic post-modification of the ring-opened lactones, we examine the effects of charge density and hydrophobicity of the polyelectrolytes on the complexation behavior, and the resulting thermomechanical properties are highlighted. By combining polyelectrolytes of varying charge densities and hydrophobicities, the salt resistance, glass transition temperature, and tensile properties of the PECs can be systematically tuned. Overall, this thesis presents synthetic strategies for polyester-based polyelectrolytes, with an emphasis on structure-property relationships. The findings advance the understanding of polyester polyelectrolyte synthesis and elucidate the influence of charge density and hydrophobicity on material properties. Physical Chemistry and Soft Matter VLAG Sustainable Chem & Techn Organic Chemistry Fysische Chemie en Zachte Materie VLAG Sustainable Chem & Techn Organische Chemie urn:nbn:nl:ui:32-81a03e76-ea44-415d-89ec-39484bf6edcb/obj 2026-05-20 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/b70c5e88-cfa0-4472-8dad-97b79eaaa4cd 2026-05-22 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-b70c5e88-cfa0-4472-8dad-97b79eaaa4cd 2026-05-22 urn:nbn:nl:ui:32-b70c5e88-cfa0-4472-8dad-97b79eaaa4cd/mods Integrative analysis of QR codes for food supply chain integrity Wageningen University dgg Li Pengfei 0000000530276507 aut K.A. Hettinga opn S.W. Erasmus opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 274 10.18174/681673 en Quick response (QR) codes are increasingly used on food packaging to provide consumers with accessible digital information. Their small size, ease of use, and ability to link to dynamic content make them promising tools for enhancing food authentication and supply chain integrity. However, effective implementation depends not only on adoption by supply chain actors but also on consumer engagement and acceptance, as various factors influence their use. Understanding stakeholders’ perceptions and consumers’ behavioral intentions is therefore essential to promote wider adoption. This thesis highlights the role of QR codes in strengthening food supply chain integrity through approaches, including literature review, interviews, surveys, and meta-analysis, which offer strategic insights for improving adoption. Additionally, the thesis proposes a novel spatial-temporal method for detecting food fraud based on consumer QR code scanning data, providing new opportunities to enhance authenticity monitoring and combat food fraud effectively. VLAG Food Quality and Design VLAG Food Quality and Design urn:nbn:nl:ui:32-b70c5e88-cfa0-4472-8dad-97b79eaaa4cd/obj 2026-05-22 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/cffe3d7d-fe13-431b-8a8b-3ed3d0e1cfa9 2026-05-21 thesis

urn:nbn:nl:ui:32-cffe3d7d-fe13-431b-8a8b-3ed3d0e1cfa9 2026-05-21 urn:nbn:nl:ui:32-cffe3d7d-fe13-431b-8a8b-3ed3d0e1cfa9/mods The impact of a negative energy balance on porcine phenotypic and granulosa cell molecular responses Wageningen University dgg Yu Qi 0000000530276494 aut J. Keijer opn K. Teerds opn N. Soede opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 202 10.18174/681449 en The aim of this thesis is to elucidate the regulatory axis linking energy status to ovarian function. I focus on mural granulosa cells (GCs), which provide nutrients and signal molecules to the oocyte. Negative energy balance (NEB) during the lactation is a well-recognized condition that induces energy stress and impairs oocyte quality in primiparous sows. Ovaries were collected from restricted and full fed sows two days after weaning, corresponding to the mid-follicular phase. This work focuses on elucidating the transcriptional and post-transcriptional mechanisms by which energy status modulates the development of mural GCs, through specific regulatory networks, key genes, and post-transcriptional small molecular mediators (microRNAs (miRNAs) and long non-coding RNAs (lncRNAs)). In the last research chapter, I studied multiparous sows to obtain a comparative insight at the physiological level. First, I investigated the effect of energy insufficiency on mural GC gene expression (chapter 2). The molecular mechanisms through which energy metabolism regulates mural GCs were thus far poorly characterized. I used laser capture microdissection (LCM) for collecting pure mural GCs for the application of unique molecular identifiers (UMIs)-based mRNA-seq. UMIs improve data quality by reducing amplification bias. The IGFBP7-AKT/FOXO1-CDKN1A-cell cycle axis was identified as a potential regulatory axis by which energy modulates the cell cycle in mural GCs, consisting of two interconnected pathways: PI3K and MAPK pathways. miRNAs can repress gene expression through mRNA destabilization and/or inhibition of translation. I investigated whether specific miRNAs participate in the regulatory axis identified in chapter 2. Interestingly, ssc-miR-24-3p and ssc-miR-296-5p likely contribute to cell cycle progress. The higher expressed ssc-miR-296-5p was predicted to target the cell cycle inhibitor CDKN1A, while lower expressed ssc-miR-24-3p was predicted to target CDK1, which drives cell cycle progression. This expression pattern suggests a coordinated regulatory mechanism that facilitates cell cycle progression. Next, I shifted my focus to lncRNAs (chapter 4). A total of 221 differentially expressed lncRNAs (DElncRNAs) were identified to co-express with regulatory axis members proposed in chapter 2 and exhibited potential regulatory interactions. Among them, four key DElncRNAs showed a strong correlation with cell cycle progression, follicle size, body weight loss, and loin muscle depth loss, providing insights for understanding the regulatory landscape in mural GCs related to energy insufficiency. In the last research chapter (chapter 5), I investigated whether multiparous sows, like primiparous sows, experience a NEB during lactation that affects follicular development. I measured lactational body condition parameters, metabolic hormones, and physiological characteristics of follicles to establish a mixed linear regression model. The results showed that the milder negative energy balance of multiparous sows did not affect follicular development. The conclusions and implications of my research are: I generated a transcriptional atlas of multilayered RNA cross-talk. This regulatory atlas provides the basis to understand at a molecular level how energy status affects mural GC proliferation and follicular development, paving the way for future applications to prevent reproductive impairment and improve reproductive outcome. I also underscore the adaptive metabolic capacity of multiparous sows to maintain follicular function under a mild negative energy balance. WIAS Human and Animal Physiology Adaptation Physiology WIAS Fysiologie van Mens en Dier Adaptatiefysiologie urn:nbn:nl:ui:32-cffe3d7d-fe13-431b-8a8b-3ed3d0e1cfa9/obj 2026-05-21 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/f837e520-dbda-4045-8881-db3558adbfe6 2026-05-21 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-f837e520-dbda-4045-8881-db3558adbfe6 2026-05-21 urn:nbn:nl:ui:32-f837e520-dbda-4045-8881-db3558adbfe6/mods Solving the methane mitigation mystery? : Effect of compost application on the atmospheric methane uptake of agricultural soils Wageningen University dgg van den Bergh Stijn G. 0000000530253217 aut W. de Boer opn P.L.E. Bodelier opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 323 10.18174/681025 en This thesis aimed to resolve the “methane mitigation mystery” by systematically investigating how compost application influences the atmospheric methane (CH₄) uptake of agricultural soils, and to elucidate the underlying microbial and physicochemical mechanisms. Given the urgent need to reduce methane emissions, and the limited capacity of intensively managed soils to function as methane sinks, this work explores compost as a potential climate-smart strategy to enhance methane mitigation by agricultural soils. A combination of field experiments and controlled laboratory studies demonstrated that agricultural soils consistently act as net sinks for atmospheric methane, but their uptake capacity is strongly modulated by management practices. While compost application did not yield consistent effects on methane fluxes under field conditions, laboratory incubations revealed a clear and significant enhancement of the agricultural soil’s methane oxidation potential following organic amendment. Soil aggregate stability emerged as a key regulator of greenhouse gas fluxes, with higher stability, which was improved by organic inputs and reduced tillage, associated with increased methane uptake but also elevated CO₂ and N₂O emissions, highlighting important trade-offs. At the microbial level, compost application unequivocally reshaped methane-cycling microbial communities, increasing total abundance while reducing diversity. Compost acted both as a vector for microbial inoculation and as a stimulant of indigenous populations. Although methanotrophs such as Methylocaldum sp. became dominant in organic-amended soils, enhanced methane uptake was primarily attributed to conventional soil methanotrophs, particularly type II methanotrophs Methylocystis sp. and Methylosinus sp. Also, different types of compost were analyzed on their intrinsic methane mitigation potential, with green compost performing best, and their indigenous methane-cycling microbial communities, which were dominated by Methylocaldum szegediense and Methanosarcina sp. Mechanistic investigations rejected several hypothesized drivers, including stimulation of in situ methanogenesis and enhanced hydrogen-mediated co-oxidation of atmospheric methane. Instead, the results support a model in which prior exposure to elevated methane concentrations enables methanotrophs to oxidize methane at atmospheric levels, consistent with a “flush-feeding” ecological strategy. Four distinct methanotrophic groups, Methylocaldum sp., Methylosinus sporium, Methylocystis sp./Methylosinus trichosporium, and members of the USCalpha cluster, were identified as methanotrophically active at (sub-)atmospheric methane concentrations. Overall, this thesis provides a mechanistic framework explaining how compost application can enhance atmospheric methane uptake in agricultural soils through interacting effects on soil structure and microbial ecology. The findings emphasize the potential of compost as a climate-smart agricultural strategy, while also highlighting the need to balance methane mitigation against other greenhouse gas emissions. They also demonstrate that compost application can enhance soil methane uptake as a climate-smart practice for farmers, while calling on policymakers and the composting industry to recognize and integrate soil methane mitigation into climate-smart agriculture through targeted policies. PE&RC Soil Biology Soil Biology Operations Manager PE&RC Bodembiologie Soil Biology Operations Manager urn:nbn:nl:ui:32-f837e520-dbda-4045-8881-db3558adbfe6/obj 2026-05-21 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/f8efcb24-06d0-4f35-96a2-de51e3355a40 2026-05-21 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-f8efcb24-06d0-4f35-96a2-de51e3355a40 2026-05-21 urn:nbn:nl:ui:32-f8efcb24-06d0-4f35-96a2-de51e3355a40/mods Light Stress in Plants : Insights from Chlorophyll Fluorescence Wageningen University dgg Bagchus Cleo Roberta Paula 0000000530253321 aut H. van Amerongen opn I.E. Wientjes opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 226 10.18174/681863 en Oxygenic photosynthesis is driven by light absorbed in photosystem (PS) I and II. Light can also inactivate photosynthesis, mainly by damage to PSII, especially the D1 core protein. Photoinhibition (the light-dependent decrease in functional PSII) is initially accompanied by an increase of excitation quenching, energy dissipation characterized by a decline in the lifetime of chlorophyll fluorescence. The effect of photoinhibition on the fluorescence lifetime of PSII of the model plant Arabidopsis thaliana was determined using time-resolved fluorescence measurements with a streak-camera setup. Measurements were performed in conditions that either closed PSII (Fm) or kept the PSII RCs open (Fo). Upon photoinhibition, a photoinhibitory quencher is formed in the PSII core complex, as indicated by measurements in the chlorina mutant. The average fluorescence lifetime of PSII in Fo conditions increased upon photoinhibition due the larger antenna size of still functional PSII. Recovery from photoinhibition requires migration of PSII core complexes from the grana to the stroma lamellae where D1 is degraded and (re)synthesized. We combined confocal Fluorescence Lifetime Imaging Microscopy (FLIM) with biochemical fractionation of the thylakoid membrane to investigate the localization of (damaged) PSII following photoinhibition in the presence of lincomycin, an inhibitor of D1 synthesis. FLIM images of structured thylakoid membranes were segmented into grana- and stroma-lamellae-enriched regions. No significant difference in fluorescence lifetime components was observed between the grana-enriched region and the stroma-lamellae-enriched regions, suggesting that damaged, quenched PSII does not accumulate in the stroma lamellae. D1 levels also uniformly decreased across grana and stroma lamellae upon photoinhibition. Thus, with this photoinhibitory treatment, photodamaged PSII is efficiently relocated and degraded without accumulation in the stroma lamellae. Non-photochemical quenching or NPQ is a collective term for photoprotective processes that safely dissipate excess light energy as heat. NPQ was studied in the moss Physcomitrium patens, which contains PsbS (indispensable for quickly reversible NPQ in vascular plants), LhcSR (indispensable for quickly reversible NPQ in green algae) and a xanthophyll cycle which interconverts violaxanthin (Vx) and zeaxanthin (Zx). NPQ induction curves were measured at a range of light intensities for WT P. patens and mutants with altered NPQ. A data analysis pipeline revealed two distinct kinetic components underlying NPQ, together with their contributions to NPQ. A slowly-rising component provides most NPQ, especially at higher light intensities. Another component contains a transient NPQ peak, providing quick protection and requires the presence of either PsbS or LhcSR. Vx to Zx conversion enhances LhcSR-related NPQ at all light intensities and within the first minute of illumination. The influence of this conversion process is thus broader than previously recognized. P. patens mutants with a constitutive presence of Zx (zep KOs) were also studied with time-resolved fluorescence measurements. In the zep KO mutant, constitutive Zx accumulation locks the photosynthetic apparatus in a pre-quenched state in the dark. This dark-adapted Zx-driven quenching is mediated by LhcSR, while PsbS-dependent quenching is strictly light-activated. Our findings indicate that PsbS and LhcSR have distinct molecular mechanisms, which might clarify the evolutionary shift towards PsbS dominance in vascular plants. EPS Biophysics EPS Biofysica urn:nbn:nl:ui:32-f8efcb24-06d0-4f35-96a2-de51e3355a40/obj 2026-05-21 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/30dd216b-1080-4034-adb8-75d238b450d9 2026-05-14 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-30dd216b-1080-4034-adb8-75d238b450d9 2026-05-14 urn:nbn:nl:ui:32-30dd216b-1080-4034-adb8-75d238b450d9/mods Rethinking Huanglongbing research : Early phloem signaling, surrogate models, and a revised evolutionary framework of Liberibacter Wageningen University dgg Wang Jing 0000000530282296 aut T. Bisseling opn X. Cheng opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 130 10.18174/680948 en Huanglongbing (HLB), or citrus greening disease, is one of the most destructive diseases of citrus worldwide. It is mainly associated with the phloem-limited bacterium Candidatus Liberibacter asiaticus (CLas), which cannot yet be cultured in vitro. This biological constraint, together with the difficulty of accessing early infection events in citrus phloem, has strongly limited mechanistic studies and the development of durable control strategies. This thesis rethinks HLB research by combining synchronized citrus infection, phloem-specific transcriptomics, rhizobial surrogate systems, and phylogenomics to better understand CLas biology and host–pathogen interactions. First, a modified micrografting-based transmission system was established to achieve rapid and synchronized CLas infection in citrus seedlings. This system enabled systemic CLas invasion within 40 days and provided a controlled platform for studying early-stage HLB before extensive secondary tissue damage occurs. By combining this system with laser-capture microdissection and RNA sequencing, early phloem-specific citrus responses to CLas were profiled. This approach identified previously unreported early-responsive genes, offering new insight into the initial molecular dialogue between CLas and citrus and providing candidate infection-inducible promoters for targeted antimicrobial strategies. Second, the evolutionary and functional relationship between CLas and rhizobia was explored using the Sinorhizobium meliloti–Medicago root nodule symbiosis as a surrogate system. Comparative expression analysis of homologous genes from CLas and the S. meliloti symbiotic plasmid pSymA revealed extensive divergence in promoter activity, suggesting that CLas regulatory networks have been reshaped during adaptation to an intracellular phloem-associated lifestyle. In addition, the CLas transcription factor RpoH was functionally tested in planta. CLas RpoH partially complemented an S. meliloti RpoH mutant, while the inhibitor rosiglitazone maleate reversed this effect and reduced CLas titers in infected citrus seedlings, demonstrating the value of rhizobial-legume systems for CLas gene-function studies and inhibitor screening. Finally, large-scale phylogenomic analyses using conserved AMPHORA proteins showed that Liberibacter is nested within the genus Rhizobium, supporting a revised evolutionary framework in which Liberibacter represents a highly specialized rhizobial lineage adapted to phloem and insect-associated niches. Together, this thesis provides conceptual and methodological advances for HLB research by revealing early phloem responses, validating tractable surrogate models, and reframing the evolutionary origin of CLas. EPS Molecular Biology (MOB) EPS Molecular Biology (MOB) urn:nbn:nl:ui:32-30dd216b-1080-4034-adb8-75d238b450d9/obj 2026-05-14 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/1b550ccd-70e6-4e8e-8fde-bae9751f9f39 2026-05-11 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-1b550ccd-70e6-4e8e-8fde-bae9751f9f39 2026-05-11 urn:nbn:nl:ui:32-1b550ccd-70e6-4e8e-8fde-bae9751f9f39/mods Protein transition in a dynanamic food environment: : a systems approach Wageningen University dgg Blokhuis Christina 0000000530218251 aut E.W.M.L. de Vet opn G.J. Hofstede opn M. Ocké opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 310 10.18174/681476 en People in Western countries eat too much animal-sourced proteins such as meat, dairy and eggs, which has negative consequences for nature, human health, and animal welfare. Shifting towards more plant-sourced proteins, such as lentils and nuts, requires a better understanding of why animal-sourced proteins remain preferred. This doctoral research connects all factors determining food choices in a system view and identifies those most influential in attaining more plant-based diets. The results indicate that animal-sourced proteins remain easier to acquire and more socially accepted than plant-sourced proteins. Moreover, lobbying by the animal-based industry, along with promotion and financial support in favour of animal-sourced proteins, reinforces this status-quo. Promising solutions aim for the deeper system layers, including shifting responsibility from consumers to governments; strengthening regulation to support production and consumption of plant-sourced proteins; and policies that change the norm of eating animal-sourced proteins. Information Technology WASS Consumption and Healthy Lifestyles Toegepaste Informatiekunde WASS Consumptie en Gezonde Leefstijl urn:nbn:nl:ui:32-1b550ccd-70e6-4e8e-8fde-bae9751f9f39/obj 2026-05-11 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/2b184f16-cb35-405c-880d-a4214aaac058 2026-05-11 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-2b184f16-cb35-405c-880d-a4214aaac058 2026-05-11 urn:nbn:nl:ui:32-2b184f16-cb35-405c-880d-a4214aaac058/mods Cacao and arbuscular mycorrhizal fungi : Breeding prospects Wageningen University dgg Ferro Lozano Natalie M. 0000000530121329 aut G.A.B. Bonnema opn T.W. Kuijper opn L.C. Mejia opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 195 10.18174/681165 en Cacao (Theobroma cacao) has been cultivated in Panama since at least 1500 BC, predominantly within traditionally managed agroforestry systems overseen by Indigenous communities. Despite this long history and the country’s strategic biogeographical position for cacao semi-domestication, the genetic identity of cacao cultivated in Panama and the management practices shaping it remain poorly documented. This research provides the first comprehensive characterization of cacao germplasm used across Panamanian farms while integrating environmental, agronomic, and microbial dimensions to understand how plant genetics and soil biota jointly influence cacao production. Across 16 farms in the provinces of Bocas del Toro and Herrera, we collected leaf and root samples from five trees per farm and genotyped them using a 96-SNP array. We also recorded detailed management practices and environmental variables, including soil nutrients and physiographic conditions. Cacao genetic diversity in Bocas del Toro displayed extensive admixture, representing all major cacao genetic groups, whereas farms in Herrera were dominated by Amelonado and Criollo germplasm, including individuals with pure Criollo ancestry. Limited germplasm exchange between provinces contributed to these distinct genetic compositions. While seed propagation was common nationwide, grafting frequency varied substantially, being more prevalent in Bocas del Toro (55%) than in Herrera (16%). These findings reveal Panama’s unrecognized cacao genetic diversity and underline its potential for strengthening national cacao improvement programs. Because cacao is a mycotrophic species reliant on belowground symbioses, we also assessed how genotypic and environmental variables shape arbuscular mycorrhizal fungal (AMF) communities associated with the sampled trees. Using molecular AMF community profiling, paired with analyses of scion and rootstock genotypes, root traits, and soil chemistry, we found that Glomus was the dominant AMF genus across all sites. AMF community structure was significantly influenced by scion genotype, root nutrient concentrations (N and P), elevation, and available soil P, whereas rootstock genotype and root morphological traits were not major determinants. High between-farm variation highlighted the sensitivity of AMF communities to local environmental contexts. These results underscore the importance of considering both host genetics and soil chemistry when designing strategies to optimize plant–fungal mutualisms in cacao agroforestry. To further explore opportunities for breeding cacao cultivars with improved symbiotic performance, we evaluated selfed progenies of three cacao clones previously selected for high yield and bean quality. Progenies were grown under four distinct AMF inocula representative of Panama’s environmental gradients, plus a non-inoculated control. Significant main effects of both AMF treatments and progeny identity were detected for aboveground biomass, with interactive effects between AMF communities and progenies. Root nitrogen content and diameter varied significantly among progenies and mycorrhizal treatments, while root tissue density and specific root length differed primarily among mycorrhizal treatments. These findings emphasize the relevance of root functional traits in mediating cacao–AMF interactions and highlight the potential to breed cacao varieties optimized for beneficial symbioses. Collectively, this research provides an integrated perspective on cacao genetic diversity, traditional management, AMF communities, and root functional traits in Panama, offering actionable insights for sustainable cacao agroforestry and future cacao improvement initiatives. PE&RC Soil Biology Plant Breeding (PBR) PE&RC Bodembiologie Plant Breeding (PBR) urn:nbn:nl:ui:32-2b184f16-cb35-405c-880d-a4214aaac058/obj 2026-05-11 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/c2748d33-d6a4-4be9-a468-ede07870b387 2026-05-07 thesis

urn:nbn:nl:ui:32-c2748d33-d6a4-4be9-a468-ede07870b387 2026-05-07 urn:nbn:nl:ui:32-c2748d33-d6a4-4be9-a468-ede07870b387/mods Financial performance outcomes of downsizing Wageningen University dgg van Boven Jasper 000000051329536X aut W.A. Dolfsma opn H.L. Aalbers opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 176 10.18174/681141 en The objective of this dissertation is to explore how and when firms engage in downsizing with one central theme: how downsizing affects the financial performance of the firm. In response to recent calls, this dissertation investigates strategic actions such as acquisitions and digital transformation, where downsizing is used applied to unlock benefits. This dissertation examines the timing and magnitude of downsizing decisions and how firms can offset negative workforce effects, thereby securing financial performance. Chapter 2 examines incumbents acquiring born‑digital firms for their digital transformation. This chapter argues that downsizing after a digital acquisition signals efficiency. The findings show that early downsizing after a digital acquisition triggers negative market reactions, while a longer interval signals successful integration and improves market response. The findings emphasizes the importance of careful implementation and employee downsizing to maximize the benefits of digital acquisitions. Chapter 3 analyzes downsizing after a digital‑technology investment. The results show that larger magnitudes of downsizing and short time spans between investment in digitalization and downsizing unlock most value. These insights contribute to the understanding of employee downsizing as digital transformation makes the firm more efficient and yields smaller, flatter structures. Chapter 4 reviews human‑capital deterioration and the need for acquisitions to replenish talent. Post‑acquisition downsizing after an acquisition can unlock synergies but may erode the replenishment potential of the acquired workforce. The findings show that only targeted redundancy in smaller acquired workforces streamlines operations. This chapter provides a nuanced understanding of when and how downsizing can enhance post-acquisition performance, emphasizing resource efficiency and integration to drive long-term success. Chapter 5 studies how firms repair psychological‑contract breaches caused by downsizing. This chapter sheds light on the violating effect of downsizing, which harms employee engagement and motivation, which in turn hurts financial performance. The results show that minor and major cuts outperform moderate ones as efficiency gains in moderate cuts fail to offset contract‑violation costs. Proactive contract repair during moderate downsizing reduces backlash and boosts performance. This chapter provides insights into how organizations can effectively recover from psychological contract violation. In closing, the findings presented in this dissertation suggest that a misjudgment of the magnitude of downsizing, wrong timing, or not taking the impact on employees into consideration can potentially lead to diminished financial performance. However, the insights gained from the various studies in this dissertation above all reinforce the awareness that downsizing under the right circumstances, strategically aligned with firm objectives, and especially with considerations for employees, both victims and survivors, can reap financial benefits. Business Management and Organisation WASS Bedrijfsvoering en Organisatie WASS urn:nbn:nl:ui:32-c2748d33-d6a4-4be9-a468-ede07870b387/obj 2026-05-07 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/8b04310e-3c1e-41ac-a799-d455b1e2c064 2026-05-07 thesis

urn:nbn:nl:ui:32-8b04310e-3c1e-41ac-a799-d455b1e2c064 2026-05-07 urn:nbn:nl:ui:32-8b04310e-3c1e-41ac-a799-d455b1e2c064/mods Steering the rhizobiome: : multi-trophic and stage-dependent responses to diversified cropping systems Wageningen University dgg Hu Shunran 0000000530191140 aut J.E. Kammenga opn S. Geisen opn Y. Chen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 186 10.18174/681776 en Agriculture faces unprecedented pressure to meet the rising food demand under global climate change while reducing negative environmental impacts. Intensive management (e.g., excessive fertilization, pesticide use and tillage) can impair soil biodiversity, reduce nutrient use efficiency, and degrade ecosystem services. Diversified cropping systems that include temporal, spatial and genetic dimensions of diversification have therefore emerged as a promising pathway towards more sustainable crop production. However, how diversified cropping systems influence the multi-trophic interactions in the rhizobiome during plant maturation remains unknown. This leads to the central aim of this thesis: to reveal the temporal shifts in the rhizobiome and its functioning in diversified cropping systems, with particular attention to the feedback consequences of these rhizobiomes for subsequent crop performance. Building on this global and conceptual context, I first examine how diversification in crop rotations modifies the rhizobiome. While increased diversification in crop rotation systems induces a plant-beneficial rhizobiome that can facilitate plant performance, I further explore how wheat maturation affects the rhizobiome and how these stage-specific rhizobiomes functionally link to maize growth. Besides the temporal diversification in rotation systems, spatial-genetic diversification also has the potential to shape the rhizobiome. I examine how increased wheat genotype diversity (from monocultures to 12-genotype mixtures) affects the rhizobiome assembly and plant performance under biotic or abiotic stresses. The focus on within-species diversity is also extended; I study how the same wheat genotype diversity gradient modulates nematode communities and their trophic links with the rhizobiome across stages. Finally, I synthesise findings from all experimental chapters into an integrated framework linking diversified cropping systems, the rhizobiome and multi-trophic interactions to crop performance. I argue that more diversity is not inherently better for plant growth and soil health, since intermediate levels of crop diversity tend to maximise complementarity and promote plant-beneficial rhizobiomes. I also emphasise that diversified cropping systems are shown to act through interconnected bottom-up and top-down pathways in the soil food web, mediated by stage-dependent recruitment of microbial functional groups and the rhizobiome predators. Therefore, diversification strategies that are trait-based, stage-dependent, and host-matched, which need to be tested through multi-scale experiments and on-farm trials, can help design resilient, low-input agroecosystems that steer the rhizobiome functioning to sustain crop production under global change. PE&RC Nematology (NEM) PE&RC Nematology (NEM) urn:nbn:nl:ui:32-8b04310e-3c1e-41ac-a799-d455b1e2c064/obj 2026-05-07 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/56a408f3-2a9e-40a2-8ff4-0312327bee78 2026-05-07 thesis

urn:nbn:nl:ui:32-56a408f3-2a9e-40a2-8ff4-0312327bee78 2026-05-07 urn:nbn:nl:ui:32-56a408f3-2a9e-40a2-8ff4-0312327bee78/mods Multilateralism for whom? : The politics of transparency in the global climate regime Wageningen University dgg van Deursen Max B.W. 0000-0002-9148-5415 0000000530253313 aut A. Gupta opn I. Boas opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 324 10.18174/681805 en Which countries are most responsible for taking climate action? Should developed countries take the lead? And what types of climate action are appropriate and count towards the global effort to address climate change? Is emission reduction the cornerstone of climate action, or is adaptation and addressing loss and damage equally important? These questions capture the essence of global climate politics. These contested politics are what makes negotiating multilateral agreements so difficult—and fascinating. The latest milestone in negotiating such multilateral agreement was the adoption of the Paris Agreement. The Paris Agreement cemented a novel approach to global climate governance. This approach does not rely on legally binding emission-reduction targets for developed countries, but instead relies on voluntary, nationally determined targets submitted by all. It is in this era of voluntary, nationally determined targets that transparency—i.e., reporting and review—has become ever more central. Transparency is widely assumed to facilitate accountability and enhanced climate action. It has even been termed the ‘backbone’ of the Paris Agreement. Yet does transparency live up to its promise in practice? Is transparency a neutral tool to facilitate climate action from all? Or does transparency intervene in the broader politics of climate action? And, if so, how? These questions remain hardly asked, let alone empirically examined. To address this gap in the literature, this thesis draws on critical transparency studies to empirically examine the steering effects of transparency in the global climate regime. Methodologically, this thesis relies on detailed analyses of multilaterally negotiated transparency rules, as well as two case studies on domestic uptake of transparency rules in India and South Africa. These sites of analysis are studied using interviews, a focus group discussion, policy documents, observations of negotiations, country submissions, and other primary documents as data sources. These data sources are analyzed qualitatively, drawing on interpretivist approaches. Based on these analyses, this thesis challenges the assumption that more transparency facilitates accountability and enhanced climate action from all. Instead, this thesis finds that transparency intervenes in the broader politics of global climate action by channeling a mitigation-centric agenda to developing countries, while obscuring responsibilities of developed countries. These steering effects are also resisted, especially by developing countries, many of whom hold other visions of what an equitable multilateral response to climate change would look like. In essence, this thesis problematizes the notion that the Paris Agreement is itself a neutral institutional mechanism to raise climate ambition for all. Not all forms of multilateralism are created equal, and this thesis calls for continued critical scrutiny of the ways in which the operationalization of the Paris Agreement’s design intervenes in the broader politics of global climate action. Environmental Policy WIMEK Milieubeleid WIMEK urn:nbn:nl:ui:32-56a408f3-2a9e-40a2-8ff4-0312327bee78/obj 2026-05-07 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/970c2c66-709c-431f-87ab-7423e01c9ae2 2026-05-08 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-970c2c66-709c-431f-87ab-7423e01c9ae2 2026-05-08 urn:nbn:nl:ui:32-970c2c66-709c-431f-87ab-7423e01c9ae2/mods With a grain of plastic : navigating the unvalidated territories of microplastic and nanoplastic analysis Wageningen University dgg Vitali Clementina 0000000530208619 aut M.W. F. Nielen opn J.G.M. Janssen opn F.S.Dr. Ruggeri opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 252 10.18174/681299 en The growing scientific and regulatory attention to microplastics (MPs) and nanoplastics (NPs) as emerging food contaminants has exposed major analytical challenges, driven by the need to characterize solid, heterogeneous, and polydisperse particles rather than dissolved molecules. Comprehensive analysis requires the reliable determination of particle number, size and shape distributions, and chemical composition. However, current methods remain limited in robustness and sensitivity, particularly at the nanoscale. A critical assessment of the field highlights key gaps, including the lack of harmonized validation criteria and quality assurance frameworks, the limited availability of high-throughput methods for large-scale monitoring, insufficient sensitivity for single-particle NP analysis, and the scarcity of representative reference materials. This thesis addresses these challenges through the development of multimodal analytical approaches for the detection and characterization of MPs and NPs. A high-throughput, automated fluorescence-based workflow for MP quantification in bottled water is developed – combining Nile Red staining, fluorescence microscopy, and AI-powered image analysis – and validated. The workflow is further extended by integrating single-particle atmospheric solids analysis probe mass spectrometry, enabling the determination of particle count, morphology, and chemical identity. At the nanoscale, a complementary workflow combining spatially confined hyper-concentration, fluorescence-guided localization, and infrared nanospectroscopy is introduced. This approach enables detailed characterization of NP morphology, composition, and surface chemistry, revealing localized oxidation and weathering patterns in NPs isolated from real samples. VLAG Organic Chemistry VLAG Organische Chemie urn:nbn:nl:ui:32-970c2c66-709c-431f-87ab-7423e01c9ae2/obj 2026-05-08 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/6641f2fb-bbc0-464b-8e13-9bfea3bcc2b0 2026-05-01 thesis

urn:nbn:nl:ui:32-6641f2fb-bbc0-464b-8e13-9bfea3bcc2b0 2026-05-01 urn:nbn:nl:ui:32-6641f2fb-bbc0-464b-8e13-9bfea3bcc2b0/mods Next generation molecular breeding in strawberry : using whole-genome sequencing based haplotypes Wageningen University dgg Koorevaar Tim 0000000530153224 aut R.G.F. Visser opn P. Arens opn J.H. Willemsen opn C.A Maliepaard opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 209 10.18174/681823 en This thesis addresses how to implement sequencing-based genotyping in a practical breeding program for cultivated strawberry. The aim was to implement a flexible WGS-based genotyping strategy that captures the (almost) all genetic variation in the breeding germplasm, allows high-throughput genotyping, and can subsequently be used for downstream applications such as haplotype-based diversity analysis, QTL mapping, and genomic selection. To achieve this, we first investigated what to sequence with high coverage to capture the relevant diversity in a commercial strawberry breeding program (Chapter 2). We combined pedigree information with genotypes data to build pedigree genomic relationship coefficients. Based on these, we selected a core collection that represents the current breeding germplasm, but also the expected future variation by prioritizing recent crossing parents. This core collection was then sequenced and became the backbone for haplotype construction, imputation, and diversity analyses in the later chapters. In Chapter 3, we addressed the problem of erroneous and misassigned SNPs that occur because the sequence similarity between subgenomes in strawberry. This similarity can cause sequencing reads to align to the wrong subgenome, which could result in erroneous SNP calls. We developed a filtering strategy a based on a combination of linkage disequilibrium (LD) and average allele balance (AAB) to detect these problematic SNPs and remove them. This reduced the number of unreliable variants and provided a high confidence SNP dataset that is suitable for phasing and downstream analyses. In Chapter 4, we used the high confidence SNP set to construct haplotypes and build haplotype reference panels for cultivated strawberry. We phased the core collection with SHAPEIT5 and then evaluated how well these haplotypes can be used for imputation of low-coverage sequencing data by downsampling to 1× and imputing with GLIMPSE2. This showed that low-coverage sequencing, when combined with a filtered and representative haplotype reference panel, can yield high accuracy. In Chapter 5, we used the improved haplotype reference panel to study haplotype diversity across different strawberry breeding programs and across breeding years. This allowed us to compare genome wide and region specific haplotype diversity over time and between breeding programs, and to identify temporal and population specific selection footprints. By doing this, we could see that haplotype diversity is not uniform across the genome, and that specific regions stand out. Together, these results showed how different breeding programs have shaped genetic diversity in cultivated strawberry and provide guidance on how to balance short term genetic gain with long term breeding potential. In Chapter 6, I translated the findings of this thesis into a practical roadmap for using WGS based genotyping in a practical breeding program. Practical considerations were discussed, such as how a haplotype reference panel should be maintained over time. I then place our findings in the context of QTL mapping and genomic selection, focusing on what this sequencing-based genotyping strategy improves in practice. Finally, I discuss where the field is heading, including long range phasing for cross predictions, and how long-read sequencing and pangenomes may improve alignment and variant calling. EPS Plant Breeding (PBR) EPS Plant Breeding (PBR) urn:nbn:nl:ui:32-6641f2fb-bbc0-464b-8e13-9bfea3bcc2b0/obj 2026-05-01 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/e7462822-f1cf-4ebf-8a12-e984c66af77a 2026-05-08 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-e7462822-f1cf-4ebf-8a12-e984c66af77a 2026-05-08 urn:nbn:nl:ui:32-e7462822-f1cf-4ebf-8a12-e984c66af77a/mods The effects of antimicrobials on aquatic ecosystems Wageningen University dgg Wu Dailing 000000053022255X aut P. van den Brink opn H. Smidt opn Guang-Guo Ying opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 215 10.18174/681478 en Antimicrobials are routinely detected in freshwaters, where organisms are exposed to complex mixtures rather than single compounds. This PhD thesis links real-world exposure patterns to ecological responses by integrating four lines of research: environmental occurrence, multi-trophic effects, internal exposure and food-web transfer, and the ecological consequences of advanced wastewater treatment. The results showed that antimicrobial contamination can propagate across connected compartments, and that mixture effects are frequently non-additive and differ across trophic levels. Microbial and community responses were highly context-dependent, varying between water and sediment and with nutrient status and organic matter, while functional endpoints revealed impacts not captured by community structure alone. Food-chain experiments further indicated that limited biomagnification does not preclude ecological risk, as dietary exposure can still impair predator performance. Finally, advanced wastewater treatment reduced chemical pressure but could also restructure microbial communities, highlighting the need to balance removal efficiency with ecological outcomes. Ultimately, this thesis provides a transferable framework to support interdisciplinary research and management of emerging contaminants in aquatic systems. WIMEK Aquatic Ecology and Water Quality Management Microbiology WIMEK Aquatische Ecologie en Waterkwaliteitsbeheer Microbiology urn:nbn:nl:ui:32-e7462822-f1cf-4ebf-8a12-e984c66af77a/obj 2026-05-08 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/fa5a2bd2-3d07-4e9e-8bbb-3c39c96d0d02 2026-05-01 thesis

urn:nbn:nl:ui:32-fa5a2bd2-3d07-4e9e-8bbb-3c39c96d0d02 2026-05-01 urn:nbn:nl:ui:32-fa5a2bd2-3d07-4e9e-8bbb-3c39c96d0d02/mods Seaweeds – Cows – Methane : Introducing seaweeds in dairy cattle diets and their effects on enteric methane production, ruminal microbiome, food safety and animal health Wageningen University dgg Muizelaar Wouter 432994378 0000-0001-7527-4469 0000000502316786 aut J. Dijkstra opn G. van Duinkerken opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 200 10.18174/681060 en The central role of livestock production in the current food system is globally reassessed due to its contribution to greenhouse gas (GHG) emissions. In ruminants, one of the end products of fermented feed in the rumen is methane (CH4), which is released via the mouth and nostrils (enteric emissions). This enteric CH4 emission from ruminants is a major contributor to all animal production related GHG emissions. Several strategies have been developed to reduce the amount of enteric CH4 emissions from ruminants, with many strategies focusing on diet composition and addition of specific ingredients that lower CH4 production. Seaweeds are considered as CH4 reducing ingredients due to their diverse chemical composition. While seaweeds are no longer a novel ingredient in animal production, their application for reducing enteric CH4 emissions is relatively recent. In the development of novel ingredients for specific purposes, there is a balance between safety and efficacy. In this case, maximizing the CH4 reduction with no adverse effects on animal health and food safety. While seaweeds have potential to reduce enteric CH4 emissions, the active compounds and other compounds that seaweeds tend to accumulate pose a risk for animal health and food safety when fed. The general objective of this thesis was to study how seaweeds can contribute to reducing enteric CH4 emissions of cattle through two research lines. These lines differentiated between the seaweed species used, resulting in a research focus on either efficacy or safety. The first research line used seaweed species originating from northwest Europe, and evaluated their efficacy in CH4 mitigation, as well as their effects on production characteristics and the rumen microbiome. The second research line used seaweed species belonging to the genus Asparagopsis, which were investigated to generate data relevant for the absorption, metabolism, excretion and dynamics of the active compound bromoform (CHBr3). Additionally, the CH4 mitigating effectiveness of synthetic CHBr3 was evaluated. Several factors limit the use of most seaweed species as enteric CH4 inhibitors. The main limitations are related to the accumulation of minerals and heavy metals, or the too low concentrations of the hypothesized active compounds in seaweeds. Refining cultivation and processing techniques can lower the concentrations of unwanted compounds, and increase concentrations or extract active compounds to increase the potential as CH4 inhibitors, but requires time and financial resources to develop. The seaweed species belonging to the Asparagopsis genus do have high concentrations of active compounds (halogenated metabolites; e.g., CHBr3) which effectively reduce enteric CH4 production. However, adverse effects regarding animal health and food safety have been associated with the use of Asparagopsis spp. as CH4 inhibitors. Also the use of synthetic CHBr¬3, which allows better control over the quality, purity and dosing, is associated adverse effects, highlighting a central role of the active compound. The underlying causes of these adverse effects are unknown, and several hypothesis are explored which require further investigation. In general, it can be expected that in practice lower concentrations of CHBr3 will be used compared to experimental settings, resulting in lower CH4 inhibition. WIAS Animal Nutrition Management WIAS Diervoeding Management urn:nbn:nl:ui:32-fa5a2bd2-3d07-4e9e-8bbb-3c39c96d0d02/obj 2026-05-01 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/e8b3943c-f3a5-42a4-ac6e-cf5748685cad 2026-05-06 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-e8b3943c-f3a5-42a4-ac6e-cf5748685cad 2026-05-06 urn:nbn:nl:ui:32-e8b3943c-f3a5-42a4-ac6e-cf5748685cad/mods Physical stability of plant protein-stabilized food emulsions: A multiscale approach Wageningen University dgg Cao Jiarui 0000000530212706 aut C.G.P. Schroen opn M.N. Corstens opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 171 10.18174/681692 en As the demand for plant‑based foods grows, we need reliable ingredients that can replace the functional properties of animal proteins. Many everyday foods, like mayonnaise, sauces, and dairy-alternatives, are emulsions: tiny oil droplets that must stay evenly mixed. To make stable plant‑based emulsions, we need to understand how plant proteins behave during real processing conditions. This thesis explored how proteins from potatoes and faba beans can help keep oil-in-water emulsions stable. I found that potato proteins are excellent at keeping oil droplets apart, even under tough conditions like heating, or other ingredient addition (salt or pectin). Faba bean proteins can also work, but only when conditions are well-controlled. Heating plays a big role: it can help by thickening the liquid, but overheating can also damage the proteins. Combining proteins with polysaccharides offers a promising strategy to improve overall emulsion performance. Overall, stability depends on several factors working together at different scales, both in the liquid and at the oil-water interface. These insights help food manufacturers formulate more stable and appealing plant-based products. Food Process Engineering VLAG Food Process Engineering VLAG urn:nbn:nl:ui:32-e8b3943c-f3a5-42a4-ac6e-cf5748685cad/obj 2026-05-06 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/aee37c8c-b770-4500-a9f3-cb68b1a733ed 2026-05-06 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-aee37c8c-b770-4500-a9f3-cb68b1a733ed 2026-05-06 urn:nbn:nl:ui:32-aee37c8c-b770-4500-a9f3-cb68b1a733ed/mods Serial combined drying strategy of mushrooms for rehydration improvement Wageningen University dgg Hu Lina 0000000530235553 aut R.G.M. van der Sman opn J. Bi opn X. Jin opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 196 10.18174/680980 en The research addressed the common problem that dried fruits and vegetables often develop poor texture and lose nutrients after rehydration. Focusing on mushrooms, the study tested a two-step drying method that first creates a porous, sponge-like internal structure for better water absorption, followed by rapid dehydration to preserve this structure—successfully producing dried mushrooms with good rehydration performance and texture after the rehydration. By investigating how the mushroom's internal structure changes during this process using advanced microscopes and 3D scanners, the researchers identified the specific structural changes that lead to good rehydration. Most significantly, they developed a drying model that can predict moisture and temperature changes in mushrooms during drying, enabling targeted experiments for process optimization saving time and resources associated with costly trial-and-error experiments. Food Process Engineering VLAG Food Technology Food Process Engineering VLAG Food Technology urn:nbn:nl:ui:32-aee37c8c-b770-4500-a9f3-cb68b1a733ed/obj 2026-05-06 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/1bc321ca-6b7b-48f1-b6e3-8fb8c0fa740e 2026-05-01 thesis

urn:nbn:nl:ui:32-1bc321ca-6b7b-48f1-b6e3-8fb8c0fa740e 2026-05-01 urn:nbn:nl:ui:32-1bc321ca-6b7b-48f1-b6e3-8fb8c0fa740e/mods Microalgal protein solate cryostructurates : Understanding their role in preserving the biological activity of Lacticaseibacillus rhamnosus GG under processing, storage, and gastrointestinal transit associated cell stressors Wageningen University dgg Fortuin Jennyfer 0000000530200406 aut V. Fogliano opn C. Soukoulis opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 251 10.18174/681732 en This thesis investigated the potential of microalgal protein isolates from Arthrospira platensis (spirulina, SPI) and Chlorella vulgaris (chlorella, CPI) as sustainable and functional matrices for probiotic encapsulation. The work focused on elucidating how these proteins stabilise Lacticaseibacillus rhamnosus GG (LGG) across multiple stress conditions encountered during processing, storage, and gastrointestinal transit, including freeze-drying, elevated water activity, acidic pH, digestive enzymes, bile salts, and intestinal adhesion. To contextualise their performance, SPI and CPI were systematically compared with conventional protein matrices, namely whey protein isolate (WPI) and pea protein isolate (PPI). The role of precursor fermentation and the functionality of hybrid sodium alginate–microalgal protein cryogels were further explored. SPI and PPI demonstrated superior lyoprotective capacity during freeze-drying, while WPI showed limited protective effects. However, storage stability varied between matrices: SPI-based systems exhibited accelerated viability losses, likely linked to lipid oxidation, whereas PPI maintained stable probiotic survival. Precursor fermentation reduced LGG viability during processing and storage but improved gastric tolerance, revealing a trade-off between technological stability and gastrointestinal robustness. Proteomic and peptidomic analyses showed that SPI exhibited the highest digestibility, with extensive peptide release during in vitro digestion. Fermentation enhanced peptide diversity and abundance across all matrices and contributed to the generation of peptides with potential bioactivities, including antihypertensive, antioxidant, and immunomodulatory effects. However, the identification of such peptides in microalgal systems remained constrained by limited protein databases. CPI-based systems provided consistent protection of LGG during processing, storage, and digestion, with particularly strong performance under gastric conditions. This effect was attributed to acid-induced protein aggregation, which reinforced matrix structure and reduced cellular losses, as supported by observed colloidal transitions. Structured delivery systems based on sodium alginate (NaAlg)–microalgal protein cryogels further enhanced probiotic stability. The high water-binding capacity of NaAlg improved survival during lyophilisation, while acid-induced gelation and protein aggregation, especially in SPI-based systems, limited probiotic loss during gastrointestinal digestion. These systems enabled controlled release of LGG in the intestinal phase and supported adhesion to mucin-producing epithelial models, indicating preserved biological functionality. Overall, this thesis demonstrates that microalgal proteins are effective and multifunctional alternatives to conventional dairy and plant proteins for probiotic encapsulation. By linking protein composition, hydration behaviour, fermentation history, and structural organisation to probiotic viability and digestive performance, this work provides a mechanistic framework for the rational design of next-generation microalgae-based delivery systems with enhanced stability and functionality. VLAG Food Quality and Design VLAG Food Quality and Design urn:nbn:nl:ui:32-1bc321ca-6b7b-48f1-b6e3-8fb8c0fa740e/obj 2026-05-01 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/6ca54b9e-c47a-484c-a90a-beed3c6835a8 2026-05-07 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-6ca54b9e-c47a-484c-a90a-beed3c6835a8 2026-05-07 urn:nbn:nl:ui:32-6ca54b9e-c47a-484c-a90a-beed3c6835a8/mods Modeling variation for learning-based and multi-task robots in fruit picking Wageningen University dgg van de Ven Robert 0009-0005-6483-6231 000000053021826X aut E.J. van Henten opn G.W. Kootstra opn A.T. Nieuwenhuizen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 182 10.18174/681709 en Modern agriculture suffers from labor shortages for delicate tasks like fruit harvesting. This thesis worked on several challenges facing selective harvesting robotics. To reduce the manual annotation effort, 3D scene reconstruction was used for pose estimation, reducing the effort by 99.6%, while maintaining high pose estimation accuracy. To optimize the fruit detachment method, multiple algorithms were implemented to learn the fruit detachment motion from expert demonstrations. In a lab environment, a 67% success rate was achieved. Next, the challenge of dealing with wind disturbances was studied. A novel algorithm was developed, which could achieve a 99% success rate. Lastly, the multi-tasking capabilities were studied in a real orchard. Apple harvesting was performed best by training with 20 demonstrations and resulted in 90% of the fruits grasped and 65% picked. Pear harvesting was performed best by training with 40 demonstrations and resulted in 65% of the fruits grasped and 50% picked. Agricultural Biosystems Engineering (ABE) PE&RC Agro Field Technology Innovations Agricultural Biosystems Engineering (ABE) PE&RC Agro Field Technology Innovations urn:nbn:nl:ui:32-6ca54b9e-c47a-484c-a90a-beed3c6835a8/obj 2026-05-07 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/fe4a2f00-d114-4885-ae09-4de6a7ca2b64 2026-05-04 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-fe4a2f00-d114-4885-ae09-4de6a7ca2b64 2026-05-04 urn:nbn:nl:ui:32-fe4a2f00-d114-4885-ae09-4de6a7ca2b64/mods Toxic but tasty : The role of flavors in e-cigarette product appeal Wageningen University dgg Hellmich Ina Marisa 0000000530208627 aut S. Boesveldt opn R. Talhout opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 254 10.18174/681671 en E-cigarettes are harmful, yet popular. They come in many different flavors and these flavors play a role in e-cigarette appeal. This PhD thesis investigates how flavorings, sensory perception, and contextual product cues influence the appeal and use of e-cigarettes, and how these insights can inform public health policy and regulation. Across a series of experimental, observational, and analytical studies, this research demonstrates that e-cigarette flavor perception is not solely determined by chemical composition. Instead, it emerges from an interaction between flavoring ingredients and product design features. Using sensory and consumer science methods, we show that visual cues such as device color can systematically bias flavor expectations and flavor experiences. For example, identical e-liquids were perceived as sweeter when presented in a red device compared to a neutral-colored device, highlighting the role of crossmodal correspondences in shaping flavor experience. At the ingredient level, this thesis applies machine learning techniques, specifically self-organizing maps, to classify flavoring profiles across a wide range of tobacco and nicotine products. The results reveal systematic relationships between chemical flavoring compositions and marketed flavor categories (e.g., fruity, sweet, minty), as well as similarities and differences across product types. These findings suggest that flavoring profiles can serve as a basis for more consistent and scalable regulatory approaches, complementing current frameworks that rely on sensory-defined “characterizing flavors.” In addition, this work evaluates the real-world impact of regulatory interventions, focusing on the Dutch e-cigarette flavor ban implemented in 2024. Survey data from adolescents, young adults, and adults who used e-cigarettes prior to the ban indicate that a substantial proportion reduced their use or quit vaping altogether following the removal of non-tobacco flavors. Importantly, these behavioral changes were not accompanied by an increase in overall smoking prevalence at the population level. However, the findings also highlight challenges related to cross-border purchasing and continued access to restricted flavors, underscoring the importance of enforcement and international policy alignment. Overall, this thesis demonstrates that flavors are a key driver of e-cigarette appeal and use, influenced by both chemical and perceptual factors. By integrating sensory science, data-driven classification methods, and policy evaluation, the research provides a comprehensive understanding of how flavors operate within the broader context of nicotine product use. These insights support the development of more effective regulatory strategies aimed at reducing the attractiveness of e-cigarettes and protecting public health. VLAG Sensory Science and Eating Behaviour VLAG Sensoriek en eetgedrag urn:nbn:nl:ui:32-fe4a2f00-d114-4885-ae09-4de6a7ca2b64/obj 2026-05-04 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/0eceb135-c24c-4e0a-8082-6ac9bf842e86 2026-04-22 thesis

urn:nbn:nl:ui:32-0eceb135-c24c-4e0a-8082-6ac9bf842e86 2026-04-22 urn:nbn:nl:ui:32-0eceb135-c24c-4e0a-8082-6ac9bf842e86/mods Tuning interfacial properties and functionalities of lupin protein-pectin complexes by particle size and morphological features : Role of 2D interfacial rheology in affecting functionality and 3D bulk rheology Wageningen University dgg Ma Xingfa 0000-0001-9763-7662 0000000530076249 aut L.M.C. Sagis opn M. Habibi opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 273 10.18174/682027 en Lupin protein-polysaccharide complexes show great potential to improve interfacial properties and functionality of lupin proteins at acidic pH. These complexes form different structures with different sizes and morphologies, which could greatly affect their interfacial properties and functionality. It is therefore necessary to identify how these different structures (i.e., sizes and morphology) could affect the stabilization of interfaces and colloidal systems (e.g., foams and emulsions). In this thesis, we systematically studied the interfacial behavior and functionality of lupin protein-polysaccharide complexes with different sizes and morphologies. We found correlations between 2D interfacial rheology and 3D bulk rheology of these systems which help to better understand their functionality for stabilizing foams and emulsions.This thesis demonstrates the role of particle size and morphological features of lupin protein-polysaccharide complexes in stabilizing colloidal systems, such as foams and emulsions. We can tune interfacial properties and functionality of the complexes by modifying the particle size and morphological features of complexes by choosing different polysaccharides and mixing ratios. Findings from this thesis could help to design stable acidic colloidal food systems based on plant proteins, such as yogurt, mayonnaises, mousses, and acidic beverages that can answer the current need for more sustainable food design. VLAG Physics and Physical Chemistry of Foods VLAG Physics and Physical Chemistry of Foods urn:nbn:nl:ui:32-0eceb135-c24c-4e0a-8082-6ac9bf842e86/obj 2026-04-22 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/baddc179-859c-4d01-a56c-931f52a220d4 2026-04-30 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-baddc179-859c-4d01-a56c-931f52a220d4 2026-04-30 urn:nbn:nl:ui:32-baddc179-859c-4d01-a56c-931f52a220d4/mods Phostering sustainability : Integrating agronomic and environmental objectives in phosphorus fertilizer recommendations Wageningen University dgg van Doorn Maarten 0000000530142138 aut W. de Vries opn A.M.D. Rotterdam-Los opn G.H. Ros opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 265 10.18174/681704 en Phosphorus (P) is an essential nutrient for food production and is therefore applied to agricultural fields to achieve or maintain optimal soil P levels for crop yields. Especially in areas with intensive animal husbandry, a history of P fertilization beyond the crop P demand has resulted in the build-up of considerable plant-available soil P pools. While increases in these soil P pools have enhanced crop yields, they have also led to increased P losses from agricultural soils to water systems, contributing to the eutrophication of aquatic ecosystems. To ensure that food production remains within environmental limits in view of water quality, it is crucial to incorporate environmental boundaries into agricultural management schemes. This includes a revision of current P fertilizer recommendation and soil testing procedures. This thesis contributes to producing food within environmental boundaries by integrating agronomic and environmental objectives in P fertilizer recommendations. Specific research objectives are to (i) assess the potential of the 0.2M acid ammonium oxalate extraction method as an integrated agri-environmental soil P test; (ii) create gridded predictions of soil contents of amorphous Fe- and Al-(hydr)oxides that affect the P sorption capacity and thereby the balance between agronomic and environmental objectives in P management decisions; (iii) investigate the risk of P losses to the water system on agricultural soils vulnerable to P losses due to high hydrological connectivity and a low P sorption capacity; and (iv) incorporate an environmental boundary in P fertilizer recommendations. These objectives are addressed in four studies (Chapters 2 to 5). Results demonstrate that transitioning from purely agronomic to agri-environmental P management requires insight into soil P quantity-intensity relationships. Such insight can be obtained by combining agri-environmental soil P testing with high-resolution digital soil mapping of soil properties influencing P quantity-intensity relationships, such as amorphous Fe and Al-(hydr)oxides. We propose the inclusion of an environmental soil P intensity threshold into fertilizer recommendations, with threshold stringency determined by the degree of hydrological connectivity between fields and surface waters. In countries where routine agronomic soil testing only includes a measurement of P quantity, this P intensity threshold can be translated into a spatially variable P quantity threshold using combined information on (proxies of) the P sorption capacity and binding affinity. Implementing environmental soil P intensity thresholds prevents soils with a low P sorption capacity from reaching a high P saturation degree and corresponding high ortho-P concentration in soil solution, which is prone to being transported to surface water via interflow, overland flow and land drainage. The use of environmental soil P intensity thresholds implies that soils with a medium to high P sorption capacity are more suitable for producing crops with high P demands, whereas soils with a low P sorption capacity are more appropriate for extensive agriculture with crops that have lower P demands, or for the provision of other ecosystem services. This perspective calls for more differentiated, context-specific fertilizer recommendations that support broader sustainability goals. WIMEK Earth Systems and Global Change WIMEK Earth Systems and Global Change urn:nbn:nl:ui:32-baddc179-859c-4d01-a56c-931f52a220d4/obj 2026-04-30 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/5e705b57-240f-4a6f-89fc-f0304d47f830 2026-05-18 thesis

urn:nbn:nl:ui:32-5e705b57-240f-4a6f-89fc-f0304d47f830 2026-05-18 urn:nbn:nl:ui:32-5e705b57-240f-4a6f-89fc-f0304d47f830/mods Soil pollution under orchards in central-eastern Portugal: sources, risks and potential solutions Wageningen University dgg Veloso Abel 0000000530142103 aut V. Geissen opn M.P. Simõe opn M. do C Horta opn V. Silva opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 213 10.18174/681537 en Pesticides and plastics play major roles in most modern agricultural systems resulting in pesticides and microplastics being important soil contaminants, especially given their persistence, mobility, and toxicity. The research behind this thesis focused on the distribution and main effects of pesticide residues and microplastics in soils under peach orchards from central-eastern Portugal. It was divided into 4 main parts. The first part covered 18 orchards. It included their pesticide application records, used for predicting pesticide dissipation, and the quantification of a total of 37 pesticide residues in 270 soil samples collected throughout a complete growing season. Glyphosate was found to be highly relevant considering its application rates, the concentration of this active substance and of its main metabolite, the aminomethylphosponic acid (AMPA), and their potential for persistence in soil. Furthermore, pesticide dissipation in soil was slower than predicted, highlighting the importance of regular soil pesticide monitoring programs. The second part was focused on microplastic levels and their potential sources to soil. Furthermore, it evaluated the microplastic distribution across 3 different soil layers (0-5 cm, 5-15 cm, and 15-25 cm). Microplastic levels were generally lower, and their particle sizes higher, in the shallower layer. Irrigation water was the largest microplastic source to the soil. The third part was based on a mesocosm study which evaluated the single and combined effects of pesticide residues and microplastics, with and without biochar, on soil nutrients, pesticide residues, and in the mycorrhizal colonisation of peach tree roots. The combined effects of pesticides, microplastics, and biochar on soil nutrients were found to be more important than their single effects. Additionally, microplastics were related to higher levels of difenoconazole and biochar was related to higher levels of most quantified pesticide residues, except for glyphosate whose levels were lower in the presence of biochar. The mycorrhizal colonisation of peach tree roots was not substantially influenced by pesticide residues, microplastics or biochar. The fourth part was related to a field study, installed in a commercial peach orchard, which intended to evaluate cover crops as alternatives to herbicides. When compared to the standard practice of herbicide applications, the cover crop treatments did not significantly impact fruit yield or quality. While cover crops did not have a strong effect on mycorrhizal colonisation of peach tree roots or on soil nutrient levels, they were related to lower levels of plant available copper, which is a promising result considering its widespread use as a fungicide and its potential to reach phytotoxic levels in soil. This thesis proposed not only to characterise the soil contamination by pesticides and microplastics, but also to evaluate its consequences and to study the viability of cover crops as a strategy with the potential to decrease the levels of pesticide residues in soil, particularly, herbicides. While interesting and promising results were obtained, further studies are needed to increase our understanding of the distribution and levels of those soil contaminants, of their consequences, and to develop strategies that could reduce their negative impact in soil. WIMEK Soil Physics and Land Management WIMEK Bodemfysica en Landbeheer urn:nbn:nl:ui:32-5e705b57-240f-4a6f-89fc-f0304d47f830/obj 2026-05-18 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/bcd3c85e-49a4-4f51-84b1-11101912b0e2 2026-04-29 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-bcd3c85e-49a4-4f51-84b1-11101912b0e2 2026-04-29 urn:nbn:nl:ui:32-bcd3c85e-49a4-4f51-84b1-11101912b0e2/mods How microbiome predator–prey interactions shape litter decomposition Wageningen University dgg Wang Yuxin 0000000530200393 aut G. Smant opn S. Geisen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 204 10.18174/681678 en Litter decomposition is a key ecosystem process regulating nutrient cycling, soil organic matter formation, and long-term soil fertility. Although microbial communities and litter properties are well known to affect litter decomposition, comparatively little attention has been given to microbiome predators, particularly protists and nematodes, in soil food webs. These microbiome predators exert top-down control on microbial communities while being simultaneously shaped by bottom-up factors such as litter properties. This thesis investigates how microbiome predator–prey interactions shape litter decomposition across multiple experimental contexts. Chapter 1 introduces the ecological roles of protists and nematodes and develops a conceptual framework that links predator–prey interactions to litter properties and decomposition dynamics. Subsequent chapters examine specific aspects through which microbiome predators influence litter decomposition. Chapter 2 tests whether protist species identity and diversity influence litter decomposition and plant performance using simplified microcosm experiments. Results show species-specific effects, with only Tetramitus thorntoni reducing litter mass loss. Although litter mass loss was positively related to plant biomass, protist presence did not directly affect plant growth. Chapter 3 evaluates whether protist body size mediates litter decomposition by altering bacterial community composition. Large-sized protists reduced litter mass loss while increasing microbial respiration, likely by promoting predation-resistant bacterial taxa. Chapter 4 examines the temporal succession of protist and fungal communities across six litter types in a one-year field decomposition experiment. Both fungal and protist communities displayed litter-type-specific successional patterns. Notably, protist-related indicators became the strongest predictors of litter mass loss during late-stage decomposition, explaining 47% of the observed variation and surpassing fungal predictors. Chapter 5 investigates whether co-adapted nematode–microbial communities influence decomposition using phase-matched and mismatched combinations. While overall Home-Interaction Advantage (HIA) values were close to zero, litter quality structured nematode succession, and greater community dissimilarity strengthened HIA effects in low-quality litter. Chapter 6 synthesizes these findings and proposes a framework for incorporating microbiome predator–prey interactions into decomposition theory. Overall, this thesis demonstrates that microbiome predators exert important, context-dependent effects on litter decomposition, driven by interactions between top-down trophic control and bottom-up litter properties. These results highlight the need to explicitly integrate microbiome predators into decomposition theory and soil biogeochemical models. PE&RC Nematology (NEM) PE&RC Nematology (NEM) urn:nbn:nl:ui:32-bcd3c85e-49a4-4f51-84b1-11101912b0e2/obj 2026-04-29 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/d71c1b82-6a9c-4b46-8139-b46532863418 2026-04-29 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-d71c1b82-6a9c-4b46-8139-b46532863418 2026-04-29 urn:nbn:nl:ui:32-d71c1b82-6a9c-4b46-8139-b46532863418/mods The power of metalcore : Iron biofortification of black soldier fly larvae as an enhanced micronutrient source Wageningen University dgg First Tomer 0000000530208635 aut V. Fogliano opn M. Mishyna opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 199 10.18174/681878 en Background and aim: Iron deficiency remains one of the most prevalent micronutrient deficiencies worldwide, while sustainable and bioavailable iron sources are still limited. Edible insects, particularly Hermetia illucens (black soldier fly; BSF), have emerged as promising alternatives due to their high mineral content and efficient feed conversion. However, the mechanisms regulating iron uptake, storage, and utilization under elevated dietary iron conditions remain poorly understood. This thesis investigates how BSF larvae respond to increasing dietary iron levels, examining effects on larval physiology, nutritional composition, iron storage, and mineral bioaccessibility, providing insight into the potential of BSF as a sustainable iron source for animal feed and human food. Methods: A multidisciplinary framework was applied, combining literature research, controlled rearing experiments, omics analyses, histological localization, and digestion studies. Chapter 2 reviewed entoferritin — the primary iron-binding protein in insects — describing its structure, function, and nutritional relevance. Chapter 3 examined the effects of increasing dietary iron, supplied as ferric ammonium citrate, on growth, survival, and mineral composition of BSF and yellow mealworm larvae. Chapter 4 combined transcriptomic and proteomic analyses to characterize the molecular response of BSF to elevated dietary iron, with parallel dissections to localize iron accumulation across larval tissues. Chapter 5 applied an in vitro digestion model coupled with iron nanoparticle characterization to evaluate mineral bioaccessibility across biofortification levels and thermal processing conditions. Results: Chapter 2 reviewed entoferritin as the primary insect iron-binding protein, highlighting its high mineralization capacity, pH stability, and structural similarity to vertebrate ferritin — properties supporting its relevance as a bioavailable dietary iron source. In Chapter 3, increasing dietary iron produced a dose-dependent rise in BSF larval iron content, reaching nearly a threefold increase at the highest treatment level, without affecting larval growth, survival, or macronutrient composition. Calcium concentration increased by approximately 20% at the highest iron level. In contrast, yellow mealworm showed limited iron accumulation and reduced survival at far lower iron concentrations, indicating substantially lower tolerance. Chapter 4 revealed pronounced transcriptomic and proteomic shifts under elevated dietary iron, including approximately 70% increases in both entoferritin subunit abundances, driven by post-transcriptional regulatory mechanisms. Histological imaging localized iron clusters to the midgut across all biofortification levels, consistent with entoferritin-based sequestration. Additional pathway changes were observed in metal transport, oxidative stress response, and exoskeletal formation. Chapter 5 demonstrated significantly higher digestible iron in biofortified larvae compared to controls. Iron nanoparticle characteristics remained consistent across treatments, indicating a conserved storage mechanism. Thermal processing reduced iron bioaccessibility while increasing calcium solubilization, demonstrating mineral-specific effects of blanching. Conclusions:This thesis demonstrates that BSF efficiently regulates and accumulates dietary iron without impairing growth or survival. Elevated dietary iron triggered coordinated molecular responses, including increased entoferritin abundance and activation of oxidative stress and metal transport pathways, accompanied by localized midgut iron storage. Digestion studies confirmed higher digestible iron in biofortified larvae, while thermal processing reduced iron bioaccessibility but enhanced calcium availability. These findings provide fundamental mechanistic knowledge supporting iron-biofortified BSF as a sustainable ingredient for animal feed and, in the future, human food. VLAG Food Quality and Design VLAG Food Quality and Design urn:nbn:nl:ui:32-d71c1b82-6a9c-4b46-8139-b46532863418/obj 2026-04-29 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/815ad96b-d7d1-4d07-8e51-48502d46bc10 2026-04-20 thesis edurep openaire public

urn:nbn:nl:ui:32-815ad96b-d7d1-4d07-8e51-48502d46bc10 2026-04-20 urn:nbn:nl:ui:32-815ad96b-d7d1-4d07-8e51-48502d46bc10/mods Exoot : De begripsgeschiedenis van invasie-ecologie, van Linnaeus tot Darwin Leiden University dgg Peeters N.G.J. aut J.W. McAllister opn G.R. de Snoo opn J.J.M. Sleutels opn text info:eu-repo/semantics/doctoralThesis Noordboek Gorredijk 2026 520 10.60602/1887-4287367 nl This dissertation examines the conceptual history of invasion ecology from the eighteenth to the nineteenth century, focusing on how alien plants came to be identified, classified, and evaluated within natural history and early ecological thought. Central to the dissertation is the claim that three semantic shifts structured changing understandings of alien plants. These shifts successively frame alien species as colonists, as invasives, and as weeds. The first shift is located in the work of Carolus Linnaeus and his student Jon Flygare, particularly in their 1768 treatise De coloniis plantarum, which offers a systematic account of plant colonization and the role of purposeful and accidental human-mediated dispersal. The second shift concerns the emergence of the concept of invasion in the nineteenth century, most notably in the writings of Charles Darwin and Charles Lyell, who begin to characterize exotic plants and animals that spread rapidly and cause the displacement or extinction of aboriginal flora and fauna as invasive. The final shift addresses the mid-nineteenth-century re-evaluation of exotic plants as weeds. This development coincides with the first reported plant plagues in Europe and the colonies and marks the emergence of a new class of weeds understood as plants that are out of place in nature. Philosophy Filosofie urn:nbn:nl:ui:32-815ad96b-d7d1-4d07-8e51-48502d46bc10/obj 2026-04-20 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/1d60068a-387f-4af6-b5c1-2c097c9a9a2a 2026-04-24 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-1d60068a-387f-4af6-b5c1-2c097c9a9a2a 2026-04-24 urn:nbn:nl:ui:32-1d60068a-387f-4af6-b5c1-2c097c9a9a2a/mods Reducing food loss and waste along the supply chain : ideas for advancing its economic assessment Wageningen University dgg Pijpers Frank H. 0000000530200414 aut D. Drabik opn H. de Gorter opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 186 10.18174/681889 en In this dissertation, I assess the economic effects of reducing food loss and waste (FLW) along the supply chain. Data suggests that 30 to 40 percent of the global food production is lost or wasted. The Sustainable Development Goals aim to reduce FLW by 50 percent, a target that requires careful assessment because food is an essential resource, and these targets are unprecedented. I aim to improve the assessment of FLW reduction policies in this dissertation. After an introduction to the topic, I propose a new FLW abatement cost function in Chapter 2. In Chapter 3, I extend this cost function by adding scale effects and inedible FLW. I apply this new abatement cost function to a farm model that disentangles food losses before, during, and after harvest in Chapter 4. In Chapter 5, I use the new abatement cost function to compare the effects of mandatory and voluntary FLW reduction policies. Chapter 6 concludes this dissertation. WASS Agricultural Economics and Rural Policy WASS Agrarische Economie en Plattelandsbeleid urn:nbn:nl:ui:32-1d60068a-387f-4af6-b5c1-2c097c9a9a2a/obj 2026-04-24 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/ced6ba1c-3bbf-4e6f-8185-5c5811cae810 2026-04-24 thesis

urn:nbn:nl:ui:32-ced6ba1c-3bbf-4e6f-8185-5c5811cae810 2026-04-24 urn:nbn:nl:ui:32-ced6ba1c-3bbf-4e6f-8185-5c5811cae810/mods Ripple effects: understanding and mitigating psychopharmaceutical pollution in freshwater Wageningen University dgg Dubey Asmita 0000000530191116 aut M. Lürling opn L.N. Senerpont Domis opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 224 10.18174/681355 en Many medicines used by people end up in rivers and lakes after passing through wastewater treatment plants. These substances, called micropollutants, are often found in very small amounts, but they can still affect aquatic life. This research focused on psychopharmaceuticals, i.e., medicines used to treat mental health conditions such as antidepressants. Even at low levels, these chemicals can change how aquatic organisms behave, move, feed, and interact with each other, which may disturb the ecosystem health. This PhD studied both the effects of these medicines on aquatic life and ways to remove them from wastewater. Experiments showed that some antidepressants can affect specific groups of organisms and alter food web processes in aquatic ecosystems. The research also tested advanced wastewater treatments, such as ozonation and granular activated carbon, to see how well they remove these pollutants. While both methods reduced pollutant levels, ozonation improved water quality and ecosystem health more clearly. Overall, the research highlights the need to better consider subtle effects of medicines in environmental protection and improve understanding of the effect of different wastewater treatments on freshwater ecosystems. WIMEK Aquatic Ecology and Water Quality Management WIMEK Aquatische Ecologie en Waterkwaliteitsbeheer urn:nbn:nl:ui:32-ced6ba1c-3bbf-4e6f-8185-5c5811cae810/obj 2026-04-24 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/b0bdebde-2d6c-4ad3-9269-6ad1d837a166 2026-04-24 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-b0bdebde-2d6c-4ad3-9269-6ad1d837a166 2026-04-24 urn:nbn:nl:ui:32-b0bdebde-2d6c-4ad3-9269-6ad1d837a166/mods MIND the gap : evaluation of the MIND diet in relation to cognitive ageing Wageningen University dgg Beers Sonja 0000000530191132 aut L.C.P.G.M. Groot opn M. de van der Schueren opn Y. Vermeiren opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 242 10.18174/681473 en Prevention of dementia, with accelerated cognitive decline as one of the hallmark features, is considered a public health priority. Diet is considered an important intervention strategy for reducing the risk of cognitive decline and dementia. However, evidence is still insufficient to determine which dietary patterns are most effective. One promising, but relatively new dietary pattern is the Mediterranean-Dietary Approaches to Stop Hypertension (DASH) Intervention for Neurodegenerative Delay (MIND) diet. The overall aim of this thesis was to evaluate the applicability and scientific evidence of the MIND diet, with particular focus on the Dutch context. Chapter 2 describes the development of the MIND-NL diet and a corresponding short Food Frequency Questionnaire (FFQ). Chapter 3 evaluates the short FFQ and demonstrates that the questionnaire is suitable to rank participants according to their MIND-NL diet adherence, which is relevant for studying diet-disease associations. This FFQ was used for subsequent analysis in this thesis. Chapter 4 presents a systematic review summarizing the existing literature on the association between the MIND diet and brain ageing outcomes. A total of 38 observational and 2 intervention articles were included. Observational evidence showed beneficial associations between MIND diet and global cognition (3 of 4 cohorts) and dementia risk (7 of 10 cohorts), with evidence predominantly originating from U.S. cohorts. Observational evidence for other brain outcomes was mixed and/or limited. In Chapter 5, adherence to the MIND-NL diet and the Dutch Dietary Guidelines is cross-sectionally examined in relation to global cognitive function among older adults at risk of cognitive decline. In the total study sample, neither dietary pattern was associated with global cognitive function. However, age appeared to moderate the association. Among older adults younger than 70 years of age, adherence to the Dutch Dietary Guidelines was positively associated with cognitive function, while for the MIND-NL diet a similar but non-significant trend was observed. Chapter 6 explores a potential biological mechanism through which diet may influence cognitive decline. Specifically, this chapter examines the association between the MIND-NL diet and tryptophan metabolism. Tryptophan is an essential amino acid that must be obtained through diet, and several of its metabolites have been linked to dementia incidence. We found that changes in MIND-NL diet adherence were associated with changes in metabolite ratios (kynurenine:large neutral amino acids and kynurenine:tryptophan) within the kynurenine pathway. This suggests that increased MIND-NL diet adherence may contribute to decreased activity of the kynurenine pathway and, in turn, potentially reduce dementia risk. Collectively, the findings in this thesis summarize the current evidence on the MIND diet and cognitive health, add new insights from the Dutch context, and explore a potential biological underlying mechanism through which the MIND diet may help to reduce cognitive decline. To further advance the field, additional research, particularly randomized clinical trials, is needed. Moreover, the influence of cultural context should be considered more explicitly when studying this food-based dietary pattern. Further research into the links among diet, cognition, and dementia risk may guide refinements to the MIND diet to optimize its preventive effectiveness. VLAG Nutritional Biology VLAG Nutritional Biology urn:nbn:nl:ui:32-b0bdebde-2d6c-4ad3-9269-6ad1d837a166/obj 2026-04-24 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/8abbe4d5-cca0-4ae6-b026-c0c5fc3f6cf1 2026-04-23 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-8abbe4d5-cca0-4ae6-b026-c0c5fc3f6cf1 2026-04-23 urn:nbn:nl:ui:32-8abbe4d5-cca0-4ae6-b026-c0c5fc3f6cf1/mods Feeding cows for climate: reducing greenhouse gas emissions from tropical dairy systems in Indonesia and Costa Rica Wageningen University dgg Apdini Titis 411275666 000000050830409X aut S.J. Oosting opn C.E van Middelaar opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 193 10.18174/680910 en Milk production contributes to food security and livelihoods in the tropics. An increase in the dairy cattle population in the tropics is likely to continue as a means to boost milk production in response to rising milk demand. However, this trend will also raise greenhouse gas (GHG) emissions from milk production, including methane (CH4) from enteric fermentation and carbon dioxide (CO2) and nitrous oxide (N2O) from feed production. Feeding strategies are widely promoted as mitigation options, but their implementation in the tropics remains limited. This thesis explores the implications of feeding strategies for GHG mitigation in tropical dairy systems, with a focus on improving assessment methods, identifying feasible mitigation options, and understanding their impacts on GHG emissions, land use, and costs. Indonesia and Costa Rica were selected to represent contrasting dairy systems in terms of their feeding practices, while both countries include feeding strategies for GHG mitigation in their national dairy development agendas. On-farm data collection was conducted on 32 smallholder dairy farms in Indonesia and 51 dairy farms in Costa Rica. In Indonesian smallholder dairy farms, results show substantially higher emission intensities during the rainy season (1.32 kg CO2-eq kg−1 fat-and-protein-corrected milk (FPCM)) than the dry season (0.91 kg CO2-eq kg−1 FPCM). When six combinations of approaches to assess feed intake and enteric CH4 emissions were applied, rankings of smallholder farms based on their CH4 emission intensities remained consistent, demonstrating that modelling offers a cost-efficient alternative in data-scarce contexts. In both Indonesia and Costa Rica, improving feed self-sufficiency can reduce GHG emission and land-use intensities. Overall, the feeding strategies assessed in this thesis have clear potential to reduce GHG emission intensity, but their cost-effectiveness and feasibility vary across contexts. Effective implementation will require policy support, investment, and careful consideration of trade-offs with other climate mitigation goals. WIAS Animal Production Systems WIAS Dierlijke productiesystemen urn:nbn:nl:ui:32-8abbe4d5-cca0-4ae6-b026-c0c5fc3f6cf1/obj 2026-04-23 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/9c90d576-a9c2-4f8a-811b-ab1f3b534b30 2026-04-23 thesis

urn:nbn:nl:ui:32-9c90d576-a9c2-4f8a-811b-ab1f3b534b30 2026-04-23 urn:nbn:nl:ui:32-9c90d576-a9c2-4f8a-811b-ab1f3b534b30/mods Held by the plants : how insights in population ecological and genetic processes can improve plant conservation and reintroductions Wageningen University dgg Bohm Sina 0000000527898639 aut Joop Schaminee opn D. Kleijn opn P. Vergeer opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 199 10.18174/681194 en Human-induced biodiversity decline urgently requires effective conservation strategies for vulnerable plant species. This thesis enhances the ecological understanding of plant populations to improve plant conservation and reintroduction efforts, focusing on three species: Primula elatior, Hypericum pulchrum, and Solidago virgaurea. Plant performance, habitat condition, and genetic diversity were investigated in wild Primula elatior populations in the Netherlands. High soil phosphate content was strongly associated with poor plant performance, indicating that eutrophication threatens the species. Bryophyte cover was linked to higher germination and recruitment, likely by regulating the microclimate. Primula elatior exhibits flower dimorphism requiring cross-pollination. Smaller populations showed skewed floral morph ratios, which was linked to reduced seed production. Seed production peaked at intermediate forest cover surrounding the population (1000 m radius), reflecting pollinators' need for heterogeneous landscapes for foraging, nesting and overwintering. Genetic diversity of Primula elatior populations declined strongly with decreasing population size, which is concerning given the species' long generation time. Populations in more heterogeneous microhabitats maintained higher genetic diversity independently of their size. Since larger habitat patches supported both larger populations and greater microhabitat heterogeneity, habitat patch size plays an important role in maintaining genetic diversity and thereby population resilience. Experimental reintroductions testing the effect of soil inoculation (i.e., transferring soil from conspecific plant populations) on plant establishment. Results showed species-specific responses: Hypericum pulchrum demonstrated improved survival, growth, and flowering; Solidago virgaurea showed increased flowering; but Primula elatior experienced reduced survival. This indicates that species from nutrient-poor environments may benefit more from soil microorganisms aiding nutrient acquisition than species from nutrient-rich habitats. Thus, soil inoculation can enhance reintroduction success for certain species, but its effectiveness varies by the species’ ecological requirements. This thesis demonstrates the complex interconnectedness of plant populations with their immediate and distant surroundings: from soil conditions on the microhabitat-level to pollinator interactions on the landscape-level. Successful population restoration requires recognizing these complex ecological relationships. Failing to consider these relationships undermines conservation and restoration success and may lead to unrealistic expectations about the reversibility of human-induced ecological disruptions. PE&RC Plant Ecology and Nature Conservation PE&RC Plantenecologie en Natuurbeheer urn:nbn:nl:ui:32-9c90d576-a9c2-4f8a-811b-ab1f3b534b30/obj 2026-04-23 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/12c0398e-2fbd-4b68-bd55-cc26da7351dd 2026-04-15 thesis

urn:nbn:nl:ui:32-12c0398e-2fbd-4b68-bd55-cc26da7351dd 2026-04-15 urn:nbn:nl:ui:32-12c0398e-2fbd-4b68-bd55-cc26da7351dd/mods Advancing renewable energy through Integrated systems design : Application to domestic electricity supply in Java and Bali, Indonesia Wageningen University dgg Diyono D. 0000-0002-2100-7776 0000000530070568 aut P. van Heijster opn K.J. Keesman opn H.J. Cappon opn K. Kujawa-Roeleveld opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 251 10.18174/681796 en The Indonesian Islands, Java and Bali, hold abundant renewable energy resources (RES) that are vital to national decarbonisation, energy security, and equitable access. However, persistent challenges, including incomplete electrification in rural and remote areas, slow deployment of renewable energy sources, and grid flexibility constraints, continue to hinder progress. With the focus on domestic (household) electricity demand, this thesis addresses these challenges by analysing renewable energy mixes, energy storage systems (ESS), and transmission optimisation in the Java and Bali network, while also proposing solutions for rural electrification. Scenario- based assessments show that wind-based energy mixes deliver the most favourable balance between cost and environmental performances, highlighting pathways for cost-effective decarbonisation. To address mismatches between variable renewable generation and fluctuating demand, the study evaluates energy storage options, demonstrating that off-river pumped hydro energy storage (PHES) outperforms lithium-ion batteries and compressed air systems in terms of economic and environmental outcomes, despite higher operational requirements. Transmission system analysis further reveals that optimised integration of renewable generation, storage, and interprovincial exchange can substantially reduce energy losses, enhance infrastructure utilisation, and strengthen regional self-sufficiency. Beyond the grid, hybrid renewable energy systems (HRES) are proposed to extend reliable electricity access to rural and remote communities. A case study results show that an HRES (solar, wind, geothermal, and biogas from animal manure) supported by biogas storage provides a more cost-effective and scalable solution than grid extension or battery storage. Taken together, the findings demonstrate that energy transition in Java and Bali for domestic and rural electricity supply is technically feasible, environmentally beneficial, and economically viable if supported by strategic deployment of renewables, robust storage solutions, efficient transmission planning, and innovative off- grid systems. WIMEK Mathematical and Statistical Methods (MAT) Environmental Technology WIMEK Mathematical and Statistical Methods (MAT) Milieutechnologie urn:nbn:nl:ui:32-12c0398e-2fbd-4b68-bd55-cc26da7351dd/obj 2026-04-15 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/687fecaa-246d-4dff-82da-bcf9daff7450 2026-04-17 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-687fecaa-246d-4dff-82da-bcf9daff7450 2026-04-17 urn:nbn:nl:ui:32-687fecaa-246d-4dff-82da-bcf9daff7450/mods Learning across boundaries : understanding maritime spatial planning through serious games Wageningen University dgg Keijser Alexander 0000-0001-5894-4467 0000000530087108 aut J.P.M. van Tatenhove opn H. Toonen opn I. Mayer opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 262 10.18174/680959 en This thesis investigates how serious games contribute to learning in Maritime Spatial Planning (MSP). MSP involves balancing different activities at sea, such as shipping, energy production, fishing, and nature protection. Although learning is widely seen as important in MSP, there is little evidence about whether learning actually happens, how it happens, and how it can be designed and facilitated. This research explores whether serious games — games designed for other purposes than primarily entertainment — can help people better understand MSP and learn from one another. The central question of this thesis is: how and to what extent do serious games contribute to learning in (transboundary) MSP? This question is answered through six sub-questions using a literature review, questionnaires, interviews, and observations. Some of the key findings per chapter are: • Chapter 2 identifies a ‘learning paradox’ in MSP. Although learning is considered important, and examples of learning do exist, learning itself is rarely made explicit. However, making learning more explicit offers several benefits. For example, it clarifies what needs to be learned and why, it provides insight into power dynamics of inclusion and exclusion, and it facilitates learning among actors and between countries. • Chapter 3 analyzes various MSP Challenge board game workshops. The MSP Challenge board game allows participants to experience the complexity of MSP in a safe and interactive way. Results show that these serious games help a wide range of participants — policymakers, scientists, stakeholders, and students — better understand MSP and engage in meaningful discussions. How much participants learn depends on various factors, such as the participants’ level of involvement in MSP. • Chapter 4 examines learning in the EU Interreg project NorthSEE, where the MSP Challenge Simulation Platform served as a discussion, data collection, and stakeholder involvement tool. Results show that project participants gained more insight into each other's planning systems, are able to contact each other more easily, and have initiated several follow-up initiatives, including the “North Sea Region MSP Collaboration Group.” Learning outcomes were influenced by time, resources, and differences in expertise among project participants. • Chapter 5 examines the MSP Challenges serious games as boundary objects. The findings shows that the effectiveness of the MSP Challenge serious games depends on the “space” wherein the games are applied—the interplay between game, activity, and context. Limitations in game design, workshop design, or the context in which the games are applied can affect participants' learning experiences. Overall, this thesis makes three main contributions: (1) it places learning in MSP on the agenda as an essential aspect of marine governance; (2) it provides analytical frameworks to understand conditions, forms, and levels of learning; and (3) it demonstrates how serious games, and more particularly the MSP Challenge serious games, can enhance learning across disciplinary and organizational boundaries. Finally, this research provides suggestions for future research, such as understanding how individual and social learning can result into organizational and policy learning, examining learning during the design phase of serious games, and exploring cultural differences in game experiences. Environmental Policy WASS Milieubeleid WASS urn:nbn:nl:ui:32-687fecaa-246d-4dff-82da-bcf9daff7450/obj 2026-04-17 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/d2edbfcf-9a55-4483-a667-371874c7c084 2026-04-17 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-d2edbfcf-9a55-4483-a667-371874c7c084 2026-04-17 urn:nbn:nl:ui:32-d2edbfcf-9a55-4483-a667-371874c7c084/mods Strength lies in differences : Diversities at the disturbance-response nexus in European forests Wageningen University dgg Patacca Marco 000000053018192X aut G.-J.M.M. Nabuurs opn M.-J. Schelhaas opn M.W.M. Lohbeck opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 249 10.18174/681632 en European forests are facing unprecedented pressures as climate change intensifies natural disturbance regimes while the legacy of centuries of management continues to shape forest structure, composition, and function. Ensuring that forests continue to provide essential ecosystem services, including carbon sequestration, biodiversity conservation, and climate regulation, requires a clearer understanding of disturbance dynamics and the development of management strategies that enhance resilience. This thesis addresses these needs through two complementary aims: 1. to analyse past trends in major natural disturbances in Europe and their effects on forest characteristics, and 2. to project future disturbance dynamics under climate change and evaluate alternative management strategies for increasing forest resilience. Four research objectives structure the work: quantifying historical trends in disturbance regimes; assessing their effects on forest functional properties; developing a modelling framework to integrate disturbance projections into a forest simulation model; and exploring future forest trajectories under alternative management systems. Chapter 2 presents a comprehensive review of natural disturbance damages in Europe, resulting in a database of over 170,000 disturbance records compiled through extensive expert collaboration. This chapter synthesises trends of wind, fire, bark beetles, and other disturbances, highlight the increase magnitude of all the disturbances in the last 70 years, and discusses their implications for forest policy and management. Chapter 3 examines how changes in disturbance regimes over the past four decades have altered the functional properties of European forests. Using a novel hyperdimensional framework, maps the functional composition of forest communities across Europe and quantify their functional reorganisation. By linking this reorganisation to remotely sensed changes in disturbance frequency, the chapter demonstrates that disturbance-influenced functional change is already underway, with trajectories varying across biomes and disturbance types. Chapter 4 develops a framework to simulate future disturbance impacts in EFISCEN-Space, focusing on wildfires as a climate-sensitive disturbance. By modelling relationships between fire regimes and climate projections and integrating these into a forest resource model, simulate fire-induced mortality under different climate scenarios for Germany, Spain, and Sweden. The results reveal strong biome-specific responses, reflecting differences in biomass, structure, fire adaptation, and expected changes in fire weather. Chapter 5 extends this framework to wind disturbance and applies the enhanced model to 13 European countries. We compare a business-as-usual management regime with three alternative strategies designed to increase structural heterogeneity, species (functional) diversity, or both, selecting species based on future climate-suitability projections. The simulations show that actively managing forest regeneration, increasing species and functional diversity provides the most robust gains in growing stock and disturbance resilience across European forests. Finally, Chapter 6 synthesises the findings and argues for a shift in forest management paradigms to account for rapidly changing disturbance regimes. Drawing on evidence from all chapters, I discuss how historical management has shaped the functional and structural properties of European forests, how these properties mediate responses to disturbance regime shifts, and how management can support forest reorganisation rather than attempt to preserve outdated conditions. I propose refinements to conceptual models of post-disturbance forest reorganisation and outline research priorities for guiding adaptive management. PE&RC Sustainable forest ecosystems Forest Ecology and Forest Management PE&RC Sustainable forest ecosystems Bosecologie en -beheer urn:nbn:nl:ui:32-d2edbfcf-9a55-4483-a667-371874c7c084/obj 2026-04-17 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/1abefce9-53b0-4a95-91ae-eddf53c1cff9 2026-04-09 thesis

urn:nbn:nl:ui:32-1abefce9-53b0-4a95-91ae-eddf53c1cff9 2026-04-09 urn:nbn:nl:ui:32-1abefce9-53b0-4a95-91ae-eddf53c1cff9/mods Development and assessment of spectroscopic techniques and advanced analysis methods for characterization of bio-based fertilizers Wageningen University dgg Wali Khan 0000-0002-8976-8096 0000000529790058 aut E.J. van Henten opn E. Meers opn M.A. Munnaf opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 148 10.18174/681390 en Bio-based wastes such as animal manures, plant residues, composts, and biosolids represent valuable sources of essential plant nutrients, including nitrogen (N), phosphorus (P), potassium (K), and organic matter, and play a critical role in sustaining soil fertility and long-term agricultural productivity. In the European Union, and particularly in the Netherlands, nutrient surpluses from animal manure exceed crop demand, creating both environmental challenges and opportunities for nutrient recycling. Effective utilization of bio-based fertilizers (BBFs) requires rapid and reliable quantification of their nutrient composition at the time of application. Conventional wet chemical analyses, while accurate, are labor-intensive, time-consuming, and unsuitable for large-scale or real-time decision-making. Consequently, there is a growing demand for fast, non-destructive sensing technologies capable of characterizing BBFs and their impacts on soil fertility.This thesis investigates the potential of spectroscopic sensing techniques visible to near-infrared (Vis–NIR), mid-infrared (MIR), and Fourier transform infrared photoacoustic spectroscopy (FTIR-PAS) combined with chemometric methods, to quantify nutrient contents in BBFs and BBF-amended soils. A key challenge addressed is the limited robustness and generalizability of existing calibration models, which often rely on single-source materials, instrument-specific calibrations, and large, chemically analyzed datasets that are difficult to obtain. In addition, commonly used performance metrics such as the coefficient of determination (R²), root mean square error (RMSE), and ratio of prediction to deviation (RPD) provide limited insight into the practical usability of spectroscopic predictions for agricultural regulation and nutrient management.The research demonstrates that Vis–NIR and MIR spectroscopy can successfully predict a wide range of chemical properties in BBFs, including macro-nutrients, plant-available nitrogen forms, micro-nutrients, and physicochemical properties. Feature selection and multi-sensor model averaging significantly improved prediction accuracy, with MIR generally outperforming NIR due to stronger and more resolved spectral features. FTIR-PAS emerged as a promising alternative technique, achieving high prediction accuracy for most macro- and micro-nutrients in BBFs. A novel tolerance-based error interval method was introduced to evaluate prediction performance relative to regulatory compliance thresholds, providing a more practical assessment of model reliability. Using this approach, FTIR-PAS achieved prediction probabilities of 94.6% for total nitrogen and 83.8% for total phosphorus within acceptable error limits.To address data scarcity in spectroscopic modeling, this thesis explored digital spectral mixing (DSM) and introduced combination-based physical data augmentation (CPDA) as strategies to expand training datasets. Both methods improved prediction performance for elemental composition, although limitations remained for plant-available nutrient forms. Finally, FTIR-PAS was evaluated for quantifying plant-available phosphorus in BBFs and BBF-amended soils, revealing strong performance for BBFs and soil-type-dependent accuracy for amended soils.Overall, this thesis demonstrates the substantial potential of infrared spectroscopy for rapid BBF characterization and soil assessment, while highlighting remaining challenges related to sample preparation, environmental sensitivity, and model robustness. The findings support more sustainable nutrient management practices and provide a foundation for future development of open-access spectral libraries and improved methods for direct measurement of plant-available nutrients. Agricultural Biosystems Engineering (ABE) PE&RC Agricultural Biosystems Engineering (ABE) PE&RC urn:nbn:nl:ui:32-1abefce9-53b0-4a95-91ae-eddf53c1cff9/obj 2026-04-09 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/e1ebb526-efc7-4dee-bcd3-03faccec6e33 2026-04-09 thesis

urn:nbn:nl:ui:32-e1ebb526-efc7-4dee-bcd3-03faccec6e33 2026-04-09 urn:nbn:nl:ui:32-e1ebb526-efc7-4dee-bcd3-03faccec6e33/mods Fungal aromatic prenyltransferases: characterization and product profiling Wageningen University dgg Chunkrua Pimvisuth 0000000530153208 aut M.A. Kabel opn J-.P. Vincken opn W.J.C. de Bruijn opn W.J.H. van Berkel opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 238 10.18174/681201 en The rise of antimicrobial resistance has intensified the search for new, potent antimicrobial agents. Prenylated aromatic compounds, an abundant class of over 10,000 molecules found across plants and microbes, have emerged as promising antimicrobial candidates. Advancing studies on their potential application as antimicrobials, however, is limited by their low natural abundance and the narrow diversity of structures available for screening. This thesis explores a biotechnological strategy to overcome these limitations by enabling the production and diversification of antimicrobial prenylated aromatic compounds. Central to this work are aromatic prenyltransferases (aPTs), enzymes that transfer prenyl groups from isoprenoid donors to aromatic acceptors. Two newly identified fungal aPTs from the dimethylallyl tryptophan synthase (DMATS) family, RePT and ScPTMY, were selected due to their anticipated substrate promiscuity. These two DMATSs were investigated for their ability to prenylate diverse substrate-scaffolds including indoles, stilbenes, and (iso)flavonoids. Both enzymes exhibited broad substrate acceptance, high conversion, and strong regioselectivity toward aromatic amino acids L-tryptophan and L-tyrosine, with stilbenes showing the highest conversion among the tested plant phenolics. RePT tolerated a wide range of tryptophan and indole derivatives, displaying notably high conversion with halogenated tryptophans and suggesting halogen-guided regioselective control. For plant phenolics, both enzymes, and ScPTMY in particular, preferentially catalyzed O-prenylation, which is a rather uncommon modification in nature, highlighting DMATSs’ potential to enable novel prenylation patterns. Phylogenetic analysis revealed substantial diversity in substrate scope and regioselectivity among fungal DMATSs, underscoring the opportunity for future work to refine sequence–function relationships for unnatural substrates. Overall, this work demonstrates the considerable potential of fungal DMATSs as biocatalysts for producing structurally diverse, antimicrobial prenylated compounds. Their broad substrate tolerance and high regioselectivity offer valuable tools for antimicrobial discovery while supporting green, enzyme-based synthetic routes. VLAG Food Chemistry VLAG Levensmiddelenchemie urn:nbn:nl:ui:32-e1ebb526-efc7-4dee-bcd3-03faccec6e33/obj 2026-04-09 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/fede2e58-25c6-4297-93e8-2478221bf334 2026-04-16 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-fede2e58-25c6-4297-93e8-2478221bf334 2026-04-16 urn:nbn:nl:ui:32-fede2e58-25c6-4297-93e8-2478221bf334/mods Breaking the mould : towards mushroom-producing fungi as high-quality protein source Wageningen University dgg Zwinkels Jasper 0000000530181946 aut E.J. Smid opn O. van Mastrigt opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 228 10.18174/682370 en The high environmental impact of current food production is largely driven by livestock farming for protein supply. To reduce this impact, a transition towards alternative, non-animal protein sources is needed. However, many plant-derived foods have a lower protein content and inferior protein quality compared to animal-based proteins. Particularly, the indispensable amino acid lysine is commonly limiting in plant-based diets that rely on staple cereals. This can compromise protein adequacy when replacing meat, especially in populations with already insufficient protein intake. The fungal kingdom harbours enormous phylogenetic diversity for the production of protein-rich and palatable foods for human consumption, yet commercially available fungal fermented foods are derived from a narrow range of species. The overall aim of this thesis was to investigate the potential of fungal mycelium, produced through solid-state and submerged fermentation, to contribute to the protein transition.Solid-state fermentation of staple cereals with the conventional food fungi Rhizopus microsporus var. oligosporus and Aspergillus oryzae produced substantial amounts of fungal biomass and improved the protein quality, mainly through an increase in lysine. To expand the phylogenetic diversity of fungi used in food fermentation beyond these conventional species, mycelium of a diverse selection of mushroom-producing fungi (Basidiomycota) was characterised and compared. Basidiomycetous mycelium contained a higher protein content and quality compared to corresponding fruiting bodies and a higher protein quality compared to mycelium of R. microsporus. Furthermore, basidiomycetous mycelia contained higher levels of umami compounds, quantified as the equivalent umami concentration. When applied in solid-state fermentation on various plant substrates, basidiomycetes improved plant protein quality through a similar mechanism as R. microsporus, primarily through lysine enrichment. Additionally, basidiomycetous fermentations showed a higher protein content, a greater reduction in the anti-nutritional factor phytic acid, and higher umami concentrations compared to conventional fungal fermentations. However, substrate composition shaped metabolic strategies, and the presence of an accessible carbohydrate source was essential to prevent excessive amino acid catabolism and consequent protein loss. To assess the nutritional and environmental relevance of these findings at a dietary level, meat and fish in the Dutch evening meal were replaced in silico with mycelium of basidiomycetes and compared to other non-animal protein sources. Mycelium-substituted meals more often contained adequate utilizable protein compared to meals substituted with plant-based meat alternatives, legumes, or mushrooms. When corrected for utilizable protein content, only meals substituted with mycelia or plant-based meat alternatives had a lower environmental impact than the standard meal. Protein quality is a key parameter for assessing both the adequacy of protein intake and the environmental impact of foods, and its relevance increases as the protein transition advances toward higher consumption of plant proteins. In this context, fungal biomass and solid-state fermented foods offer a natural way to enhance nutritional quality, flavour, and texture of plant-based foods. By unlocking the enormous diversity in the phylum of Basidiomycota, a larger diversity of fungal fermented foods with novel properties, such as the combination of higher protein quality and umami taste, can be obtained. VLAG Food Microbiology VLAG Levensmiddelenmicrobiologie urn:nbn:nl:ui:32-fede2e58-25c6-4297-93e8-2478221bf334/obj 2026-04-16 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/c4acaf8e-97e0-4478-9d1e-a44863337aea 2026-04-09 thesis

urn:nbn:nl:ui:32-c4acaf8e-97e0-4478-9d1e-a44863337aea 2026-04-09 urn:nbn:nl:ui:32-c4acaf8e-97e0-4478-9d1e-a44863337aea/mods From diverse farming systems to diverse diets : A path to improving children’s diets in rural Ethiopia Wageningen University dgg Chinasho Tibebu Monges 0000000530153195 aut I.D. Brouwer opn J.C.J. Groot opn F. Baudron opn R. Remans opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 217 10.18174/680881 en Agricultural based interventions have recently gained increasing attention to sustainably transform food systems, not only to improve dietary outcomes but also to end hunger, achieve food security, improve nutrition, and promote sustainable agriculture (SDG2). However, its potential to improve access to and consumption of healthier diets remains unknown. The main objective of this thesis was to explore the potential of diverse farming systems to enhance the provision of adequate diets and nutrients among children in smallholder farm households in Ethiopia.The exploration of farming systems for adequate diets in this thesis followed the DEED framework (Describe-Explain-Explore-Design) across subsequent chapters. It began with a description of farming system diversity at different scales (national and sub-national) and an explanation of variations in dietary outcomes among children in rural Ethiopia. The national level analysis covered 228 representative rural clusters, classified into 10 dominant patterns of farming activities (Chapter 2), while the sub-national analysis focused on three zones or clusters differing in production diversity along the agricultural intensification gradient (Chapter 3). The main question addressed was: “To what extent does the diversity of farming systems at different scales influence (micro)nutrient intakes among rural children?”. The result revealed that the diet and quantities of nutrients consumed among children were inadequate. Seasonal fluctuations further exacerbated the inadequacies. However, the predictive power of farming systems diversity for explaining the variation in consumption varied considerably depending on the scale of analysis; strong at national scale while its influence weakened at smaller geographic scale.We extended our focus to the household level using farm survey collected from 172 sub-sampled households in three zones (Chapter 4). To better capture the household level heterogeneity, we developed a typology using principal component analysis and hierarchical cluster analysis. Accordingly, five distinct farm types were identified, primarily differentiated by farm size, livestock ownership and self-reliance for food. The analysis aimed to examine how household production could support consumption of healthy diets among households and children across farm types. The findings revealed that households and children in high-to-medium resource endowed farm types tended to have greater access to and consumed larger quantities of healthy diets than their counterparts in low resource-endowed farm types. Yet the consumption levels across all farm types fell short of meeting the national recommendations.The analysis then moved into an exploration of alternative options using intervention scenarios that could potentially enhance dietary outcomes and other household objectives (Chapter 5). The results demonstrated that high resource endowed farm types showed substantial potential to improve access to healthy diets, household free budget and SOM through nutrition sensitive interventions. In contrast, achieving healthy diets and maintaining a positive SOM and household free budget balance proved challenging for low-resource endowed farm types.Although agricultural interventions has the potential to enhance diets, realizing this potential requires an integrated analysis of the system. The findings from this thesis provided a farming systems approach to disentangle the complexity of the system to examine how current production and various intervention scenarios can improve household and children’s diets. PE&RC Global Nutrition Land Systems Team Plant Production Systems (PPS) Farming Systems Ecology (FSE) PE&RC Wereldvoeding Land Systems Team Plant Production Systems (PPS) Farming Systems Ecology (FSE) urn:nbn:nl:ui:32-c4acaf8e-97e0-4478-9d1e-a44863337aea/obj 2026-04-09 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/17211769-7991-4552-b3a5-d5aefded57c4 2026-04-09 thesis

urn:nbn:nl:ui:32-17211769-7991-4552-b3a5-d5aefded57c4 2026-04-09 urn:nbn:nl:ui:32-17211769-7991-4552-b3a5-d5aefded57c4/mods Decoding leafy head formation in Brassica using machine learning Wageningen University dgg Sun Wei 0000000530070592 aut A.B. Bonnema opn X. Wang opn A.D.J. van Dijk opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 149 10.18174/681460 en Leafy head formation in Brassica crops represents one of the most remarkable morphological innovations in plant domestication history. Chinese cabbage (Brassica rapa) and cabbage (Brassica oleracea) independently evolved this trait through separate domestication events in East Asia and Europe, respectively, both driven by human selection for inward-curving leaves that form compact, storage-stable heads. Despite its significant agricultural importance, the genetic and developmental mechanisms underlying this transformation from flat rosette leaves to tightly packed leafy heads remain poorly understood. This thesis applies a series of machine learning approaches to systematically investigate the genetic architecture of leafy head formation, progressing from fundamental mechanisms of leaf curvature to genome-wide phenotype prediction across Brassica species.In the first study, we established a computational foundation by investigating leaf adaxial-abaxial polarity, a key developmental process governing leaf curvature. Using Arabidopsis thaliana as a model system, we trained a Random Forest model incorporating known polarity genes, expression features, and ChIP-seq data to predict novel polarity-related genes. Differential expression analysis of manually separated adaxial and abaxial tissues, combined with single-cell transcriptome profiling, revealed candidate genes with preferential expression in lower epidermal cells. Critically, conserved expression patterns were identified between Arabidopsis and B. rapa orthologs, establishing a transferable computational pipeline applicable to crop species.The second study expanded this framework directly to Brassica crops, integrating machine learning with gene regulatory network analysis to identify heading-related genes in both B. rapa and B. oleracea. Random Forest models trained on known heading genes achieved strong predictive performance in both species, with several high-confidence candidate genes shared between them. Gene regulatory network analysis uncovered both species-specific and conserved regulatory modules enriched for heading-associated biological processes, including leaf polarity establishment, meristem regulation, and auxin-mediated growth. Network centrality analysis further identified key transcription factors as potential master regulators of heading development. The convergence of molecular mechanisms identified in both independently domesticated species provided mutual validation and suggested parallel evolution at the molecular level.The third study developed a deep learning framework combining prior-guided attention mechanisms with contrastive learning, integrating SNP and transcriptome data from both species. The model achieved high classification accuracy for heading versus non-heading phenotypes, and phylogenetic analysis confirmed parallel evolution of heading morphotypes. However, gene masking validation revealed an important limitation: the model relied on collective gene signals for phenotype classification rather than learning individual gene-level patterns, constraining its utility for novel gene discovery.Together, these studies demonstrate both the power and limitations of machine learning in decoding complex agronomic traits. While these approaches effectively handle high-dimensional biological data and generate biologically meaningful predictions, traits shaped by deep evolutionary history and polygenic architecture present fundamental challenges for individual gene-level discovery. This work provides a valuable computational framework for investigating heading formation and offers broader insights into applying machine learning to complex trait genetics in polyploid crop species. EPS Plant Breeding (PBR) EPS Plant Breeding (PBR) urn:nbn:nl:ui:32-17211769-7991-4552-b3a5-d5aefded57c4/obj 2026-04-09 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/b1016b2e-33b8-4cff-9a2f-0e0a21e60c73 2026-04-08 thesis

urn:nbn:nl:ui:32-b1016b2e-33b8-4cff-9a2f-0e0a21e60c73 2026-04-08 urn:nbn:nl:ui:32-b1016b2e-33b8-4cff-9a2f-0e0a21e60c73/mods Farmer-friendly climate information services for climate-smart rice disease management in Coastal Bangladesh Wageningen University dgg Mousumi Moriom Akter aut F. Ludwig opn S. Paparrizos opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 258 10.18174/681127 en Rice farming communities in coastal Bangladesh are greatly affected by climate change and unpredictable weather patterns. Climate change and variability have direct impacts on rice yields through, for example, heat stress and changes in rainfall. Climate change-driven fluctuations in temperature, humidity, and rainfall also affect pest and disease incidence. As a result, the occurrence and spread of climate-induced rice diseases are expedited, further decreasing crop yields. Climate-based disease management is necessary to reduce the impacts of these diseases. In this case, the development of participatory climate information services (CIS) to provide farmers with climate-based rice disease forecasts and management information can assist them. Currently, coastal farmers have limited access to need-based, accurate, timely, and location-crop-specific CIS to forecast and manage diseases in advance. However, there remain scientific challenges for developing climate-based disease forecasting models through collaboration between farmers and scientists. The central question is how CIS can be tailored based on local farmers' needs to assist them in climate-smart disease management by providing actionable information. Furthermore, a bottom-up approach for developing CIS for disease management has not been explored yet. In this dissertation, I aim to co-produce CIS using a mobile application DROP app with farmers in coastal Bangladesh and assist them in up-taking rice disease forecasts and better managing diseases. Therefore, the objectives of the research were to assess the impact of changing climate on rice yield and diseases in coastal Bangladesh, to understand the common sources and needs of CIS for forecasting and managing rice disease, to co-produce participatory CIS to assist farmers in accessing disease forecasts and management information, and to evaluate the impact of tailored CIS on farmers’ pesticide use and income.A multidisciplinary research approach was employed for this research. This research revealed that long-term variability of temperature, rainfall, and humidity negatively affects rice yield in coastal Bangladesh. Additionally, sheath blight disease of rice is increasing more rapidly than blast and bacterial blight disease of rice due to rising temperature and humidity. Farmers usually have access to weather and climate information through personal experiences, peer farmers, agricultural extension officers, and local knowledge to predict and manage rice diseases. Most farmers (85%) were eager to receive disease forecasts information with 7 days lead time to take early measures. This research confirms that tailored CIS focusing on their needs, local crops, and weather conditions can help farmers to improve disease management. The co-production study reports that the co-creation of service using the DROP app through stakeholder collaborations, regular participation, and capacity building of farmers and field extension officers leads to better access to information. Besides, this also enhances the uptake and understanding of disease forecast information and farmers take early action to manage diseases. The co-produced services reduce pesticide use, increase crop yield and farmers' income. This makes farmers environmentally concerned about using less pesticides and fertilizers in crop fields. Finally, the participatory co-production of CIS for rice disease forecasting and management reduces climate-induced crop disease risk, makes farmers resilient, and sustains rice production under climate change. WIMEK Earth Systems and Global Change WIMEK Earth Systems and Global Change urn:nbn:nl:ui:32-b1016b2e-33b8-4cff-9a2f-0e0a21e60c73/obj 2026-04-08 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/9da78a87-f642-4899-8b0d-1108ab0a5d7c 2026-04-08 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-9da78a87-f642-4899-8b0d-1108ab0a5d7c 2026-04-08 urn:nbn:nl:ui:32-9da78a87-f642-4899-8b0d-1108ab0a5d7c/mods Utilising diagnostic features to define the safe operating space for nutrient management in smallholder farming systems Wageningen University dgg Reda Gidena Tasew 0000-0002-9470-0029 0000000530121281 aut R.E. Creamer opn D. P. Wall opn A.G. Reda opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 134 10.18174/680919 en Smallholder farming systems dominate Ethiopian’s agricultural landscape and are central to national food security and rural livelihoods. Despite their importance, these systems are often characterised by limited access to soil testing services, constrained use of external inputs, and a continued reliance on blanket fertiliser recommen-dation. Such uniform approaches overlook the considerable heterogeneity of soil and agro-ecological conditions, which frequently leads to inefficient nutrient use. Under-application of fertiliser in nutrient limited but responsive soils constraints crop productivity, while over-application in poorly responsive soils increases the risks of nutrient losses, soil degradation and environmental pollution. These challenges pose a significant barrier to achieving Ethiopia’s national objectives of improving agricultural productivity, enhancing nutrient use efficiency and promoting sustainable intensification. This thesis explores the potential of utilising diagnostic soil features as a practical and cost effective framework for defining a safe operating space for nutrient management in small-holder farming systems. The safe operating space is conceptualised as the range of nutrient inputs within which crop productivity can be enhanced while minimising risks to soil health and the environment. By anchoring nutrient management decisions in pedological knowledge, this framework offers an alternative to both blanket fertiliser recommendation and resource intensive soil testing approaches, that remain largely inaccessible in smallholder contexts. The findings show that diagnostic features capture key soil forming processes that strongly influence nutrient supply and retention, highlighting their value as indicators for soil specific nutrient man-agement. In parallel, the study examines constraints to phosphorus availability by analysing phosphorus pools, sorption capacity and chemical indicators such as calcium to phosphorus and aluminum to phosphorus ratios. These analyses reveal substantial variation in phosphorus supply potential among soils, driven by differences in mineralogy and chemical binding mechanisms. The assessment of farm-gate nutrient balances and nutrient use efficiency further demonstrates how fertiliser inputs and crop nutrient outputs interact with diagnostic soil features under smallholder management conditions. Nutrient use efficiencies vary markedly across soils, reflecting differences in nutrient retention capacity, loss pathways, and crop responsiveness. Overall, the thesis demonstrates that diagnostic soil features provide an operational basis for defining safe operating spaces for nutrient management in smallholder farming systems. Ultimately, this work contributes to strengthening the long term productivity, resilience and environmental sustainability of smallholder farming systems in Ethiopia. PE&RC Soil Biology PE&RC Bodembiologie urn:nbn:nl:ui:32-9da78a87-f642-4899-8b0d-1108ab0a5d7c/obj 2026-04-08 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/774fd3e3-d55b-4d02-b347-c40a55b8a1f7 2026-04-09 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-774fd3e3-d55b-4d02-b347-c40a55b8a1f7 2026-04-09 urn:nbn:nl:ui:32-774fd3e3-d55b-4d02-b347-c40a55b8a1f7/mods Advancing conservation biological control: a multidimensional perspective on microbial suppression of plant-parasitic Nematodes Wageningen University dgg van Himbeeck Robbert A.F. 0000000529767982 aut J. Helder opn G. Smant opn S. Geisen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 206 10.18174/681807 en Exploiting the nematode-suppressive capacity of microorganisms inhabiting suppressive soils is often proposed as a sustainable management strategy for controlling plant-parasitic nematodes, commonly referred to as microbial control. Microbial control of plant-parasitic nematodes is generally divided into two approaches, namely the inoculation of exogenous biological control agents (i.e., augmentative biological control) and enhancing the suppressiveness mediated by the native microbial antagonists (i.e., conservation biological control). In this thesis I aimed to advance our understanding of microbial control of plant-parasitic nematodes, principally within the framework of conservation biological control. We first developed a workflow to characterize soil nematode communities by sequencing the whole 18S rRNA gene using nanopore sequencing, which offered mostly species-level resolution. We then successfully tested this workflow in an experiment investigating the influence of cover crops on nematode communities. We then revealed the occurrence of soils that are naturally suppressive to potato cyst nematodes in the Netherlands, which was associated with various known fungal and bacterial nematode antagonists. This suppressiveness varied within a single field, highlighting that such differences in soil microbiome composition can influence the local establishment of a phytopathogen. Next, we demonstrated the global prevalence of fungal antagonists in soils and that this is affected by climatic conditions. Furthermore, soil pH was a key predictor of antagonist relative abundance in croplands. We revealed that fungal nematode antagonists are remarkably prevalent in croplands, providing opportunities to promote the abundance and activity of some of these taxa in arable fields to induce soil suppressiveness. Thereafter, we reasoned that plant phenotyping could serve as a proxy for determining nematode suppressiveness of a soil, circumventing the need for laborious suppressiveness-bioassays. We therefore explored the potential of aboveground chlorophyll fluorescence analysis to study potato cyst nematode infections and confirmed its high sensitivity and rapid response. Overall, this thesis advances the field of microbial control of plant-parasitic nematodes by demonstrating the native nematode-suppressive potential of arable soils and expanding the methodological toolkit available for this field of research. PE&RC Nematology (NEM) PE&RC Nematology (NEM) urn:nbn:nl:ui:32-774fd3e3-d55b-4d02-b347-c40a55b8a1f7/obj 2026-04-09 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/45a271aa-8180-428f-8e92-e1f7a11e9beb 2026-04-09 thesis

urn:nbn:nl:ui:32-45a271aa-8180-428f-8e92-e1f7a11e9beb 2026-04-09 urn:nbn:nl:ui:32-45a271aa-8180-428f-8e92-e1f7a11e9beb/mods A brassicaceae’s life : the eco-evolutionary dynamics of induced defence to multi-herbivore attack Wageningen University dgg Delamore Zoë 0000000530127464 aut E.H. Poelman opn K.J. Kloth opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 216 10.18174/681813 en Plants harbour diverse insect communities, from mutualistic pollinators to antagonistic herbivores. To defend against herbivores, plants have evolved a myriad of defence strategies. How plants evolved these defence strategies against multiple types of herbivores that feed simultaneously or sequentially (i.e. cross-resistance) is poorly understood. This thesis aimed to bridge the gap between the ecology and evolution of cross-resistance to herbivores, to explain how plants evolved defence strategies against multi-herbivory. To achieve this, I assessed plant defence strategies and insect community assembly across the Brassicaceae plant family. Chapter 2 reviewed which ecological factors affect plant induced responses to sequential herbivory by performing a meta-analysis. The results revealed that sequential herbivory generally leads to induced resistance by reducing herbivore performance but not herbivore preference. Moreover, plants managed to reduce damage but did not reduce biomass loss effectively. The lack of studies reporting on plant reproductive output show a serious knowledge gap into the cost of induced responses to sequential herbivory and the consequences for plant defence evolution. Chapter 3 studied the evolution of induced responses to sequential herbivory. In 83 plant species of the Brassicaceae family, I assessed macroevolutionary patterns in constitutive, induced and cross-resistance by exposing the plants to either single or sequential attack by two herbivores (Myzus persicae and Pieris brassicae). Cross-resistance related positively to induced resistance, indicating that plants responding strongly to P. brassicae remained resistant even with previous herbivory by another species. This suggests that the variation in resistance to sequences of herbivores is mainly explained by the evolution of resistance to specific herbivore species. Chapter 4 assessed how induced responses to the early-season herbivore Pieris rapae can affect plant fitness through changes in the insect community and plant growth. I manipulated P. rapae presence by either excluding them or by manually infesting plants with P. rapae caterpillars. The legacy effects of early-season herbivory affected the subsequent insect community and plant growth, resulting in a combination of direct and indirect effects on plant fitness. These findings indicate that the herbivore community as a whole could shape the evolution of plant defences rather than each single herbivore alone. Chapter 5 assessed how the evolutionary history and mating system of a plant help to explain variation in the insect community and discuss how this may influence plant defence evolution. I performed a common garden experiment with 26 annual Brassicaceae species with varying resistance to common herbivores on which we monitored the herbivore and pollinator communities and recorded plant growth, leaf and flower traits. The results revealed that showed that evolutionary shifts in mating system not only affect inducibility but has consequences for the entire community. Chapter 6 discusses how the findings in the different chapters contribute to understanding the ecological interactions that have been shaped by plants’ adaptations against herbivores and how current interactions may shape future plant defence evolution. Finally, I provide an outlook on future research to further entangle the complexities of eco-evolutionary feedback between plants and insects. PE&RC Entomology (ENT) PE&RC Entomology (ENT) urn:nbn:nl:ui:32-45a271aa-8180-428f-8e92-e1f7a11e9beb/obj 2026-04-09 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/56c21a6b-3585-40be-8777-22a534ccc7b2 2026-04-09 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-56c21a6b-3585-40be-8777-22a534ccc7b2 2026-04-09 urn:nbn:nl:ui:32-56c21a6b-3585-40be-8777-22a534ccc7b2/mods Digitalizing sustainability governance in aquaculture : Implications for smallholder inclusion Wageningen University dgg Kruk Sake R.L. 0000-0001-5646-1613 0000000529714514 aut S.R. Bush opn H.M. Toonen opn S. Kloppenburg opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 190 10.18174/681081 en This thesis investigates how digitalization reconfigures sustainability governance in aquaculture, with a particular focus on implications for smallholder inclusion. Aquaculture, the world’s fastest-growing food sector, heavily relies on smallholders. Digital technologies from mobile apps and sensors to traceability platforms and automated feeders promise improved efficiency, traceability, and environmental management. Several stakeholders promote digitalization as a pathway toward sustainability and inclusion, particularly by integrating smallholders into knowledge, finance, and markets. Critical scholarship, however, highlights how these technologies may also reinforce inequalities, concentrate power among agribusiness and technology firms, and constrain farmers’ autonomy. Against this backdrop, the thesis asks: In what ways does digitalization reshape the inclusion of smallholders in aquaculture sustainability governance?Methodologically, the thesis follows digital technologies across sites of design, farm-level use, value chain coordination, and global data ecosystems. It draws on interviews, observations, and document analysis, while building on perspectives from algorithmic governance, social practice theory, and global value chain governance.The empirical core consists of four chapters. Chapter 2 analyses ten sustainability initiatives to examine how digital technologies are designed to engage smallholders, identifying three archetypes of participation - the tutorial, the dashboard, and the platform - that shape roles and responsibilities. Chapter 3 presents a case study of a fish farming platform in Indonesia, showing how everyday practices such as feeding and harvesting are reorganized through datafication, synchronization, calibration, and aggregation, enabling the platform to orchestrate wider economic and governance functions. Chapter 4 examines digital sustainability assurance in value chains, revealing how reliance on digital information elevates “digital lead actors” who coordinate these processes and redefine governance power. Chapter 5 maps emerging digital data architectures in aquaculture globally, identifying a fragmented ecosystem and outlining three possible futures. It argues that federated data ecosystems hold the greatest potential for aligning digitalization with sustainable development.Overall, the thesis demonstrates that digitalization does not merely support existing governance arrangements in aquaculture but actively reconfigures them in three ways. First, digital technologies reorganize actor constellations, connecting diverse stakeholders but also concentrating influence in the hands of those who design and maintain digital technologies, resulting in a dynamic but fragmented governance landscape. Second, digital technologies shape participation mechanisms through their design and everyday use. Design choices prefigure participation and processes of datafication, calibration, and synchronization determine how smallholders participate in practice. Third, digital technologies increasingly embed decision-making functions within platforms, reshaping how sustainability is defined, assessed, and acted upon by prioritizing quantifiable metrics and rescaling decision-making.As a result of this reconfiguration, digital technologies create new capacities for coordination and oversight, yet their contribution to smallholder inclusion depends on who controls digital infrastructures, how systems are designed, and how data are interpreted in practice. By developing a vocabulary – archetypes of participation, practices of digital work, digital lead actors, data ecosystems – the thesis sharpens the analysis of this reconfiguration and contributes to broader debates on digital agriculture, algorithmic governance, and sustainability transitions, and highlights the need for active governance of digitalization to ensure it supports inclusive and sustainable food systems. Environmental Policy WASS Milieubeleid WASS urn:nbn:nl:ui:32-56c21a6b-3585-40be-8777-22a534ccc7b2/obj 2026-04-09 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/3871bc95-7fa5-4cee-ac03-96fc7eed1e20 2026-04-02 thesis

urn:nbn:nl:ui:32-3871bc95-7fa5-4cee-ac03-96fc7eed1e20 2026-04-02 urn:nbn:nl:ui:32-3871bc95-7fa5-4cee-ac03-96fc7eed1e20/mods Early-life galactose for later-life metabolic health Wageningen University dgg Sun Peixin 0000000530070613 aut J. Keijer opn E.M. van Schothorst opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 222 10.18174/681382 en The global prevalence of obesity underscores the urgent need for effective preventive strategies. Targeting nutrition during early-life developmental windows offers a great opportunity to aid in the prevention of adult obesity.Breastmilk, the optimal source for infant nutrition, is known to exert beneficial programming effects on later-life health. A key component of breastmilk is lactose. Upon digestion, lactose is cleaved into glucose and galactose. However, whether early-life galactose consumption exerts beneficial programming effects on later-life health remains less understood. Therefore, this thesis investigates the nutritional programming effects of early-life galactose on metabolic health in the mouse (Mus musculus) model and lifespan in the fruit fly (Drosophila melanogaster) model.Chapter 2 demonstrated that partial replacement of glucose with galactose in an early-life post-weaning diet for three weeks, followed by a high-fat diet for nine weeks, significantly increased the expression of adiponectin encoding gene in white adipose tissue and serum adiponectin levels, and decreased the expression of skeletal muscle Insulin receptor substrate 2 in later-life without alterations in fat mass, inflammation status, and glucose tolerance.Chapter 3 showed that galactose in the context of maltodextrin in a post-weaning diet significantly decreased body weight, fat mass, and lean mass in both sexes, and reduced energy expenditure and respiratory exchange ratio in females in early-life. However, following a nine-week obesogenic challenge, nutritional programming effects were largely absent except for decreased liver insulin-like growth hormone 1 mRNA in females.Chapter 4 revealed that galactose, compared to isocaloric glucose, as the sole carbohydrate in the larval diet, extended developmental time during the larval period, increased pupal volume, and reduced mitochondrial mass with no change in respiration per body weight. In later-life, larval galactose exerted programming effects on increased body weight, reduced triacylglycerol content, and reduced survival in adult females when adult flies were fed a standard glucose diet, with no programming effects under an obesogenic diet challenge later in life or in males.Chapter 5 demonstrated that equimolar galactose plus glucose co-consumption, compared to isocaloric glucose, produced similar, but milder, early-life effects to those observed in Chapter 4. In later-life, co-consumption of galactose and glucose programmed adult lifespan in a sex-specific manner: a shortened lifespan in males, but an extended lifespan in females. The extended lifespan in females was accompanied by a healthier lipid profile, which was characterized by increased polyunsaturated glycerophospholipids and decreased monounsaturated glycerophospholipids. This was potentially driven by higher expression of transcripts involved in cuticular hydrocarbon biosynthesis, a pathway that preferentially consumes saturated and monounsaturated fatty acids, but not polyunsaturated fatty acids.Overall, galactose exerts distinct, context-dependent, programming effects, ranging from subtle metabolic effects on insulin/IGF1 signaling in mice to significant, sex-specific effects on lifespan and lipid metabolism in flies. Future research should elucidate the mechanisms underlying galactose's context-specific programming effects. Eventually, understanding the long-lasting effects of early-life galactose exposure may contribute to optimizing infant nutritional guidelines and improving long-term metabolic health. VLAG Human and Animal Physiology VLAG Fysiologie van Mens en Dier urn:nbn:nl:ui:32-3871bc95-7fa5-4cee-ac03-96fc7eed1e20/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/3e5cc829-14b0-4704-8d00-61bddaca4683 2026-04-02 thesis

urn:nbn:nl:ui:32-3e5cc829-14b0-4704-8d00-61bddaca4683 2026-04-02 urn:nbn:nl:ui:32-3e5cc829-14b0-4704-8d00-61bddaca4683/mods Unravelling teacher development : exploring the mechanisms, conditions, and continuity of teacher learning in pedagogical development programmes in higher education Wageningen University dgg Vreekamp Marloes 0009-0000-1803-3458 000000049328075X aut P. den Brok opn J. Gulikers opn P. Runhaar opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 238 10.18174/681130 en In higher education, teachers are expected to continuously improve their teaching and respond to changing educational demands. To support and recognise these efforts, universities offer pedagogical development programmes (PDPs), in the Netherlands for example the University Teaching Qualification (UTQ). This dissertation reports on a study that examines how teachers learn during these programmes and explores which programme characteristics are associated with different types of learning outcomes.---The dissertation brings together four part studies using complementary methodologies to address the overarching question: Via what mechanisms and under what conditions does teacher learning unfold over time during participation in a PDP? The Interconnected Model of Professional Growth (Clarke & Hollingsworth, 2002) served as a conceptual framework to analyse the dynamic interactions between PDP characteristics, learning outcomes, and the processes through which learning unfolds.---A systematic literature review presented in Chapter 2 examined how characteristics of PDPs and the context wherein these programmes take place, are related to different domains of teacher development’. The findings revealed a wide range of teacher development outcomes (e.g. personal domain, domain of practice, domain of consequence) and identified multiple relationships between programme and contextual characteristics and learning outcomes. For instance, PDP training was reported to affect the domain of practice via activities including instruction, collaboration, discussion, feedback, and designing teaching.---Chapter 3 reports a survey study investigating how participation in collaboration activities in a PDP related to teacher learning and the subsequent changes in student learning. Participation in information-exchange activities was positively associated with changes in student learning, via changes in teachers’ attitudes and teaching practices. Co-creation activities appeared to influence student learning more directly, warranting further investigation into the underlying mechanisms.---Chapter 4 explored the development of teachers’ conceptions of the academic teacher during a PDP and how this is related to their teaching practices at the start of the PDP. Half of the 11 participating teachers changed their conception, either by becoming more or becoming less student-centred or by enriching their existing conceptions. These changes appeared unrelated to teachers’ conceptions and teaching practices at the start of the PDP, illustrating the diverse and non-linear nature of professional learning.---A longitudinal multiple case study in Chapter 5 investigated how teachers learned within a PDP and how their learning continued over time. Two patterns of continued learning were identified. The impact-driven pattern was characterised by a direct continuation of an intervention trialled in the classroom after observing positive impact of the implemented changes. The insight-driven pattern originated from reflection, leading first to changes in knowledge, attitudes, or vision, followed by continued development through refinement, transfer to other courses or contexts, or further exploration. Several context factors were found to stimulate (e.g. having autonomy) or hinder (e.g. time-constraints) this continuation of learning, or function as catalyst of learning (e.g. increasing student numbers, shortage of teaching staff).---Overall, this dissertation demonstrated that PDPs meaningfully stimulate teacher development. Teacher learning often begins with small changes that continue over time and contribute to lasting improvement in education. WASS Education and Learning Sciences WASS Onderwijs- en leerwetenschappen urn:nbn:nl:ui:32-3e5cc829-14b0-4704-8d00-61bddaca4683/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/ca7504c5-ae3d-45ca-84b0-dc3cce95acd5 2026-04-01 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-ca7504c5-ae3d-45ca-84b0-dc3cce95acd5 2026-04-01 urn:nbn:nl:ui:32-ca7504c5-ae3d-45ca-84b0-dc3cce95acd5/mods Characterisation of apple pectin structure in relation to apple fruit processability Wageningen University dgg Liu Dazhi 0000000530070648 aut H.A. Schols opn Jinfeng Bi opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 238 10.18174/680976 en Apples, one of the most widely harvested fruits globally, come in thousands of cultivars that can be consumed fresh or processed into products like juice and puree. They are rich in polysaccharides, particularly pectin, which varies in quantity and structural features among different sources. This structural complexity imparts a wide range of physicochemical properties to pectin. Variations in characteristics such as sugar content, backbone linearity, and degree of methyl esterification (DM) lead to differing functionalities like thickening and stabilization. This thesis aims to explore the differences in pectin structures across various apple cultivars and how these variations influence the physical properties of apple products.Pectins were extracted from different apple cultivars in two harvest years and characterized using various methods to elucidate their structural features, such as sugar composition and DM. Beyond DM analysis, an enzymatic fingerprinting approach assessed methyl ester distribution. Pectins were hydrolyzed with endo-polygalacturonase and pectin lyase to release diagnostic oligomers, which were identified using HILIC-MScombined with HPAEC. Parameters such as the degree of blockiness of methyl esterified oligomers provided insights into methyl esterification distribution patterns. Additionally, apples were processed into juice and puree, with product qualities like turbidity, zeta - potential, and rheological properties measured. Statistical analyses were conducted to explore the relationships between apple product quality and their native pectin structures.The findings reveal significant differences in pectin structures among apple cultivars, particularly in methyl esterification distribution patterns, even among pectins with the same DM. These structural variations influence product quality. Using metabolomic techniques, the research also links pectin structures to metabolic profiles, uncovering crucial connections between pectin characteristics and apple biosynthesis pathways.Understanding the variation in pectin structure and its effects on product quality is valuable for the apple processing industry. The differences in pectin structure across cultivars highlight each apple's unique processing potential. Additionally, pectin from the same cultivar but harvested in different years can be differentiated based on structural characteristics. These results provide valuable insights for product development and quality control within the apple processing industry. VLAG Food Chemistry VLAG Levensmiddelenchemie urn:nbn:nl:ui:32-ca7504c5-ae3d-45ca-84b0-dc3cce95acd5/obj 2026-04-01 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/317b994c-f0ea-459d-8220-f009f63626bf 2026-04-01 thesis

urn:nbn:nl:ui:32-317b994c-f0ea-459d-8220-f009f63626bf 2026-04-01 urn:nbn:nl:ui:32-317b994c-f0ea-459d-8220-f009f63626bf/mods Flavivirus infections in poultry : from transmission and host adaption to vaccination strategies Wageningen University dgg Li Luzhao 0000000530070584 aut M.M. van Oers opn G.P. Pijlman opn Z. Li opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 188 10.18174/681506 en Mosquito-borne flaviviruses (MBFVs) include several important pathogens such as Yellow fever virus, Dengue virus, West Nile virus, Japanese encephalitis virus, and Zika virus. Many of these viruses use birds as natural reservoirs. Poultry, characterized by large population sizes, high-density farming, and close contact with humans, may therefore play an important role in the ecology and emergence of flaviviruses. In 2010, an outbreak of Tembusu virus (TMUV) occurred in duck farms in China, causing severe economic losses and highlighting the importance of monitoring flavivirus infections in poultry. However, the mechanisms underlying host range, transmission, and adaptation of flaviviruses in poultry remain poorly understood. In this thesis, we first investigated the pathogenicity and transmission routes of a cluster 3 TMUV strain (SD) in ducks and chickens. TMUV SD infected both species, but virus shedding from the oropharyngeal and cloacal routes and direct contact transmission were observed only in ducks. In contrast, no virus shedding or direct transmission occurred in chickens. However, Culex pipiens mosquitoes were able to acquire the virus from infected chickens and subsequently transmit it to naïve chickens, indicating that mosquito vectors remain essential for TMUV transmission in chickens. To explore the molecular basis of host expansion, we compared an early cluster 2 TMUV strain (FX2010) with the recent cluster 3 strain (SD). While SD replicated systemically in chickens, FX2010 couldn’t infect chicken. Using chimeric virus approaches, we identified the viral envelope (E) protein as a key determinant of host range. In particular, a serine residue at position 69 was required for efficient infection, pathogenicity, and tissue tropism in chickens, and this residue has become predominant in recent cluster 3 strains. We further examined the role of the prM and E proteins from different flaviviruses by introducing their prME regions into a common TMUV-FX2010 backbone. Comparative analyses in duck and mouse models demonstrated that the prME region is a major determinant of viral infectivity in ducks and of the ability to initiate infection via the intranasal route in mice. Finally, using the TMUV vaccine strain FX2010-180P as a backbone, we developed chimeric live-attenuated vaccine candidates expressing the prM-E proteins of West Nile virus. These candidates induced strong neutralizing antibody responses in ducks, demonstrating that the TMUV vaccine platform can be used for the development of flavivirus vaccines for poultry. Overall, this work improves our understanding of flavivirus host adaptation and transmission in poultry and provides insights for surveillance, prevention, and vaccine development against emerging flaviviruses in poultry. PE&RC Virology (VIR) PE&RC Virology (VIR) urn:nbn:nl:ui:32-317b994c-f0ea-459d-8220-f009f63626bf/obj 2026-04-01 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/71dcd52c-5e74-48c8-9a9c-8e5cc53842a2 2026-04-01 thesis

urn:nbn:nl:ui:32-71dcd52c-5e74-48c8-9a9c-8e5cc53842a2 2026-04-01 urn:nbn:nl:ui:32-71dcd52c-5e74-48c8-9a9c-8e5cc53842a2/mods The ecology of arthropods in a nature-inclusive farming system Wageningen University dgg Litovska Iryna 000000053007055X aut D. Kleijn opn F. van der Plas opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 167 10.18174/681837 en Arthropod populations are experiencing drastic declines that are to a considerable extent driven by agricultural intensification. To halt the decline of arthropods, changes in farming practices and management of surrounding habitats are needed. Nature-inclusive farming is a novel approach and a possible solution for these challenges since it aims to combine crop production with biodiversity conservation. This thesis investigated how nature-inclusive farming affects arthropod abundance and diversity, as well as the ecosystem services they provide. Based on this thesis, semi-natural habitats are the backbone of biodiversity in agricultural landscapes, while crops with a high plant cover early in the season (e.g. winter wheat) benefit arthropods in spring and summer. Moreover, despite higher pest abundance in nature-inclusive farming, potato yield quantity and quality did not differ from conventional farming. Overall, this thesis shows that nature-inclusive farming can boost arthropod biodiversity, yet, since it requires agricultural land taken out of production, less land is available for farming. PE&RC Plant Ecology and Nature Conservation PE&RC Plantenecologie en Natuurbeheer urn:nbn:nl:ui:32-71dcd52c-5e74-48c8-9a9c-8e5cc53842a2/obj 2026-04-01 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/d150d6c0-558f-438f-a9e8-c5b165d33729 2026-04-28 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-d150d6c0-558f-438f-a9e8-c5b165d33729 2026-04-28 urn:nbn:nl:ui:32-d150d6c0-558f-438f-a9e8-c5b165d33729/mods Going local? environmental impacts of nutrient cycling in food systems at different scales : The Netherlands as a case study Wageningen University dgg Tamsma Durk W. 000000051785830X aut M.K. van Ittersum opn I.J.M. de Boer opn A.G.T. Schut opn C.E. van Middelaar opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 241 10.18174/681282 en Achieving a sustainable food future requires restoring nutrient cycles and minimizing losses in more circular food systems. The scale at which nutrient loops can be restored and the resulting environmental outcomes depend strongly on local conditions. This thesis evaluates the environmental impacts of restoring nutrient loops at different spatial scales. It first explores why current food systems are not circular and how local context shapes opportunities for nutrient circularity. It then assesses how circular food systems in the Netherlands with varying levels of local food sourcing within provinces affect land use, nitrogen losses and greenhouse-gas emissions. Results show that circular food systems substantially reduce land use, nitrogen inputs and losses, and greenhouse-gas emissions. Local production conditions in conjunction with scale were a strong driver of environmental impacts. In parts of the Netherlands local food sourcing aligned well with local environmental targets, while in other parts this was not the case. PE&RC Plant Production Systems (PPS) Animal Production Systems PE&RC Plant Production Systems (PPS) Dierlijke productiesystemen urn:nbn:nl:ui:32-d150d6c0-558f-438f-a9e8-c5b165d33729/obj 2026-04-28 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/2f53f6f1-fe09-4b25-a819-9058b589e843 2026-05-18 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-2f53f6f1-fe09-4b25-a819-9058b589e843 2026-05-18 urn:nbn:nl:ui:32-2f53f6f1-fe09-4b25-a819-9058b589e843/mods Integrating crop modelling with remote sensing : Application on data-limited small-scale farming systems Wageningen University dgg Dlamini Luleka 0000000530076230 aut C.J. Ritsema opn J. van Dam opn O. Cresco opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 166 10.18174/681297 en Climate change and variability present increasing threats to agricultural productivity and food security in southern Africa, particularly for small-scale, rainfed farming systems constrained by limited resources, fragmented landholdings, and weak institutional support. Although digital technologies such as crop growth models (CGM) and remote sensing (RS) show growing potential for improving yield estimation and adaptation planning, their practical use in small-scale contexts remains limited. This thesis examined how CGM and RS can be integrated and applied in data- and resource-limited small-scale maize farming systems to improve yield estimation, climate adaptation, and institutional decision-making. The study was conducted in South Africa’s Eastern Cape Province, a region that exemplifies the socio-economic and climatic challenges of small-scale agriculture in southern Africa. A mixed-methods approach was used, combining a systematic review, crop modelling experiments, climate impact assessments, and institutional surveys. Chapter 2 provided a systematic overview of global CGM–RS integration through data assimilation, identifying key trends, limitations, and research gaps, particularly the concentration of applications in large-scale, high-input systems and the lack of studies in African small-scale contexts. Building on these insights, Chapter 3 applied a recalibration-based data assimilation method using Sentinel-2–derived Leaf Area Index (LAI) to improve the performance of the WOFOST crop model at the farm scale. The model was parameterized and validated using field data from small-scale maize plots, demonstrating that assimilating LAI significantly improved yield estimation accuracy by more than 90% compared to baseline simulations. Chapter 4 used this locally recalibrated model to simulate maize phenology, water stress, and yield responses across three future climate scenarios derived from multiple Global Climate Models (GCMs) and Shared Socioeconomic Pathways (SSPs). Results indicated that projected increases in temperature and rainfall variability will substantially reduce maize yields, though adaptive measures such as adjusted planting dates and changing varieties can partially offset these losses. Chapter 5 assessed the awareness, use, and institutional readiness of agricultural extension officers to adopt CGM and RS tools. Survey and interview data revealed high interest but low practical use, primarily due to limited training, technical complexity, and weak institutional infrastructure. Overall, the findings show that integrating CGM with RS is technically feasible and operationally valuable in small-scale systems, provided it is supported by institutional capacity-building and policy alignment. Methodologically, introducing a yield gap factor and assimilating high-resolution RS data are pragmatic innovations for adapting modelling frameworks to data-poor environments. Scientifically, the research advances understanding of how digital tools can improve yield forecasting and climate adaptation at local scales. Practically, it highlights the pivotal role of extension officers in bridging the gap between digital innovation and on-farm application. By linking the technical, climatic, and institutional dimensions, this thesis offers a pathway to democratize digital agriculture and build more resilient, data-informed small-scale farming systems across southern Africa. WIMEK Soil Physics and Land Management WIMEK Bodemfysica en Landbeheer urn:nbn:nl:ui:32-2f53f6f1-fe09-4b25-a819-9058b589e843/obj 2026-05-18 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/7f022416-9202-4079-91b9-09e5659466e5 2026-03-31 thesis

urn:nbn:nl:ui:32-7f022416-9202-4079-91b9-09e5659466e5 2026-03-31 urn:nbn:nl:ui:32-7f022416-9202-4079-91b9-09e5659466e5/mods On the side of the plant cell : Proteomic insights into lateral cell polarity Wageningen University dgg Pukhovaya Evgeniya 0000000530153216 aut D. Weijers opn C. Albrecht opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 214 10.18174/681502 en Cell polarity is uneven distribution of cellular components. It controls asymmetrical cell division, directional growth and transport during the organism development. Proteins involved in cell polarity are concentrated at the plasma membrane (PM) facing certain directions – polarity domains. Plant cell polarity domains are aligned with organismal shootward-rootward and inner-outer axes. Mechanisms that target proteins to these cellular domains, and by extension control cell polarity, are poorly understood.Plant-specific SOSEKI proteins localize to different cell edges and are associated with the PM. Several SOSEKI interactors are also polar, indicating the existence of connected polar pathways in plant cells. In this work, we used SOSEKI and their interactors to dissect PM targeting mechanisms for plant polar proteins. Additionally, we studied their functions downstream of plant cell polarity.In order to find out if plant cells have general directional mechanisms of polar protein targeting, we used a proximity labelling proteomics approach. We created a set of overexpression Arabidopsis lines of 12 previously identified polar proteins (baits), including SOSEKI’s and their interactors, fused with a biotin ligase enzyme that labels the proteins in the bait proximity. We analyzed resulted interactomes and recovered 2457 proteins that are significantly enriched with at least one of the baits in seedlings. The interactors were clustered according to the enrichment level with each bait. One such cluster contained high enrichment values only in the baits localized to the lateral polar domain of the root meristem cell, and contained SOSEKI interactors and two newly identified polar proteins families – PAT19 (S-Protein-acyl-transferase 19) and IRKI (IRK interactors). Thus, we identified a connected lateral polar protein module.Using a set of reporter lines, we showed that the lateral module is ubiquitously expressed and polarized, suggesting generic developmental function. We studied the functions of two lateral module components with enzymatic activity – a cytosolic kinase SIK4 and PM-localized PAT19. We showed that SIK4 is an atypical kinase emerged early in the land plant evolution. However, knocking out the only Arabidopsis SIK4 homolog did not lead to any significant developmental and polarity defects. Therefore, SIK4 is not essential for cell polarity establishment and likely serves an unknown downstream function under certain conditions.PAT are known to take part in protein membrane targeting by modifying their cysteine residues to make a protein substrate more hydrophobic. Several polar proteins, including SOSEKI, require this modification for their PM association. To investigate if PAT19 can create a polar bias in PM targeting, we constructed SOSEKI reporter lines in the background of pat19 mutants and found out that the mutants exhibit cell division orientation defects and a partial loss of SOSEKI PM association. Therefore, PAT might be involved in the lateral targeting of the factors important for the orientation of cell division.Overall, this work presents a large proteomic resource allowing systematic dissection of polarity mechanisms in plants. We used it to discover a lateral polar protein complex and propose a mechanism of lateral polar targeting through a directional bias in S-acylation. EPS Biochemistry EPS Biochemie urn:nbn:nl:ui:32-7f022416-9202-4079-91b9-09e5659466e5/obj 2026-03-31 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/7fe2e13c-0c47-4c2f-aaa0-5571dae4429e 2026-03-27 thesis

urn:nbn:nl:ui:32-7fe2e13c-0c47-4c2f-aaa0-5571dae4429e 2026-03-27 urn:nbn:nl:ui:32-7fe2e13c-0c47-4c2f-aaa0-5571dae4429e/mods From fields to forests : how young tropical forests adapt to global change Wageningen University dgg Kok Jazz J.M. 000000053007063X aut L. Poorter opn Masha T. van der Sande opn Lucy Amissah opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 171 10.18174/681112 en Amid ongoing global change, young tropical forests are regrowing under climatic and landscape conditions that may alter their recovery. As these forests establish under hotter, drier, and more fragmented environments, understanding drought adaptation during early succession becomes essential. Because early-successional forests are dominated by fast-growing, short-lived species, they can reorganize more rapidly than old-growth forests and may therefore adapt more quickly to shifting conditions. This thesis investigates drought adaptation across three dimensions: the species dimension, which assessed drought strategies of early-successional species; the spatial dimension, which examined how forest type and surrounding landscape shape community drought adaptation; and the temporal dimension, which evaluated how these adaptations influence forest productivity through time. Together, these dimensions provide an integrated understanding of how young tropical forests adapt and function under increasingly variable environments.The species dimension examined whether early-successional tree species form a single functional group or differ in drought strategies. Studying 30 dominant species from dry and wet forests revealed functional differentiation: dry-forest species were more drought tolerant with slower light-saturated gas exchange, whereas wet-forest species showed the opposite suite of traits. Two trade-offs (drought tolerance vs. gas exchange; leaf toughness vs. nutrient concentration) produced four strategies: fast-and-rich, tolerant-and-tough, tolerant-and-rich, and fast-and-tough. These findings show that early-successional species are functionally diverse rather than a homogeneous group and provide the basis for a simple bi-trait proxy (wood density × leaf mass per area) to guide species selection in forest restoration.The spatial dimension examined how climate and landscape context filter species strategies into community-level drought adaptations. Across 37 young secondary forest plots, dry-forest communities were dominated by drought-tolerant traits, whereas wet-forest communities showed acquisitive traits. Landscape composition further shaped these patterns: agriculture promoted communities with drought-delaying leaves, secondary-forest cover favoured acquisitive species in dry regions, and old-growth cover favoured conservative species in wet regions. These findings show that macroclimate and landscape jointly filter community drought adaptation in regenerating forests and highlight the importance of maintaining forest patches and nearby seed sources to promote regenerating communities with broader functional compositions.The temporal dimension examined how community-level drought adaptation develops through time and affects productivity. Basal area growth across 50 plots spanning a decade showed that wet forests grew rapidly but slowed early, whereas dry forests grew more gradually yet remained stable. Communities dominated by drought-tolerant species showed lower productivity, revealing a trade-off between tolerance and growth. These findings suggest that ongoing shifts toward more drought-adapted communities may slow forest recovery, and highlight the importance of balancing drought-tolerant and fast-growing species to sustain productivity under increasing global change.The findings of this thesis also point to the need for reframing succession. Forests develop under continually changing environmental and social conditions. Rather than a predictable sequence within a static context, succession is better viewed as a dynamic, interconnected process shaped by shifting relationships among species, climate, landscape, and human influence. This “shapeshifting-web” perspective highlights the importance of accounting for temporal variability in both drivers and responses and helps explain why tropical forests follow diverse recovery pathways. PE&RC Forest Ecology and Forest Management PE&RC Bosecologie en -beheer urn:nbn:nl:ui:32-7fe2e13c-0c47-4c2f-aaa0-5571dae4429e/obj 2026-03-27 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/a344538b-0cf8-4194-b27f-201874ba2c26 2026-03-27 thesis

urn:nbn:nl:ui:32-a344538b-0cf8-4194-b27f-201874ba2c26 2026-03-27 urn:nbn:nl:ui:32-a344538b-0cf8-4194-b27f-201874ba2c26/mods S. cerevisiae’s general stress response : a tool to save energy and uncouple protein production from growth Wageningen University dgg Temelli Nuran 0000000530070621 aut R.A. Weusthuis opn M.M.M. Bisschops opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 202 10.18174/681247 en This thesis investigates the importance and the function of the General Stress Response (GSR), regulated by the transcription factors Msn2 and Msn4, in Saccharomyces cerevisiae during nutrient-limited, slow-growth conditions. Using advanced cultivation techniques, including chemostat, fed-batch, and retentostat cultivations, the research highlights a novel role for the GSR beyond stress resistance.A key finding is that GSR activation promotes energy conservation by significantly reducing the Maintenance Energy Requirement (MER), particularly at slow growth rates. Furthermore, the study demonstrates that protein production strategies must be tailored to the localization of the product. Optimal yields for intracellular versus secreted proteins require distinct promoter strategies such as using stress induced PHSP12 vs. constitutive PTEF1. Finally, the research explores adaptation under extreme nutrient limitation, establishing that the GSR is essential for cellular robustness and viability. Overall, these results provide deep insights into fundamental role of GSR and its application in bioprocess engineering. Bio Process Engineering VLAG Bio Process Engineering VLAG urn:nbn:nl:ui:32-a344538b-0cf8-4194-b27f-201874ba2c26/obj 2026-03-27 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/c34c1cf6-ee93-4caf-8fa2-b323aca6e0d3 2026-03-20 thesis

urn:nbn:nl:ui:32-c34c1cf6-ee93-4caf-8fa2-b323aca6e0d3 2026-03-20 urn:nbn:nl:ui:32-c34c1cf6-ee93-4caf-8fa2-b323aca6e0d3/mods The microbial fingerprint of drought : patterns and drivers of microbiome assembly in the rhizosphere of water-stressed plants Wageningen University dgg Berdaguer Roland 0000000529735307 aut C. Testerink opn R. Karlova opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 232 10.18174/681302 en The research presented in this thesis aims at improving our understanding of rhizosphere microbiome assembly under drought through three comparative studies between different plants, at three different evolutionary scales, addressing both common and different research questions. Overall, I aim to shed light on rhizosphere microbiome assembly under drought by focusing on (i) commonalities and differences between different plants, (ii) evolutionary patterns and (iii) plant mechanisms shaping this microbiome.In chapter 1, the general introduction, I present the current state of knowledge on the rhizosphere microbiome and how it is shaped by plants, in particular through root exudation. This is also placed in an evolutionary context. I then elaborate how plants and the rhizosphere microbiome respond to drought stress, and how their interaction affects plant fitness and drought resilience.In chapter 2, we study the microbiome associated with the rhizoids, named rhizoid-sphere, of three bryophyte plant species. We compare these microbiomes and their changes under drought between these three species and with two angiosperm species. This reveals some consistent compositional changes in the rhizosphere microbiome under drought. We also show that certain bacterial taxa known for their plant growth promoting properties show strong differences in abundance between bryophyte species, suggesting that the interaction with these bacterial taxa may have evolved at an early stage of land plant evolution.In chapter 3, we compare the rhizosphere microbiome of 24 different plant species under drought and well-watered conditions. We show that these microbiomes show very similar compositional shifts under drought, but also some differences, which we correlate with the host plant species’ drought resilience. We also show that host species specificity patterns of rhizosphere microbes can be linked to the host plants’ phylogeny, but this pattern is weakened under drought. Lastly, we correlate rhizosphere microbiome data with untargeted liquid chromatography – mass spectrometry (LC-MS) of root metabolites to generate hypotheses regarding specific root metabolites that may play a role in the recruitment of specific microbial taxa in the rhizosphere.In chapter 4, we zoom into intra-species variation in the rhizosphere microbiome of tomato. We analyze the rhizosphere microbiomes associated with 139 different tomato genotypes, under drought and well-watered conditions. We show differences in these tomato genotypes’ rhizosphere microbiome composition and link them to host genotype dissimilarity. Like in chapter 3, we show that this link is weakened under drought. We further identify which bacterial taxa show a high heritability, i.e. of which the relative abundance is strongly influenced by the host genotype. Finally, we perform genome-wide association studies (GWAS) to identify plant genetic loci associated with plant biomass and drought resilience, and with the relative abundance of specific bacteria in the rhizosphere.In chapter 5, the general discussion, I draw some parallels between the three experimental chapters and put the research presented in this thesis in the context of the latest scientific literature. I further discuss how fundamental research on the rhizosphere microbiome can feed into applied research and give an outlook on its potential impact on agriculture. EPS Plant Physiology (PPH) EPS Plant Physiology (PPH) urn:nbn:nl:ui:32-c34c1cf6-ee93-4caf-8fa2-b323aca6e0d3/obj 2026-03-20 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/d38dcabc-d919-432b-9bbb-8e647d5abf5c 2026-03-20 thesis

urn:nbn:nl:ui:32-d38dcabc-d919-432b-9bbb-8e647d5abf5c 2026-03-20 urn:nbn:nl:ui:32-d38dcabc-d919-432b-9bbb-8e647d5abf5c/mods Ethnobotanical study of wild food plants used by farmers in Konso, Ethiopia : Gathering and consumption of specific wild food plants mark the levels of household food stock Wageningen University dgg Lemessa Ocho Dechassa 0000000443759455 aut P.C. Struik opn L.L. Price opn Ensermu Kelbessa † opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 239 10.18174/680773 en The collection and consumption of wild food plants (WFPs) play an important role in the diet in Ethiopia, where food shortage is recurrent and stressful. WFPs are key to survival strategies used by rural farming households at times of food stresses. However, little is studied on the subject, especially for Konso. Humanitarian partners have used the gathering and consumption of WFPs as early warning indicators in assessing seasonal food availability in chronically food insecure areas. This general assumption is misleading.This study was therefore conducted to specify the WFPs whose gathering and consumption could be used as early warning indicator of household food situation and to generate botanical data that could help assess the importance of WFPs in the food security of the study area by analyzing occurrence, abundance, diversity, seasonal availability of WFPs, their biophysical characteristics, and by identifying microenvironments where WFPs are gathered.We used household interviews, key informant interviews, focus groups discussions, physical field observations, and market surveys, in collecting of ethnobotanical data. We identified 15 microenvironments where WFPs are locally gathered. Botanical data were generated from inventories of WFPs in these 15 microenvironments and their occurrence, abundance, and species diversity were studied.We found 136 (S)WFPs, crop parts, and crop residues gathered and consumed in the study area. These provided 152 products: 120 products from (S)WFPs, 21 products from crop parts, 10 from crop residues, and one from recycled food stuff. 119 (S)WFPs were volunteered during free-listing exercises while the rest were obtained through key informant interviews, focus group discussions, field visits and observations, and head counting of the plants during the sampling of the 15 microenvironments. Of the 152 plant products, 52 were gathered and consumed only in severe food stress period (red light traffic metaphor), 35 products in amber light, and the remaining 65 products could be gathered even in normal times. Therefore, this study showed that in Konso, the gathering and consumption of the 65 plant products cannot be used as indicator of food stress as they are part of normal diets of the community.The gathering and consumption of the plants under different levels of food availability indicate that (S)WFPs are integral parts of the food security situation of the Konso community both in normal and in food stress times. The study identified food stress times and analyzed the coincidence of food shortage/stress period with the availability/unavailability of the (S)WFPs and analyzed how the (S)WFPs are used in filling the food gap which clearly showed the strategic role and importance of (S)WFPs in the food security situation of the study area.The study revealed a wealth of preserved ethnobotanical knowledge and associated traditional use and management of (semi-)wild food plants of farmers in Konso. It further established that regardless of the type and number of (S)WFPs species or diversity indexes provided, and the size of the habitats, all 15 microenvironments studied were important gathering places of the plants as sources of food for farmers in Konso and in preserving specific species. PE&RC Centre for Crop Systems Analysis (CSA) PE&RC Centre for Crop Systems Analysis (CSA) urn:nbn:nl:ui:32-d38dcabc-d919-432b-9bbb-8e647d5abf5c/obj 2026-03-20 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/0cdec10d-0848-42fe-8a7a-dce7b6e36292 2026-03-26 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-0cdec10d-0848-42fe-8a7a-dce7b6e36292 2026-03-26 urn:nbn:nl:ui:32-0cdec10d-0848-42fe-8a7a-dce7b6e36292/mods Genetic variation in the lettuce pangenome Wageningen University dgg van Workum F.J.M. 0000-0001-6247-5499 0000000529690225 aut D. de Ridder opn S. Smit opn M.E. Schranz opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 154 10.18174/681451 en Lettuce (Lactuca sativa L.) is an important and valuable leafy vegetable showing extensive morphological and genetic variation. However, due to constantly evolving pathogens and changing natural environments, there is a need for effectively harnessing the available natural variation in lettuce and its crop wild relatives (CWRs). This necessitates a pangenomic approach, going beyond the traditional reference-based analysis. This thesis therefore investigates current and future pangenomic approaches to summarising, analysing and harnessing the genetic variation of L. sativa and its CWRs.First, we assembled, annotated and analysed the first complete genome of Lactuca virosa in Chapter 2. Although the assembly is not chromosome-level, we show it is highly contiguous and complete. Lactuca virosa is characterised by its large genome size, which we found is caused by an expansion of long terminal repeats (LTRs). In addition, we identified several inversions with respect to Lactuca saligna and L. sativa, potentially hampering the introgression of genes from these regions.Next, we compiled a super-pangenome overview of L. sativa and its three most important CWRs: Lactuca serriola, L. saligna and L. virosa. In Chapter 3, we uncovered extensive presence/absence variation (PAV) of genes in lettuce: only about 50% of genes per accession is core Lactuca. The PAV of genes can be used as accurate genetic markers, which we showed through performing genome-wide association studies (GWAS) based on PAVs. We identified several non-reference peaks and we could trace likely introgression origins through the super-pangenome.While ultimately aiming to link genetic variation to phenotypic variation, targeting expression variation was the next logical step. Therefore, in Chapter 4, we developed the Lettuce Expression Browser (LEB). This is a resource compiling expression data of lettuce across tissues, species and conditions.Given the rate of sequencing of crop varieties and their wild relatives, it is crucial to prepare for a future where pangenomics is the standard, and many high-quality, comparable genomes are needed as input. To aid in the generation of such genomic resources (for lettuce, but also for other crops), we developed MoGAAAP in Chapter 5. MoGAAAP is a standardised modular workflow for the assembly, annotation and subsequent quality assessment of genomes.Finally, in Chapter 6, aiming to make large, complex pangenome graphs useful for practical (breeding) research, we developed an approach to study the genetic variation in a region of interest (ROI), such as a quantitative trait locus. It explores not only genomes in the pangenome, but also resequenced accessions by efficiently using information from the pangenome graph.Overall, this thesis provides a first pangenomic view of the genetic variation in the genus Lactuca focussing on accessions and traits relevant to lettuce breeding. While the approaches we discuss and develop are mostly applied to lettuce, they are generalisable to other (plant) pangenomes too. EPS Plant Physiology (PPH) Bioinformatics (BIF) EPS Plant Physiology (PPH) Bioinformatics (BIF) urn:nbn:nl:ui:32-0cdec10d-0848-42fe-8a7a-dce7b6e36292/obj 2026-03-26 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/184948b1-09c9-4d3e-99d2-ea76825a1910 2026-03-20 thesis

urn:nbn:nl:ui:32-184948b1-09c9-4d3e-99d2-ea76825a1910 2026-03-20 urn:nbn:nl:ui:32-184948b1-09c9-4d3e-99d2-ea76825a1910/mods Genomic diversity of a globally invasive crop pest, the fall armyworm Spodoptera frugiperda Wageningen University dgg Zhang Lei 0000000530070576 aut M. Eric Schranz opn Robin van Velzen opn Vera I.D. Ros opn Yutao Xiao opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 159 10.18174/681740 en The fall armyworm (Spodoptera frugiperda, FAW) is a highly destructive migratory pest native to tropical and subtropical regions of the Americas. Since its first detection in West Africa in 2016, FAW has rapidly expanded across Africa and Asia to Australia and New Zealand, and has recently reached southern Europe. Despite its rapid global spread, the genetic characteristics, invasion sources, and outbreak mechanisms of invasive FAW populations remain insufficiently understood. This thesis investigates the genomic diversity, invasion history, and microbial associations of global FAW populations using molecular markers and whole-genome sequencing approaches.Population genomic analyses based on resequencing data from native and invasive populations revealed strong genetic differentiation associated with the Tpi gene in native populations, whereas invasive populations exhibited high genetic homogeneity. The invasive populations were genetically closer to the American corn-strain populations, indicating that North and Central America are likely the primary sources of invasion. Comparative analyses of the full-length Tpi gene among representative FAW strains led to the development of improved molecular markers for strain identification. Application of these markers to Chinese populations showed the absence of the rice strain and a low frequency of the Zambia strain.Further analyses using expanded genomic datasets identified ancestry-informative markers distinguishing rice- and corn-strain populations. The invasive populations displayed a highly heterozygous genetic background and evidence of introgression from rice-strain lineages. Integrating molecular marker and whole-genome analyses suggests that invasive populations may have originated from a source population related to those from Suriname. In addition, microbiome analyses revealed variation in microbial community composition among FAW populations and identified several microbial pathogens with potential applications in biological control.Overall, this thesis expands genomic resources for FAW across both native and invasive ranges and provides new insights into the genetic structure, invasion origins, and microbial associations of this globally important pest, contributing to improved understanding and management strategies for FAW invasions. Biosystematics (BIS) PE&RC Virology (VIR) Biosystematics (BIS) PE&RC Virology (VIR) urn:nbn:nl:ui:32-184948b1-09c9-4d3e-99d2-ea76825a1910/obj 2026-03-20 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/d249479e-bf63-4269-832f-e2ff9fb0dcc0 2026-03-25 thesis

urn:nbn:nl:ui:32-d249479e-bf63-4269-832f-e2ff9fb0dcc0 2026-03-25 urn:nbn:nl:ui:32-d249479e-bf63-4269-832f-e2ff9fb0dcc0/mods 3D modelling of maize to design high-yielding ideotypes for future environments Wageningen University dgg Liu Fusang 0000000529785339 aut P.C. Struik opn X. Yin opn X.G. Zhu opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 234 10.18174/681829 en Global food security faces mounting pressure from population growth and climate change. Sustaining crop productivity under higher planting densities, elevated temperatures, and increasing resource limitations requires new strategies that transcend conventional breeding and static crop models. In maize, yield gains have historically relied on genetic improvement and intensified nitrogen inputs. Yet future performance will depend increasingly on complex genotype × environment × management (G × E × M) interactions, demanding predictive frameworks that integrate architecture, physiology, and genetics across scales.This thesis develops an integrative three-dimensional (3D) whole-plant modelling framework that mechanistically links canopy and root architectures, their spatial micro-environments, and genomic information to enable environment-specific ideotype design.The work began with a high-throughput virtual experimentation pipeline to quantify how canopy architectural variation shapes photosynthetic performance. Using 3D point-cloud–based organ segmentation and architecture perturbation, I explored variation in leaf area and angle and introduced canopy occupation volume (COV), a 3D metric describing how leaves occupy canopy space. COV outperformed conventional metrics such as leaf area index in explaining canopy photosynthetic capacity, providing a scalable criterion for architectural optimization.To capture physiological realism, the canopy model explicitly represented spatial heterogeneity in leaf nitrogen and temperature. SPAD measurements informed nitrogen distributions, a Bayesian framework parameterized C4 photosynthesis, neural radiance fields reconstructed 3D structure, and ray-tracing coupled with energy-balance modelling resolved local light and thermal environments. Simulations demonstrated that ignoring nitrogen heterogeneity biases canopy carbon gain estimates, while neglecting temperature heterogeneity—particularly under heat stress—substantially underestimates performance penalties. These findings highlight the necessity of spatially explicit physiology for evaluating genetic variation in canopy function.For the belowground system, I developed a high-throughput approach to quantify root anatomical traits and integrated them into a multi-scale root model linking genes to root-system function. Root occupation volume (ROV) emerged as a key architectural trait connecting root structure to resource uptake. Both simulations and experiments showed that lateral-root morphology strongly modulates nitrogen use efficiency. Greater lateral-root diversity increased ROV and improved nitrogen uptake efficiency with limited carbon cost, revealing a promising root ideotype.By coupling canopy and root modules within shared 3D micro-environments, I established the first fully integrated 3D whole-plant model linking realistic above- and below-ground architectures. Optimization across density × temperature scenarios revealed environment-specific trait combinations that maximize daily canopy photosynthesis per unit ground area. Importantly, productivity was not maximized by increasing COV or ROV independently; instead, optimal performance emerged from coordinated above–below ground occupation. Under high density and high temperature, optimized architectures increased simulated daily photosynthesis up to 3.6-fold relative to a reference genotype. Integration with multi-trait genomic selection further mapped these ideotypes to genetically realizable allele combinations.Overall, this thesis provides a unified 3D, whole-plant, genotype-to-phenotype framework that integrates high-throughput 3D phenotyping, spatially explicit canopy and root modelling, and genomic prediction to deliver mechanistic and genetically actionable insights for climate-adaptive maize ideotype design and to unravel complex G × E × M interactions. Library PE&RC Centre for Crop Systems Analysis (CSA) Library PE&RC Centre for Crop Systems Analysis (CSA) urn:nbn:nl:ui:32-d249479e-bf63-4269-832f-e2ff9fb0dcc0/obj 2026-03-25 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/bcc584f9-58d9-4070-b23f-7e32a7efbc37 2026-03-23 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-bcc584f9-58d9-4070-b23f-7e32a7efbc37 2026-03-23 urn:nbn:nl:ui:32-bcc584f9-58d9-4070-b23f-7e32a7efbc37/mods Agronomy of true potato seed-based cultivation pathways Wageningen University dgg van Dijk Luuk Christiaan Maria 408486953 0000-0001-8625-5247 0000000529774007 aut P.C. Struik opn W.J.M. Lommen opn M.E. de Vries opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 180 10.18174/680874 en The innovation of hybrid potato breeding on the diploid level comes with opportunities to re-design potato multiplication and cultivation systems. The conventional system has significant challenges regarding the multiplication of starting materials which happens clonally, belowground and comes with low multiplication rates, combined with a rapid pest and disease built-up. Moreover, the seed tuber infrastructure is cumbersome and costly due to the seed tuber’s bulky and perishable nature. In contrast, the multiplication of starting materials in the novel hybrid diploid systems gives the opportunity of sexual reproduction through the production of true potato seed (TPS) at very high rates, which are free from diseases, small in size, and not perishable. However, to utilise the opportunities of hybrid TPS to the maximum extent the potato cultivation system should be re-designed from seed-tuber grown crops to TPS-grown crops. This dissertation studied two novel TPS-based cultivation pathways for future seed or ware tuber production by using greenhouse-raised transplants or pelleted TPS for field-sowing.In the transplanting system, additional hilling of conventional ridges did not affect total tuber yields. However, hilled ridges resulted in higher tuber numbers compared with non-hilled ridges. In contrast, non-hilled ridges were able to produce more larger-sized tubers compared with maximum hilled ridges.A different timing of transplanting can influence final tuber yield. It was found that transplanting in early spring will increase the risk of crop and yield loss because of colder weather conditions and frost. Delayed transplanting resulted in lower marketable yields compared with transplanting in mid-spring. However, some experimental genotypes benefited more from the total length of the crop cycle rather than the transplanting date.Potato stem density manipulation can change total yield and more specifically the yield in various size classes. Transplant density trials showed that total yields of 107 Mg/ha were achieved by using a density of 200 plant/m2 in a 1.5 m wide bed-system. For commercial classes Baby Bakers and Seed Tubers maximum yields of 64 Mg/ha were recorded, which showed that transplanting seedlings at increased densities is a feasible way to produce seed tubers or tubers for potato outlets including smaller-sized tubers.Field sowing is another cultivation pathway to successfully produce a hybrid TPS potato crop as shown by dozens of trials over multiple seasons in this research. Total tuber yields of 50 Mg/ha or larger were measured in some trials, which makes field sowing of hybrid TPS a relevant pathway for future potato production. The field sowing pathway excludes a relevant share of labour and greenhouse costs associated with transplanting pathways, and avoids risks with transplants as vulnerable, living material.However, hybrid potato breeding should work on the introduction of traits associated with larger tuber sizes to boost yields and enhance the future acceptation of both novel cultivation pathways by potato growers particularly and the sector more generally. The introduction of improved potato genetics and TPS-materials will have a significantly larger impact for farmers and the livelihoods of rural people in Sub-Saharan Africa than in North-West Europe. PE&RC Centre for Crop Systems Analysis (CSA) PE&RC Centre for Crop Systems Analysis (CSA) urn:nbn:nl:ui:32-bcc584f9-58d9-4070-b23f-7e32a7efbc37/obj 2026-03-23 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/61f021f1-052d-494d-aba0-b06a02112d36 2026-03-20 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-61f021f1-052d-494d-aba0-b06a02112d36 2026-03-20 urn:nbn:nl:ui:32-61f021f1-052d-494d-aba0-b06a02112d36/mods For a circular future : Implementation of additive manufacturing and circularity in cities Wageningen University dgg Hernandez Valera Elias 0000000529774023 aut E. van Leeuwen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 211 10.18174/681203 en Currently, our cities operate under linear systems where resources are discarded after use. This reduces the capacity for resource recovery and decreases their value. Humanity is at a critical juncture as pollution and overexploitation reach tipping points. The adoption of new technologies and a circular approach is urgently needed to transition from linear to circular systems, reducing waste and fostering local, sustainable practices. Circular Additive Manufacturing (AM) promotes the creation of localized labs for the development of circular practices, contributing to sustainable transitions. This dissertation explores circular practices in AM, the urban context, and the importance of material recovery in cities. Chapters 2 and 3 reflect on the current state of AM worldwide, while Chapters 3 and 4 focus on the implementation of circular practices across different industries and within the AM innovation ecosystem. Chapter 5 presents multiple solutions for circular AM and the vision of creating a Circular AM Lab. This research provides a clear pathway for entrepreneurs, businesses, researchers, public institutions, and NGO’s to develop circular solutions through AM and create Circular AM Labs, promoting sustainable transitions driven by circular AM practices. WASS Urban Economics WASS Urban Economics urn:nbn:nl:ui:32-61f021f1-052d-494d-aba0-b06a02112d36/obj 2026-03-20 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/ffc049db-d3a3-4bc9-8eaf-3ac4465e9354 2026-03-23 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-ffc049db-d3a3-4bc9-8eaf-3ac4465e9354 2026-03-23 urn:nbn:nl:ui:32-ffc049db-d3a3-4bc9-8eaf-3ac4465e9354/mods On dynamics and stagnation in the use of varieties and improved seed of potato in Kenya Wageningen University dgg Atieno Elly Ouma 0000000529774015 aut P.C. Struik opn C.J.M. Almekinders opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 170 10.18174/680946 en Potato has evolved into a critical food, nutrition, and income security crop for smallholder farmers in Kenya. Substantial investments over the past two decades, have targeted productivity improvement through the introduction of improved varieties, rapid multiplication technologies, and decentralised seed production models. However, other persistent challenges including limited adoption of high-quality seed, weak market systems, inadequate regulatory enforcement, and recurrent pest and disease pressures continue to constrain sector growth. Despite sustained interventions, national yields remain stagnated at approximately 10 t/ha, far below attainable potential. The underlying drivers of this performance are insufficiently documented from a systems perspective. This thesis employed a mixed-methods research design that integrated qualitative and quantitative approaches to investigate historical, structural, technical, and behavioural determinants influencing seed system performance and productivity outcomes. Four research questions addressed: (i) sector drivers, constraints, and developmental trends over the past two decades; (ii) the effectiveness of rapid multiplication techniques for early-generation seed; (iii) the performance and sustainability of the decentralised seed multiplier (DSM) model; and (iv) tuber characteristics that farmer use in seed selection and their motivations for doing so. Findings reveal that a an overly emphasis on improving seed and varietal supply has expanded varietal diversity and increased private sector participation yet has not translated into meaningful smallholder productivity gains. Comparative analysis of rapid multiplication techniques (rooted apical cuttings, aeroponics, and sand hydroponics) showed substantial differences in multiplication efficiency, production costs, and commercial viability. Evaluation of the DSM model demonstrated that DSM and certified seed were comparable in performance better than farmer-saved seed, but long-term viability of this model is threatened by pests and disease outbreaks, weak market integration, and limited starter seed renewal. Examination of farmer seed choice behaviour identified 38 attributes prioritized by farmers, centred on characteristics associated with higher yields and income, with notable gender differences and recognition of certified seed benefits even among non-users. The study highlights that technological innovation alone is insufficient to drive meaningful growth in Kenya’s potato sector. Sustainable productivity gains require integrated and coordinated strategies that prioritize smallholder farmers, strengthen market and institutional frameworks, enhance regulatory and disease management capacity, and align innovation pathways with socio-economic and behavioural realities. A holistic, system-wide approach is essential to achieve resilient and equitable development of Kenya’s potato sector. PE&RC Centre for Crop Systems Analysis (CSA) PE&RC Centre for Crop Systems Analysis (CSA) urn:nbn:nl:ui:32-ffc049db-d3a3-4bc9-8eaf-3ac4465e9354/obj 2026-03-23 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/f54dd297-d837-4b7b-a3da-ec7a358dded1 2026-03-19 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-f54dd297-d837-4b7b-a3da-ec7a358dded1 2026-03-19 urn:nbn:nl:ui:32-f54dd297-d837-4b7b-a3da-ec7a358dded1/mods Tyrosine-based click chemistry to access potent anti-cancer antibody conjugates Wageningen University dgg Shajan Irene 0000-0002-2163-4606 0000000529774031 aut H. Zuilhof opn F.L. Delft opn B. Albada opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 147 10.18174/681300 en The work described in this thesis focuses on the development of chemoenzymatic methods to prepare targeted therapeutics based on monoclonal antibodies, with a particular focus on anticancer drugs, and includes preliminary biological evaluations. Given the ongoing pursuit of safer and more effective cancer treatments, antibody-based therapeutics have garnered significant attention within the biopharmaceutical industry. In particular the field of antibody-drug conjugates (ADCs) has obtained significant momentum, following the approval in 2011 of Adcetris®, and 13 more in the years following. Notably, whereas the first generation of ADCs were typically generated as a stochastic mixture of compounds with an average loading of payloads (typically around 4), recent years have shown an increasing trend toward site-specific modification of therapeutic antibodies with a higher drug-to-antibody ratio (DAR). Currently two such high DAR ADCs Enhertu® and Trodelvy®, both DAR8 have received market approval, and a multitude of others are in various stages of clinical trials. Besides, there is an increasing variety of ADC formats, based on different payload mode-of-action (MOA), linker chemistries, antibody formats (in particular bispecific antibody conjugates) and other variants.In this thesis, we explored the generation of different classes of antibody conjugates for cancer therapy, utilizing strain-promoted oxidation-controlled ortho-quinone (SPOCQ) cycloaddition as a key bioconjugation strategy. Our modular chemoenzymatic approach provided access to DAR2 ADCs, dual-payload ADCs, and two formats of bispecific T cell-engagers. In the context of this thesis, we were primarily interested in generating antibody conjugates from native antibodies. To this end, native IgG1 was sequentially treated with PNGase F, to deglycosylate N297, and mushroom tyrosinase (mTyr) in the presence of a strained alkyne (here BCN), enabling selective modification of one of the two tyrosine residues proximal to N297 (i.e., Y296 or Y300). These chemoenzymatic reactions facilitated the installation of a chemical handle on the antibody, which was subsequently functionalized with appropriately labeled cytotoxic agents or proteins with complementary biological functions to yield site-specific antibody conjugates. VLAG Organic Chemistry VLAG Organische Chemie urn:nbn:nl:ui:32-f54dd297-d837-4b7b-a3da-ec7a358dded1/obj 2026-03-19 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/497c8ee0-9b06-4002-b02b-df677ae79239 2026-03-19 thesis

urn:nbn:nl:ui:32-497c8ee0-9b06-4002-b02b-df677ae79239 2026-03-19 urn:nbn:nl:ui:32-497c8ee0-9b06-4002-b02b-df677ae79239/mods Adapting to climate change, does it work? : Effects of climate change and adjusted management on biodiversity of roadside grasslands Wageningen University dgg Bakker Wiene 0000000529770911 aut D. Kleijn opn P. Vergeer opn J. Scheper opn W. Ozinga opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 126 10.18174/681555 en This research investigates the drivers of biodiversity decline in semi-natural grasslands, particularly Dutch roadside grasslands, and potential management adjustments to mitigate their effects. Analyses of vegetation change (2004-2020) revealed that winter warming, especially under high nitrogen deposition, was a major driver of plant diversity loss and community shifts. Winter warming promoted competitive species, particularly grasses, through extended growing seasons and increased biomass production, disadvantaging non-competitive species, especially forbs. Concurrent shifts in management, in productive sites particularly a reduced mowing frequency, likely further contributed to this decline. In contrast, summer drought events generally reduced the competitive dominance of tall perennial species, creating opportunities for subordinate species. However, benefits were not observed for species of conservation concern and were more short-lived (and thus overall weaker) than the effects of winter warming.A field experiment applying management adjustments demonstrated that increasing mowing frequency from once to twice per year and delaying the final cut substantially restored plant diversity, vegetation composition, and aboveground biomass to near pre-climate-change levels in productive roadside grasslands. Delayed mowing also enhanced arthropod biomass regardless of site productivity, and the increased mowing frequency supported ground-dwelling arthropods and early-season pollinators in productive roadside grasslands, although mowing created temporary resource gaps, indicating the importance of phased implementation of mowing regimes.Together, these findings identify winter warming as an overlooked driver of grassland biodiversity loss and demonstrate that altered mowing regimes can effectively counteract its impacts. PE&RC Plant Ecology and Nature Conservation PE&RC Plantenecologie en Natuurbeheer urn:nbn:nl:ui:32-497c8ee0-9b06-4002-b02b-df677ae79239/obj 2026-03-19 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/dd001905-0bc0-484e-9a84-68ab79c3af39 2026-03-16 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-dd001905-0bc0-484e-9a84-68ab79c3af39 2026-03-16 urn:nbn:nl:ui:32-dd001905-0bc0-484e-9a84-68ab79c3af39/mods Design of multi coverage path-planning for collaborative manure-removing robots in dairy barns Wageningen University dgg Ponce Pacheco Luis Angel 0000000530061645 aut G.W. Kootstra opn C. Sun opn M. Derks opn C. Lokhorst opn W. Ouweltjes opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 99 10.18174/680247 en Maintaining clean barn floors is essential for dairy farms to ensure animal welfare, reduce disease, and meet environmental regulations. As herd sizes grow and labor availability declines, many farms have adopted autonomous manure-removing robots (MrRs). However, these robots typically operate in isolation, limiting their effectiveness in large or complex barns. This project explores how multiple MrRs can work together to improve cleaning efficiency while minimizing disruption to animals. The primary focus is on optimizing multi-robot coordination through effective task allocation and complete coverage path-planning (CCPP), while minimizing disturbances to cows and maximizing cleaning efficiency. Key challenges included managing cow movement, avoiding robot-cow collisions, distributing cleaning workloads fairly, and ensuring full area coverage without redundancy. Given the ethical and logistical difficulties of real-world experimentation, the study was conducted entirely through advanced simulation. Using the Boderc design methodology, a structured process was followed to identify stakeholder needs, translate them into system requirements, and evaluate potential solutions. A simulation tool was developed to model realistic barn scenarios, including cow behavior and robot interactions. Various coordination strategies, such as splitting the barn into smaller zones or dynamically assigning tasks, were implemented and tested. The results highlight trade-offs between robot efficiency, predictability, and animal welfare. Some strategies improved cleaning speed but increased stress on cows, while others reduced collisions but led to more dirtiness in the barn. These insights provide actionable guidance for robot developers, farm managers, and researchers interested in deploying collaborative robotic systems in agriculture. This work delivers a validated simulation framework and a set of tested strategies that can support future development of intelligent, animal-friendly, and scalable robotic cleaning solutions for dairy farms. v Agricultural Biosystems Engineering (ABE) Animal Health & Welfare Emissions & Manure Valorisation Agricultural Biosystems Engineering (ABE) Dierenwelzijn en gezondheid Emissie & Mestverwaarding urn:nbn:nl:ui:32-dd001905-0bc0-484e-9a84-68ab79c3af39/obj 2026-03-16 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/e7ec8010-200b-4495-969f-516da491f361 2026-03-14 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-e7ec8010-200b-4495-969f-516da491f361 2026-03-14 urn:nbn:nl:ui:32-e7ec8010-200b-4495-969f-516da491f361/mods Design, analysis and implementation of synthetic carbon fixation pathways Wageningen University dgg Rainaldi Vittorio 0000000529770903 aut N.J. Claassens opn S. D'Adamo opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 182 10.18174/681570 en Biological carbon fixation is a fundamental process sustaining life on Earth, yet it is constrained by the efficiency and diversity of naturally occurring metabolic pathways. Rising global challenges such as climate change and the demand for sustainable bioproduction have renewed interest in rethinking carbon assimilation at the molecular level. This thesis explores the design, discovery, and contextualization of new and hidden metabolic routes for carbon fixation and assimilation. Through computational pathway design, experimental implementation, evolutionary discovery, and biotechnological assessment, it highlights how synthetic and natural metabolism can be expanded to unlock new opportunities for sustainable production of chemicals and food.Chapter 1 provides a general introduction to the topic of metabolism and carbon fixation starting from thermodynamics and biochemistry while also examining existing carbon fixation pathways and methods for pathway design.Chapter 2 begins with the rational design and experimental validation of the reductive methylaspartate cycle (rMASP), a novel ATP-efficient aerobic CO2 fixation pathway. Four rMASP variants producing glyoxylate or acetyl-CoA were computationally analyzed, and a modular engineering approach was used to reconstitute these modules in Escherichia coli. Growth-coupled selection and isotopic labeling confirmed module activity in vivo, building on and expanding previous research in the field.Chapter 3 expands the search space for new carbon fixation pathways. Using a bioretrosynthetic approach informed by enzyme promiscuity and the latent biochemical reaction space, eight novel pathway designs were identified and evaluated in comparison with both natural and previously proposed synthetic cycles. Thermodynamic, stoichiometric, and kinetic analyses revealed potential advantages over the Calvin-Benson-Bassham cycle, while also underscoring the importance of enzyme engineering for pathway realization. This work systematically broadens the landscape of candidate pathways for future CO2 fixation strategies.Chapter 4 then turns to evolutionary innovation in metabolism, showing how enzyme promiscuity can give rise to new biochemical functions. Using a strain of E. coli lacking canonical isoleucine biosynthesis, experimental evolution uncovered a previously unknown route dependent on the reactivation of acetohydroxyacid synthase II. This enzyme was shown to catalyze a novel condensation reaction between glyoxylate and pyruvate to form 2-ketobutyrate, establishing a recursive pathway to isoleucine. Unlike earlier “underground” isoleucine pathways, this one uses central metabolites under aerobic conditions, suggesting a potential role in natural E. coli metabolism and extending the known biosynthetic space of amino acids.Chapter 5 situates these findings within the emerging field of synthetic C1 metabolism, where methanol, formate, hydrogen, and CO2 are explored as sustainable feedstocks for microbial bioproduction. A comparative analysis of natural and synthetic pathway architectures highlights progress toward growth rates and biomass yields that rival or exceed those of natural C1-assimilating organisms. Remaining challenges for industrial application are identified, including the need to optimize product spectra, titers, and yields, as well as to expand host organism versatility.Chapter 6 examines the whole thesis work in the broader context of scientific, social, political and economic challenges. VLAG Microbial Synthetic Genetics and Metabolism Microbiology VLAG Microbial Synthetic Genetics and Metabolism Microbiology urn:nbn:nl:ui:32-e7ec8010-200b-4495-969f-516da491f361/obj 2026-03-14 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/d48cefea-74db-4f05-aa33-1dd584d3672f 2026-05-18 thesis

urn:nbn:nl:ui:32-d48cefea-74db-4f05-aa33-1dd584d3672f 2026-05-18 urn:nbn:nl:ui:32-d48cefea-74db-4f05-aa33-1dd584d3672f/mods Pesticide use in Bangladesh: farmers perceptions, and implications for soil health and foodsafety Wageningen University dgg Akter Mousumi 0000000529735294 aut V. Geissen opn X. Yang opn E. Huerta Lwanga opn H. Mol opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 171 10.18174/680839 en Worldwide, expanded pesticide use has reduced crop losses and boosted agricultural productivity by controlling insects, pathogens, and weeds. However, these gains have raised concerns about food safety, environmental contamination, and human health. Misuse, overapplication, and weak regulation intensify these risks, especially in developing countries with limited monitoring. In Bangladesh, pesticide use has risen sharply in intensive vegetable farming. Economic pressure drives frequent spraying beyond recommended doses. Although farmers are generally aware of hazards, safety measures during handling and storage are often neglected, leading to soil degradation, contaminated produce, and health risks for farmers and consumers.This thesis investigates three interconnected dimensions of pesticide use and environmental risk in vegetable farming systems in northern Bangladesh. First, it examines farmers’ knowledge, attitudes, and practices regarding insecticide use and associated health implications. The findings reveal that education level, age, farming experience, and access to training significantly influence protective behaviours. Younger and better-educated farmers are more likely to follow safety guidelines, whereas older farmers—who often dominate rural agriculture due to youth migration—tend to rely on habitual practices and peer advice. Unsafe behaviours such as mixing pesticides by hand, storing chemicals inside homes, and discarding empty containers in open fields remain common. Despite awareness of potential health and environmental impacts, over-application persists, particularly in high-value crops such as eggplant, chilli, and tomato. The results highlight a critical gap between awareness and implementation, underscoring the need for participatory, community-based training and improved risk communication strategies.Second, the thesis evaluates the persistence and movement of obsolete organochlorine insecticides in the terrestrial food chain. Although banned decades ago, residues of compounds such as DDT, HCHs, aldrin, endosulfan, chlordane, heptachlor, chlordecone, mirex, and hexachlorobenzene were detected in soil, vegetables, and cow’s milk. Subsoil often contained higher concentrations than surface soils, indicating long-term persistence and limited degradation. While most detected levels were below international Maximum Residue Limits, the co-occurrence of multiple residues in single food items raises concerns regarding cumulative exposure. Potential contamination sources include historical use, and illegal marketing of banned pesticides. These findings emphasize the importance of regular residue monitoring, strict enforcement of regulations, and comprehensive risk assessments that consider chronic low-dose exposure.Third, the ecological component investigates the impacts of widely used insecticides cypermethrin, imidacloprid, and chlorantraniliprole on non-target soil biota, the anecic earthworm Lumbricus terrestris. Experimental findings demonstrate that earthworm activity plays a critical role in regulating pesticide mobility within soil profiles. Imidacloprid exhibited the highest toxicity and mobility, while insecticide mixtures significantly enhanced vertical biogenic transport through burrow networks. Pesticide residues were consistently higher in burrow linings than in adjacent bulk soil, especially at depths of 15–30 cm, confirming that earthworm-mediated biogenic transport can facilitate deeper soil contamination, a pathway often underestimated in conventional leaching models.Overall, this study reveals the complex interplay between farmer behaviour, chemical persistence, and ecological processes in shaping pesticide-related risks. It calls for integrated governance approaches combining farmer education, regulatory strengthening, ecological risk assessment, and sustainable agricultural practices to safeguard environmental and public health in Bangladesh. WIMEK Soil Physics and Land Management WIMEK Bodemfysica en Landbeheer urn:nbn:nl:ui:32-d48cefea-74db-4f05-aa33-1dd584d3672f/obj 2026-05-18 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/72e08a49-6fb8-4f8f-8c75-189d1a79c677 2026-03-12 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-72e08a49-6fb8-4f8f-8c75-189d1a79c677 2026-03-12 urn:nbn:nl:ui:32-72e08a49-6fb8-4f8f-8c75-189d1a79c677/mods From light signals to sediment pathways : developing luminescence as a sediment tracing tool Wageningen University dgg de Boer Anna Maartje 0000000529677901 aut J. Wallinga opn B.C. van Prooijen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 203 10.18174/681304 en The Netherlands has a long history of living with the sea, a challenge that is intensifying under climate change. The Wadden Sea, a UNESCO World Heritage site with unique ecosystems and landscapes, is particularly vulnerable. Protecting the coast while preserving this fragile environment requires understanding how sand moves along and across tidal channels and beaches. One common approach to keep up with (local) erosion is sand nourishment: adding sand to the coast and letting natural forces reshape the shoreline. Yet, how this added sand mixes with native sediments has remained largely unknown. This thesis introduces a novel method to trace sand movement using luminescence which is a property of sand grains that records their light exposure history. By measuring these luminescence signals in individual sand grains, it is possible to get insight into sediment pathways and dynamics in complex coastal environments. The method was developed by optimizing luminescence imaging techniques (EMCCD camera), performing field experiments to quantify the in-situ subaqueous bleaching of the luminescence signals and by applying the method to the Ameland Inlet in the Dutch Wadden Sea. PE&RC Soil Geography and Landscape PE&RC Bodemgeografie en Landschap urn:nbn:nl:ui:32-72e08a49-6fb8-4f8f-8c75-189d1a79c677/obj 2026-03-12 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/6bd7c789-f7ce-4f89-b3c5-768c54e6834f 2026-03-09 thesis

urn:nbn:nl:ui:32-6bd7c789-f7ce-4f89-b3c5-768c54e6834f 2026-03-09 urn:nbn:nl:ui:32-6bd7c789-f7ce-4f89-b3c5-768c54e6834f/mods Sustainability in vertical farming across scales : from crop to city Wageningen University dgg Karpe Margarethe Sophie 0000000529706952 aut L.F.M. Marcelis opn E. Heuvelink opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 243 10.18174/681920 en In future cities, indoor vertical farms may play a key role in growing fresh greens and some fruit crops. These systems use electric rather than solar light, requiring much energy. However, they are highly efficient in the use of land, water and nutrients, and in principle no pesticides need to be applied. In my research, I applied various methods to assess vertical farm sustainability at crop-, farm-, and city-scale: I conducted trials on plant spacing and far-red lighting for tomatoes, achieving improved crop yield and quality. I also calculated and discussed carbon footprints of vertical farms, emphasizing the need for clean energy. Finally, I gathered expert views on urban farming’s sustainability and potential, showing that perceived environmental benefits drive the expansion of vertical farms. Horticulture and Product Physiology (HPP) PE&RC Horticulture and Product Physiology (HPP) PE&RC urn:nbn:nl:ui:32-6bd7c789-f7ce-4f89-b3c5-768c54e6834f/obj 2026-03-09 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/2e4c80e7-ec28-4ba7-b390-935b957b2ac9 2026-05-18 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-2e4c80e7-ec28-4ba7-b390-935b957b2ac9 2026-05-18 urn:nbn:nl:ui:32-2e4c80e7-ec28-4ba7-b390-935b957b2ac9/mods Towards “set-in-stone” co-deployment of enhanced rock weathering and biochar : an experimental study on their CO2 removal and agronomic co-benefits Wageningen University dgg te Pas Emily E.E.M. 0000000529691084 aut R.N.J. Comans opn M. Hagens opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 253 10.18174/681512 en To limit global temperature rise well below 2⁰C, Carbon Dioxide (CO2) Removal (CDR) strategies, such as Enhanced Rock Weathering (ERW) and biochar, are urgently required. Besides CDR, ERW releases nutrients and trace metals, while biochar surfaces may bind these weathering products. The main objective of this research was to experimentally study whether and through which processes ERW, and biochar co-deployment, can promote carbon sequestration, while limiting trace metal risks and providing agronomic co-benefits. A soil column experiment showed a high enhanced weathering potential for the mineral wollastonite, while the potential of olivine was limited by its nickel release. Two greenhouse pot experiments revealed that biochar co-deployment can reduce these trace metal risks. A two-year lysimeter field experiment showed that the increase in soil pH was the main agronomic co-benefit of ERW. While the potential CDR of ERW was substantial, the actual CDR observed was limited by soil retardation mechanisms. WIMEK Soil Chemistry WIMEK Soil Chemistry urn:nbn:nl:ui:32-2e4c80e7-ec28-4ba7-b390-935b957b2ac9/obj 2026-05-18 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/d25a011d-3f67-4c14-bcc5-c1e1cbbf3638 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-d25a011d-3f67-4c14-bcc5-c1e1cbbf3638 2026-04-02 urn:nbn:nl:ui:32-d25a011d-3f67-4c14-bcc5-c1e1cbbf3638/mods Post-COVID in primary care : evaluation of allied healthcare and dietary treatment Wageningen University dgg Slotegraaf A.I. 0000-0001-7162-5348 0000000492249769 aut M.A.E. de van der Schueren opn E.J.M. Feskens opn H.M. Kruizenga opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 254 10.18174/681563 en The global COVID-19 pandemic had a major impact on physical and mental health, and healthcare use. Although the pandemic is over, some people continue to experience persistent complaints after COVID-19, also known as post-COVID. This thesis describes the recovery trajectories and experiences with primary care allied healthcare among people with persistent complaints, with specific focus on support from primary care dietitians. The findings show that people receiving primary care allied healthcare made clinically relevant progress, but continued to report persistent complaints. The course of persistent complaints is difficult to predict, and the typical post-COVID patient does not seem to exist. Primary care allied healthcare professionals play an important role in providing mental support, helping patients cope with complaints, feeling heard, and acceptance. Dietitians are crucial in the management of post-COVID as malnutrition, low fat-free mass, nutrition-related complaints, and an increased risk of sarcopenia are common. A patient-centred approach is essential for successful (dietary) treatment. VLAG Global Nutrition VLAG Wereldvoeding urn:nbn:nl:ui:32-d25a011d-3f67-4c14-bcc5-c1e1cbbf3638/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/699b6bd9-0a75-42ef-81a4-a58f811c50d7 2026-05-18 thesis

urn:nbn:nl:ui:32-699b6bd9-0a75-42ef-81a4-a58f811c50d7 2026-05-18 urn:nbn:nl:ui:32-699b6bd9-0a75-42ef-81a4-a58f811c50d7/mods Understanding fire resilient landscapes across science and practice Wageningen University dgg Newman Thacker Fiona E. 0000000529746508 aut C.R. Stoof opn C. Ritsema opn H.M. Bartholomeus opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 211 10.18174/681778 en Wildfires are a natural ecological process, but in recent decades extreme wildfire events have been increasing around the world, with associated negative consequences. Concurrently, years of wildfire suppression policies have left many ecosystems in a fire deficit, also resulting in negative environmental consequences.This thesis looks towards the concept of fire resilient landscapes as a contributing solution to the current wildfire crisis. In this research, the need for fire resilient landscapes is outlined by exploring suffering linked both with extreme wildfires, but also with a lack of fire. This research then provides a holistic definition of fire resilient landscapes from a socio-ecological perspective, and explores the application of this definition with two case studies from Spain and the Netherlands. Finally, two methodologies are utilised to assess specific case study sites across the Americas and Europe in terms of their fire resilience. PE&RC Soil Physics and Land Management PE&RC Bodemfysica en Landbeheer urn:nbn:nl:ui:32-699b6bd9-0a75-42ef-81a4-a58f811c50d7/obj 2026-05-18 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/6396a374-0da5-480e-b181-168c5174a15e 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-6396a374-0da5-480e-b181-168c5174a15e 2026-04-02 urn:nbn:nl:ui:32-6396a374-0da5-480e-b181-168c5174a15e/mods Rational design of dry fractionation : a deconvoluted approach Wageningen University dgg Wetterauw Koen 0009-0001-3065-7615 0000000529714522 aut Maarten A.I. Schutyser opn Remko M. Boom opn Erik van der Linden opn Paul Venema opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 214 10.18174/681811 en The transition towards an environmentally sustainable diet necessitates the consumption of plant-based foods. Ingredients for such foods are often isolated via aqueous separation processes and energy intensive drying steps to obtain a powder. A more sustainable alternative is the dry milling of seeds into a flour, from which different components such as starch and protein can then be sorted into enriched fractions using technologies that separate in air instead of in water. However, switching to such processes requires clear understanding of how to operate them to reach specific compositions or ingredient properties in general. Optimization is typically required when changing the seed or the equipment, which can pose a costly hurdle.Therefore, the aim of this thesis was to identify and control the critical aspects that drive efficient dry fractionation of grains and legumes, by establishing generic relations that quantify how the microstructure of seeds and the settings of dry separation processes affect the composition of resulting ingredients. This is achieved through a combination of experiments involving various raw materials and model development.The first research chapter compares how three different dry fractionation technologies, namely sieving, air classification and electrostatic separation, recover starch-rich endosperm fragments from a malted barley side-stream that was rich in husk. All technologies could achieve similar purities, with air classification resulting in the best yields. The next two chapters then establish how air classification performance is affected by microstructures that contain oil, as present in a maize germ side stream and chickpea, and how pressing, solvent extraction or the addition of silica flow aids can be used to restore the separation. Based on these microstructural insights, the final research chapter develops a generic model links the size of particles in starch-rich, low-oil pulse flours to a specific composition, and shows that this enables prediction of the composition of air-classified ingredients, as function of operating settings. The model was verified for adzuki bean, faba bean, mung bean and yellow pea. In the general discussion, this model is also used to reflect on the findings for oil-rich systems, and gives directions to also predict component separation by electrostatic separation.The findings are then placed in the context of using less refined ingredients to produce more sustainable plant-based foods, to which this work contributed by mapping the composition space that is accessible via dry fractionation, using mechanistic relations between key seed characteristics and process settings. Food Process Engineering VLAG Food Process Engineering VLAG urn:nbn:nl:ui:32-6396a374-0da5-480e-b181-168c5174a15e/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/f6ce7763-8e0d-4a18-95b1-f535164c8d3e 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-f6ce7763-8e0d-4a18-95b1-f535164c8d3e 2026-04-02 urn:nbn:nl:ui:32-f6ce7763-8e0d-4a18-95b1-f535164c8d3e/mods Rational design of ruthenium complexes: P,Arene-Chelation and Anion effects in bond activation and catalysis Wageningen University dgg Zhou Yifei 0000000529660667 aut H. Zuilhof opn F. Miloserdov opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 191 10.18174/681293 en This dissertation explores the rational design of ruthenium complexes with a focus on how ligand architecture and anion identity affect bond activation and catalytic performance. Two complementary strategies are developed: stabilization of low-valent Ru(0) species through P,arene-chelation, and modulation of Ru(II)-catalyzed asymmetric hydrogenation via sulfonate anions.Ruthenium(0) complexes exhibit exceptional potential for atom-economical transformations and inert bond activation, yet their practical use is severely limited by the intrinsic conflict between high reactivity and poor stability, particularly in phosphine-based systems prone to cyclometalation. In Chapter 2, a novel carbonyl-free phosphine-based Ru(0) complex, Ru(BINAP)(PPh₃), is designed and synthesized via dehydrohalogenation. Structural characterization reveals a unique P,arene-chelation mode in which one phosphine donor and a naphthalene moiety from the BINAP ligand simultaneously coordinate to the Ru(0) center. This hemilabile coordination confers remarkable thermal stability while preserving high reactivity. The complex behaves as a “masked” 16-electron species, readily undergoing ligand exchange with alkenes and dienes, and enabling the activation of C–H, N–H, and even inert C–N bonds under mild conditions. These findings demonstrate a viable strategy to reconcile stability and reactivity in phosphine-based Ru(0) chemistry.In Chapter 3, the P,arene-chelation concept is extended to biaryl monophosphine ligands, including MOP and Buchwald-type ligands. A practical one-pot synthetic route to Ru(0) complexes from [Ru(p-cymene)Cl₂]₂ using Zn/LiCl as a mild reductant is developed. Comparative studies reveal how subtle differences in ligand topology and electronic properties dramatically influence coordination behavior and bond activation pathways, offering new insights into the structure–reactivity relationships of low-valent ruthenium complexes.Beyond neutral ligand design, this work also addresses the often-overlooked role of anionic ligands in catalysis. Chapter 4 systematically investigates sulfonate anions (OMs⁻, OTs⁻, and OTf⁻) in Ru(II)-BINAP-catalyzed asymmetric hydrogenation. A facile one-pot synthesis of Ru(diphosphine)-bis-sulfonate complexes is established. These catalysts exhibit enhanced activity and robustness compared to conventional acetate analogues, underscoring the critical influence of weakly coordinating, highly labile anions on catalytic performance.Collectively, this dissertation demonstrates that both coordinating and anionic ligands can be deliberately engineered to control the delicate balance between stability, reactivity, and selectivity in ruthenium catalysis. The concepts developed herein provide new design principles for low-valent and cationic ruthenium complexes, contributing to the broader goal of advancing practical, efficient, and sustainable transition-metal catalysis. VLAG Organic Chemistry VLAG Organische Chemie urn:nbn:nl:ui:32-f6ce7763-8e0d-4a18-95b1-f535164c8d3e/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/a7c3ebf9-9532-4428-bde8-3efd2edf6aa1 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-a7c3ebf9-9532-4428-bde8-3efd2edf6aa1 2026-04-02 urn:nbn:nl:ui:32-a7c3ebf9-9532-4428-bde8-3efd2edf6aa1/mods Step by step: a healthy dietary start for mothers and children: exploration and development of an mHealth dietary support tool for the first 1,000 days Wageningen University dgg Faessen Janine P.M. 0000000529702580 aut Edith J.M. Feskens opn Elske M. Brouwer-Brolsma opn Desiree A. Lucassen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 366 10.18174/681402 en A healthy diet during the first 1,000 days—from conception to a child’s second birthday—is critical for both maternal and child’s health. However, current dietary status is yet suboptimal in the first 1,000 days. This thesis details the exploration and development of a dietary support app designed through a user-centred approach.The research began by establishing a measurement tool, the Dutch Healthy Diet for pregnant women index, which proved to be a reliable method for assessing dietary status during gestation. Subsequent evaluations of the current dietary support revealed shortcomings in available pregnancy apps. An analysis of 57 existing pregnancy apps found a lack of expert involvement and scientific evaluation, with limited interactive features and many providing information inconsistent with national guidelines. Additionally, surveys and interviews with healthcare professionals highlighted that barriers like limited time and knowledge prevent them from providing dietary guidance to postpartum women.We also acquired much input from target users to understand their experiences and needs regarding diet and dietary support. Studies involving over 1,600 women identified physical discomfort during pregnancy and time constraints postpartum as primary barriers to healthy eating. Women expressed a strong desire for a non-judgmental, science-based digital tool that offers practical strategies like meal planning and personalized goal setting.Using these insights, the first prototype of the PRISTA app was developed, featuring diet quality assessment using the Eetscore diet screener, tailored feedback based on self-determined goals and the option to monitor progress. Usability testing through "think-aloud" interviews indicated moderate to good satisfaction in app use. Participants suggested refinements to e.g., goal setting, icon clarity and progress tracking, which were integrated into subsequent iterations to enhance the user experience.The thesis also explored broader aspects of the first 1,000 days. Focusing on preconception, research into the link between diet and fertility highlighted the complexity of this period, noting that higher diet quality was unexpectedly associated with decreased pregnancy chances in the studied group. Additional studies regarding infant feeding were performed. Investigations into breast and bottle feeding experiences revealed a need for practical and social support and the reduction of stigma, particularly regarding bottle feeding. A pilot of the Caring Bites program showed promise in improving maternal confidence and skills during the introduction of solid foods, though it highlighted a potential need for greater partner involvement.This thesis demonstrates that mHealth apps are promising tools for dietary support when they are grounded in user needs and evidence-based science. Future efforts must focus on inclusivity, specifically reaching women with lower educational levels, and integrating these tools into standard clinical care. By leveraging artificial intelligence for personalization and ensuring strict regulatory oversight for accuracy, digital interventions can provide the trustworthy, tailored support families need during this foundational life stage. VLAG Global Nutrition VLAG Wereldvoeding urn:nbn:nl:ui:32-a7c3ebf9-9532-4428-bde8-3efd2edf6aa1/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/0fc17420-1e52-4277-a583-fe27aa1ab21f 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-0fc17420-1e52-4277-a583-fe27aa1ab21f 2026-04-02 urn:nbn:nl:ui:32-0fc17420-1e52-4277-a583-fe27aa1ab21f/mods Revealing dynamics of individual mucin glycan utilisation by gut bacteria : The interaction between dietary- and mucin glycans and the intestinal bacteria Wageningen University dgg de Ram Carol 0000000529687034 aut H.A. Schols opn C. Belzer opn G.J.E.J. Hooiveld opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 331 10.18174/681627 en Human intestinal health is impacted by the interaction between bacteria residing in the intestine and available glycans from diet and host. Analysis of microbial composition in relation to glycan degradation and utilisation in the gut can help to understand the mechanisms practiced by the bacteria to use mucin glycans and reside in the mucosal surface of the gut.For this purpose, a robust and reliable method was set up and validated during this thesis for the analysis of intact O- and N-glycans by MALDI-TOF MS and PGC-LC-MS/MS. Using this method, the impact of pasteurised bacteria A. muciniphila, B. fragilis, and R. gnavus on glycosylation in in vitro mucus produced by HT29-MTX-E12 cells revealed an increase in sialylated O-glycans and high-mannose N-glycans. Next, the degradation of glycans by prominent intestinal bacteria A. muciniphila, R. torques, and B. thetaiotaomicron was investigated by incubation of the bacteria in monocultures, co-cultures, and a synthetic community on porcine gastric mucin (PGM). R. torques favoured degradation of fucosylated O-glycans and A. muciniphila and B. thetaiotaomicron equally favoured degradation of fucosylated and non-fucosylated O-glycans. The three bacteria favoured degradation of first core 2 O-glycan structures relative to core 1 O-glycan structures. A. muciniphila, R. torques, and B. thetaiotaomicron partially degraded N-glycans and these were only completely degraded by the synthetic community. Enzyme extracts from the bacterial growth experiment were incubated with human milk oligosaccharides, sulphated glycan structures, and O-glycans removed from PGM and bovine submaxillary glands mucin (BSM) to investigate cleavage of specific glycan linkages and structures. Proteomics was performed to characterise produced enzymes and these results were linked together to reveal favoured cleavage of beta1-4 linked Gal, beta1-3 linked GlcNAc, alpha1-2 linked Fuc, and alpha2-6 linked Sia by A. muciniphila, degradation of all tested linkages except sulphate by R. torques, and favoured cleavage of beta1-4 linked Gal and alpha2-6 linked Sia by B. thetaiotaomicron. Incubation of a synthetic community, consisting of mucin glycan degraders and cross-feeders, on different mucin types revealed a high relative abundance of A. muciniphila, R. gnavus, R. torques, and Faecalibacterium duncaniae when grown on PGM. Addition of sialylated structures to PGM resulted in an increase in relative abundance of A. muciniphila and a decrease in relative abundance of Ruminococcus spp. Incubation of A. muciniphila, R. torques, and B. thetaiotaomicron on galacto-oligosaccharides (GOS) + PGM resulted in increased GOS degradation by A. muciniphila, decreased GOS degradation by R. torques, and minimal influence on GOS degradation by B. thetaiotaomicron. GOS and PGM O-glycans were simultaneously degraded by the co-cultures illustrating the need for a diverse bacterial community to degrade and utilise all available carbohydrate resources.The results presented in this thesis show new insights in understanding the mechanisms of glycan degradation by prominent gut bacteria. The tested bacteria differently degrade and utilise mucin glycans and the bacteria demonstrate unique interactions in co-culture and as part of a synthetic community. VLAG Nutrition, Metabolism and Genomics Microbiology Food Chemistry VLAG Voeding, Metabolisme en Genomica Microbiology Levensmiddelenchemie urn:nbn:nl:ui:32-0fc17420-1e52-4277-a583-fe27aa1ab21f/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/6f8c7da0-35c2-4e04-986d-f69077c9e0c1 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-6f8c7da0-35c2-4e04-986d-f69077c9e0c1 2026-04-02 urn:nbn:nl:ui:32-6f8c7da0-35c2-4e04-986d-f69077c9e0c1/mods From curvy hens to the laying curve : The influence of dietary strategies on body composition and laying persistency in hens Wageningen University dgg van Eck Lieske 0000000529691113 aut R.P. Kwakkel opn H. Enting opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 327 10.18174/681766 en With a growing world population, eggs are an important and affordable nutrient source to nourish the world. The lifetime egg production capacity of laying hens has increased tremendously, with production targets currently extending to 600 eggs at 120 weeks of age. To sustain this laying persistency, nutrition is crucial to support the hen and provide the right nutrients for egg formation. In general, three key physiological systems are critical for maintaining laying persistency. These are discussed in detail in Chapter 2, but can be briefly summarized: (1) the oviduct and ovary are needed to produce the eggs, (2) the liver metabolizes most of the egg nutrients and (3) body adipose tissue, through its purpose to maintain energy homeostasis. Moreover, adipose tissue might influence the hens reproductive capacity, as it also functions as endocrine tissue.This thesis aimed to understand how dietary energy and amino acids intake, from rearing to laying, influence body composition and metabolic processes, to support long-term egg production. It was hypothesized that (1) amino acid and energy intake during rearing have long-term effects on egg production by changing body weight and body composition. Lower body fat levels during rearing would result in higher laying persistency. (2) Higher amino acid and energy intake during laying would result in a longer peak-production phase and a smaller rate of decline, improving overall laying persistency. Lastly, (3) body fat levels during laying would be influenced by lipid intake and a natural process of molting, and influenced long-term laying rate through adipokine production. To test these hypotheses, five studies were conducted, which are described in six chapters.Results showed that in the rearing phase, increasing dietary nutrient density (both energy and amino acids) increases body weight (BW) from 2 weeks of age onwards. Until approximately 12 weeks of age, growth was primarily driven by crude protein (CP) deposition. From week 5 to 6 onwards, relative crude fat deposition increases, influenced by diet density from week 2 onwards. At 15 weeks of age, BW increases linearly when dietary apparent fecal digestible (AFD) Lys levels increase, independent of dietary metabolizable energy (ME). Relative abdominal fat pad weight at 5 and 15 weeks of age mainly increases with a higher ME to AFD Lys intake ratio. During the laying phase, laying persistency was increased when dietary energy was reduced over time, thereby increasing feed intake. This is probably mediated through increased lipid intake. Moreover, feeding low lipid diets increases de novo lipoprotein synthesis for yolk formation and increases liver crude fat levels, as well as the risk of developing fatty liver disease. No direct correlation between adipose tissue during the production period and laying persistency were found, but indirectly, adipose tissue influenced adipokine production, which was in turn related to BW, egg weight and liver fat, as well as energy metabolism. WIAS Animal Nutrition WIAS Diervoeding urn:nbn:nl:ui:32-6f8c7da0-35c2-4e04-986d-f69077c9e0c1/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/688c5216-2e5b-42e9-a1b9-75347738c562 2026-04-02 thesis

urn:nbn:nl:ui:32-688c5216-2e5b-42e9-a1b9-75347738c562 2026-04-02 urn:nbn:nl:ui:32-688c5216-2e5b-42e9-a1b9-75347738c562/mods Rethinking community conservation and forest governance in the Peruvian Amazon Wageningen University dgg van der Zon Maria C. 0000000529667930 aut B.J.M. Arts opn W.A. de Jong opn R.G.A. Boot opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 136 10.18174/682086 en Community-based conservation and community forest management (CC-CFM) have become central pillars of present-day forest governance, particularly in tropical regions where Indigenous peoples and local communities play a vital role in conserving forest resources. Despite widespread adoption and strong normative support, many CC-CFM initiatives struggle to deliver lasting conservation outcomes. This thesis investigates why such efforts often fall short and how conservation design can better align with the socio-ecological systems (SES) in which they operate.The thesis argues that a key challenge in advancing CC-CFM lies in the limited understanding of the complexity and dynamism of local SES. Conservation policies and projects are frequently designed as standardized models, based on fixed assumptions about governance, incentives, and compliance. However, local forest governance systems are shaped by interacting social, institutional, ecological, and historical factors that vary substantially across contexts and change over time. When conservation designs fail to account for this complexity, they often struggle to fit local realities, undermining legitimacy, effectiveness, and long-term sustainability.Drawing on empirical research with Indigenous peoples and local communities in the Peruvian Amazon, this thesis examines how internal community characteristics and contextual factors shape the capacity for effective forest management within diverse SES. The analysis focuses in particular on internal governance capacity, including the presence of clear local rules, legitimate and context-appropriate enforcement mechanisms, and functioning leadership and institutions. The findings demonstrate that communities with strong internal governance arrangements are more likely to achieve positive conservation outcomes, even in situations where formal land tenure is weak or incomplete. Conversely, secure tenure alone does not guarantee effective forest management in the absence of these internal capacities.A central contribution of the thesis is its analysis of enforcement practices as a key institutional component of SES. The research shows that effective enforcement is highly context-dependent and adapts to local social relations, ecological conditions, market pressures, and histories of interaction with the state. Uniform enforcement models imposed from outside frequently fail to gain local legitimacy and may weaken existing governance arrangements. In contrast, conservation approaches that recognize and build upon locally embedded rules and enforcement practices tend to perform better.Overall, the thesis advances a context-sensitive perspective on CC-CFM grounded in SES thinking. It highlights the importance of moving beyond one-size-fits-all conservation blueprints toward adaptive and enabling approaches that engage with the diversity and dynamism of local socio-ecological systems. By foregrounding institutional fit and internal governance capacity, the research contributes to ongoing debates on how conservation policies and projects can more effectively support community-led forest management. WASS Forest and Nature Conservation Policy WASS Bos- en Natuurbeleid urn:nbn:nl:ui:32-688c5216-2e5b-42e9-a1b9-75347738c562/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/d1c2ef09-575d-4e37-8cb8-edc5ebbee5ce 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-d1c2ef09-575d-4e37-8cb8-edc5ebbee5ce 2026-04-02 urn:nbn:nl:ui:32-d1c2ef09-575d-4e37-8cb8-edc5ebbee5ce/mods Greenhouse gas dynamics in Siberia: interannual, seasonal, and diurnal insights from the ZOtino Tall Tower observatory Wageningen University dgg Tran Dieu Anh 0000000529601018 aut J. Vila-Guerau de Arellano opn S. Zaehle opn I.T. Luijkx opn C. Gerbig opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 243 10.18174/682773 en Siberia is a key component of the global carbon–climate system, storing vast quantities of carbon in boreal forests, wetlands, and permafrost soils while exchanging large fluxes of carbon dioxide (CO2) and methane (CH4) with the atmosphere. Rapid warming in recent decades has altered permafrost, hydrological, and phenological conditions, potentially destabilising these ecosystems and amplifying greenhouse gas emissions. This thesis investigates how these changes are reflected in atmospheric CO2 and CH4 variability using long-term observations from the ZOtino Tall Tower Observatory (ZOTTO) in Central Siberia.The study is based on continuous, multi-level measurements of greenhouse gas mole fractions and meteorological variables, enabling analysis of local to regional-scale processes and their temporal evolution. More than a decade of CO2 observations (2010–2021) reveal an emerging asymmetry in the seasonal carbon cycle. While the onset and termination of the growing-season carbon uptake remain relatively stable, the winter carbon release period is increasingly prolonged and intensified. Spring warming enhances the strength of carbon uptake, whereas late-summer and autumn warming amplify cold-season respiration, resulting in no net increase in annual CO2 uptake. Extreme events, such as the 2012 wildfire season, are clearly detectable in the atmospheric record. Comparison with atmospheric inverse modelling shows that the inclusion of ZOTTO observations improves the representation of interannual variability in regional CO2 fluxes.Analysis of CH4 observations over the same period indicates a steady upward trend and a pronounced late-summer concentration peak, the amplitude of which has increased over time. This enhancement is primarily driven by stronger local nighttime CH4 fluxes associated with warmer and wetter soil conditions. Isotopic measurements (delta13C-CH4 and delta2H-CH4), combined with atmospheric transport modelling and source attribution, reveal an increasing influence of biogenic emissions. Late-summer CH4 enhancements are dominated by wetland emissions originating mainly from Central West Siberia, while wintertime enhancements reflect a more diverse source mixture, including wetlands, fossil fuel combustion, and biomass burning.Overall, this thesis demonstrates that both CO2 and CH4 fluxes in Siberia are becoming increasingly sensitive to climate warming and disturbance. The results highlight the critical importance of long-term, high-frequency tall-tower observations in remote regions for detecting trends, constraining models, and improving understanding of land–atmosphere carbon exchange in a rapidly changing climate. WIMEK Air Quality Meteorology Meteorology and Air Quality WIMEK Luchtkwaliteit Meteorologie Meteorologie en Luchtkwaliteit urn:nbn:nl:ui:32-d1c2ef09-575d-4e37-8cb8-edc5ebbee5ce/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/1fdc9123-6c64-45e9-86d5-0a8071af180d 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-1fdc9123-6c64-45e9-86d5-0a8071af180d 2026-04-02 urn:nbn:nl:ui:32-1fdc9123-6c64-45e9-86d5-0a8071af180d/mods Advancing polymeric nanotechnology for functional improvements : from particles to purpose Wageningen University dgg Mali Alvja 0000000529691121 aut M. Srinivas opn D. Vorselen opn Paul W. White opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 387 10.18174/682273 en Nanomedicine has emerged as a powerful paradigm in modern healthcare, enabling targeted drug delivery, advanced diagnostic imaging, and the development of multifunctional and personalized therapeutic strategies. Despite substantial academic progress, however, clinical translation remains limited, largely due to challenges in reproducibility, long-term stability, scalable manufacturing, and safety validation. Addressing these barriers is essential to enable the reliable clinical implementation of nanoscale systems.This thesis focuses on polymeric nanoparticles (NPs), with particular emphasis on poly(lactic-co-glycolic acid) (PLGA), a biodegradable and biocompatible polymer with established regulatory acceptance. The overarching aim was to advance PLGA-based nanoplatforms toward multifunctional imaging, active targeting, and gene delivery within a translational framework. Perfluorocarbon (PFC)-loaded PLGA NPs were employed as a central model system, serving both as quantitative probes for fluorine-19 magnetic resonance imaging (19F MRI) and as a sensitive platform for evaluating formulation stability and process-dependent variability.Perfluoro-15-crown-5-ether (PFCE)-loaded PLGA NPs were shown to exhibit exceptional long-term colloidal stability, maintaining particle size, morphology, polydispersity, and encapsulation efficiency over storage periods exceeding six years. This finding addresses a major translational bottleneck in nanomedicine, where instability frequently limits clinical progress. Building on this robust formulation, multifunctional imaging capabilities were introduced through co-encapsulation of gadolinium chelates, yielding dual-mode proton/19F MRI nanoprobes. The results demonstrate that magnetic relaxation enhancement is strongly governed by nanoparticle ultrastructure, highlighting how internal nanoscale organization directly shapes imaging performance.Building on this structure-function relationship, the work enabled the development of pH-responsive MRI probes. The system displayed a reversible “on–off” 19F signal, with suppression at physiological pH and recovery under acidic conditions characteristic of tumor microenvironments and intracellular lysosomes, establishing a strategy for activatable 19F MRI based on architectural responsiveness. In parallel, bio-orthogonal click-chemistry approaches were developed to enable PD-L1-targeted surface functionalization while preserving formulation integrity.Beyond imaging, the thesis extends PLGA NP technology to gene delivery within a collaborative effort aimed at non-viral therapies for hereditary anemias. Finally, reproducibility was systematically investigated for PLGA-PFCE NPs by assessing the impact of subtle variations in materials, handling, and equipment. The findings highlight that consistent nanoparticle performance requires standardized workflows, transparent reporting, and rigorous operator training.Overall, this work demonstrates how robust and reproducible PLGA-based nanoplatforms can integrate imaging and therapy, contributing practical strategies toward more reliable and translatable nanomedicine. WIAS Cell Biology and Immunology WIAS Celbiologie en immunologie urn:nbn:nl:ui:32-1fdc9123-6c64-45e9-86d5-0a8071af180d/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/73538603-9b5f-4281-88a9-87bc5cee6aab 2026-04-02 thesis

urn:nbn:nl:ui:32-73538603-9b5f-4281-88a9-87bc5cee6aab 2026-04-02 urn:nbn:nl:ui:32-73538603-9b5f-4281-88a9-87bc5cee6aab/mods Market innovation for sustainable soil health management in Ghana Wageningen University dgg Amoabeng Nimako Solomon 0000000529706944 aut P. Ingenbleek opn S. Dittoh opn A. Gouzaye opn Prem Bindraban opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 221 10.18174/681587 en Smallholder agriculture underpins food security, rural livelihoods, and economic transformation across sub-Saharan Africa, yet its sustainability is increasingly undermined by widespread soil degradation. Sustainable Soil Health Management (SSHM)—the integrated and responsible use of mineral fertilizers with organic and ecological practices—offers a pathway to restore soil productivity while enhancing resilience and environmental performance. Despite its well-documented agronomic and ecological benefits, SSHM adoption among smallholder farmers remains limited. Existing explanations have largely focused on farmer-level constraints such as awareness, attitudes, or resource endowments. This thesis reframes the problem as one of market system design, arguing that SSHM adoption depends fundamentally on how agricultural markets organize, coordinate, and align the inputs, services, incentives, and institutions required to make adoption feasible and rewarding for farmers.The thesis develops and applies a market innovation perspective, grounded in complexity theory and enriched by socio-technical transition thinking, behavioral analysis, and resource–capability perspectives, to examine how smallholder agricultural markets in Ghana can be intentionally transformed to support SSHM adoption. Markets are conceptualized as complex adaptive socio-technical systems whose evolution can be deliberately steered through coordinated reconfiguration of market functions, relationships, and governance arrangements.Four interlinked studies operationalize this framework. Chapter 2 advances a complexity-informed model of smallholder market transformation, reconceptualizing market change as an emergent, iterative process shaped by interaction, feedback, and resource recombination among stakeholders. Chapter 3 applies the multi-level perspective to analyze Ghana’s soil health system using 73 stakeholder interviews and six farmer focus groups. It shows that although policy and environmental pressures are fostering niche initiatives related to SSHM, these remain fragmented, top-down, and weakly aligned, limiting their scalability and systemic impact. Chapter 4 responds by conceptualizing these initiatives as components of farmer-centered incentive systems and empirically eliciting farmer preferences for them through a conjoint experiment with 744 farmers. Results show that farmers strongly prefer integrated bundles that combine inputs, finance, advisory, sustainability support, and coordination mechanisms over isolated or purely motivational incentives. Chapter 5 assesses the feasibility of implementing these farmer-preferred configurations through a market-envisioning study, combining quantitative willingness ratings and qualitative interviews to evaluate stakeholder motivation, opportunities, and capabilities to reconfigure their roles.Across the studies, the thesis demonstrates that SSHM adoption hinges not on isolated functions performed by market stakeholders but on their alignment and relational fit. While most functions to support SSHM exist in the market system, they operate in silos, creating coordination failures that undermine adoption. Effective SSHM scaling therefore requires deliberate orchestration across actors and levels. The thesis proposes a layered coordination architecture comprising macro-level policy alignment, meso-level orchestration led by ICT platforms, and micro-level delivery through intermediaries such as aggregators and service-linked credit arrangements.By integrating market innovation theory with empirical system diagnosis, design, and feasibility analysis, the thesis contributes a unified framework for transforming “thin” agricultural markets toward sustainable outcomes. Practically, it offers actionable design principles and collaboration pathways for policymakers, development agencies, and private actors seeking to embed sustainability within commercially viable smallholder market systems in Ghana and similar contexts. Marketing and Consumer Behaviour WASS Marktkunde en Consumentengedrag WASS urn:nbn:nl:ui:32-73538603-9b5f-4281-88a9-87bc5cee6aab/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/c2f339d0-dc0f-460b-87d2-bb72256184b1 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-c2f339d0-dc0f-460b-87d2-bb72256184b1 2026-04-02 urn:nbn:nl:ui:32-c2f339d0-dc0f-460b-87d2-bb72256184b1/mods Caring for dignity in food assistance : Navigating norms and moralities Wageningen University dgg Andriessen Thirza 0000-0002-1786-2059 0000000529665548 aut J.S.C. Wiskerke opn H.M. van der Horst opn O. Morrow opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 241 10.18174/681058 en This dissertation examines how practices of charitable food assistance in wealthy countries shape recipients' dignity. Although food insecurity affects millions of people in affluent societies, responses have increasingly relied on charity-based and privatised food aid rather than rights-based welfare solutions. Scholars have criticised such approaches for depoliticising food insecurity, individualising responsibility, and undermining recipients’ dignity through inadequate food provision and stigma. At the same time, charitable food assistance has evolved, with food banks adapting their formats and new third-sector initiatives emerging that seek to provide food in non-stigmatising and more dignified ways. Despite these developments, limited research has examined how dignity is enacted within contemporary food assistance practices. Addressing this gap, this dissertation asks how evolving practices of charitable food assistance in affluent countries shape recipients’ dignity.The research combines a social dignity lens with an empirical ethics approach. Dignity is understood as socially enacted and relational, linked to the ability to meet normative standards that confer belonging and social value. Because such norms can themselves be exclusionary, the study critically examines how they are shaped by institutional, ideological, and structural forces, including consumer culture, neoliberal welfare arrangements, and charitable moralities. Ethnography forms the core methodology. Fieldwork was conducted in three food assistance initiatives in Belgium and the Netherlands, using participant observation, semi-structured and walk-along interviews, and a focus group. Embedded within this ethnographic design, the empirical ethics approach illuminates how moral judgments and normative expectations are enacted and negotiated in practice.The findings consist of one scoping review and three ethnographic case studies. The scoping review synthesises 37 studies from twelve high-income countries and identifies five dimensions through which dignity is shaped: access to food assistance, social interactions, the food provided, physical spaces, and needs beyond food. Across these dimensions, dignity emerges as relational and continually negotiated within specific institutional and cultural contexts. The three case studies focus on consumer-oriented food assistance initiatives characterised by food choice, (symbolic) pricing, and market-like exchanges. Together, they demonstrate that aligning food assistance with consumer norms can support dignity by enabling recipients to perform socially valued roles and reducing the visibility of charity. However, these models also embed neoliberal moralities of responsibility and self-management, which may reproduce moral judgment and exclusion. Using a relational autonomy perspective, the dissertation shows that autonomy in food assistance is not a matter of independence but of supported self-determination embedded in relations of care, institutional safeguards, and managed dependencies. While money-based assistance enhanced choice and social inclusion, it also introduced new vulnerabilities related to surveillance and welfare governance.The dissertation concludes that dignity in food assistance is not inherent to any specific aid model but is enacted through situated practices, moral negotiations, and relationships. It advances the concept of relational dignity to capture how dignity is co-produced through interpersonal interactions, institutional arrangements, and socio-political structures. By combining ethnography with empirical ethics, the research offers both empirical insights and a conceptual approach for developing more just, care-oriented, and dignified responses to food insecurity in affluent societies. WASS Rural Sociology Consumption and Healthy Lifestyles WASS Rurale Sociologie Consumptie en Gezonde Leefstijl urn:nbn:nl:ui:32-c2f339d0-dc0f-460b-87d2-bb72256184b1/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/3a30cce5-34c5-4fe1-ae6f-239cbd58fe3e 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-3a30cce5-34c5-4fe1-ae6f-239cbd58fe3e 2026-04-02 urn:nbn:nl:ui:32-3a30cce5-34c5-4fe1-ae6f-239cbd58fe3e/mods On the frond row : Sporophyte development in the fern Ceratopteris richardii Wageningen University dgg Woudenberg Sjoerd 0000000529561167 aut D. Weijers opn J.J. Ramalho opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 197 10.18174/681501 en A major event during land plant evolution was the establishment of a dominant sporophyte generation, which is coupled to the origin of vascular plants approximately 450 million years ago. Many important plant organs like roots, shoots and vasculature only develop within the sporophytic generation. Ferns are unique in having both a free-living gametophytic and a free-living sporophytic generation, providing an excellent experimental model to better understand the developmental necessities of sporophyte development. Therefore, in this thesis, we use and develop the fern Ceratopteris richardii as a model, to better understand sporophyte establishment during embryogenesis and development.From reviewing the literature, it becomes clear that barely any molecular data exists on non-seed plants and non-bryophyte models, whilst those taxa are the most important to understand the evolutionary framework. Subsequently, we compare on a molecular level what the prerequisites are the sporophytic body plan. Thereby, I identify hormonal regulation as a key defining characteristic between the two generations in Ceratopteris. To extend the bioinformatic analysis to experimental work, next, we focus on the plant hormone auxin and its role during development in both the gametophytic and sporophytic generations. We observe that gametophytes respond similarly to bryophytes whilst the sporophytes’ response is similar to that of seed plants. Manipulating auxin accumulation in the gametophyte leads to the ectopic formation of roots and vascular tissue in the gametophyte, suggesting that ontogeny is only correlated to development, and that changes in auxin signalling are an important factor to distinguish the two generations in Ceratopteris.Lastly, we switch gears to embryogenesis as the direct link between the two generations. We compare the reproductive structures in which embryogenesis takes place across all land plants. Embryogenesis takes place in highly divergent structures, and recent advances in Arabidopsis embryo research suggest an important role of mechanical stress in embryogenesis, next to a more canonical form of chemical regulation. Therefore, we characterize embryogenesis in the fern Ceratopteris. Embryogenesis occurs in a very predictable fashion, and patterning appears to happen early. The early patterning is further confirmed by a transcriptome analysis. The polarization of the embryo can be traced back to an asymmetric division in the zygote. We were able to disturb late embryo development by applying exogenous auxin; however, early embryo patterning remained unaffected. Besides, a strong correlation is present between maternal tissue morphology and zygotic division orientation. We explore this correlation in detail with finite-element modelling. The modelling suggests that heterogeneity in cell wall stiffness between the meristem and more differentiated cells generates tissue stresses that we propose to orient the zygotic division in such a way that the future sporophytic root points towards the gametophytic rhizoids, thereby inheriting the axis of development.All these different aspects let us to better understand the developmental principles for sporophyte establishment and development, and view this in a broader evolutionary context. EPS Biochemistry EPS Biochemie urn:nbn:nl:ui:32-3a30cce5-34c5-4fe1-ae6f-239cbd58fe3e/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/60ab18df-f231-4b3b-b9d2-0d2ef7182aa2 2026-04-02 thesis

urn:nbn:nl:ui:32-60ab18df-f231-4b3b-b9d2-0d2ef7182aa2 2026-04-02 urn:nbn:nl:ui:32-60ab18df-f231-4b3b-b9d2-0d2ef7182aa2/mods Hold on tight and let go : Electrically-responsive adsorption and desorption on polypyrrole Wageningen University dgg de Boer Kieke 000000052966553X aut C. Schroën opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 273 10.18174/681672 en Separation processes play a key role in food production. This includes the extraction and purification of fractions from agricultural starting materials, recovery of valuable components, and removal of undesirable components, ultimately contributing to the production of safe food ingredients and products. The selection of an appropriate separation strategy depends on what needs to be separated, what else is present in the mixture, and how pure the final product must be. When high purity is desired, a precise technique like chromatography is often employed. This method usually relies on chemical changes, such as variations in the acidity or salt concentration, to release the target molecule, which can be costly and environmentally harmful. This thesis explores a more sustainable alternative: capturing and releasing molecules through electrical stimulation. To achieve this, new materials need to be designed. We focused on a material called polypyrrole, which can change its surface properties when an electrical signal is applied. The goal was to develop a material that can capture and release both charged molecules, like proteins, and uncharged molecules, like flavor compounds.Polypyrrole can switch between two electrical states, oxidized and reduced, which alters its surface properties. These properties, in turn, determine whether and how strongly the surface interacts with a target molecule, resulting in either adsorption (capture) or desorption (release). By adjusting how the material is produced, such as the preparation method or the starting solution, its properties could be tuned. The polypyrrole material was subsequently tested by exposing it to electrical signals and observing whether it could capture and release different molecules. For proteins, the extent of adsorption could be related to the electrical state of the material. This made it possible to capture proteins and (partially) release them over multiple cycles. For flavor molecules, capture depended strongly on the type of flavor, but releasing them using electrical signals proved to be difficult. However, the selectivity of the material could be improved using a technique called molecular imprinting, in which cavities were formed in the material that matched the shape of a specific flavor molecule.In addition, the research investigated the underlying switching mechanism upon electrical stimulation, including changes in the surface structure and composition. This showed that the reversibility and stability of the switching behaviour could be tuned by how the material was made. Overall, this work provides insights and future directions for developing more sustainable electrically-driven separation technologies. Food Process Engineering VLAG Food Process Engineering VLAG urn:nbn:nl:ui:32-60ab18df-f231-4b3b-b9d2-0d2ef7182aa2/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/0a95eb34-3f22-4bc4-9ca8-78a63d663036 2026-05-18 thesis

urn:nbn:nl:ui:32-0a95eb34-3f22-4bc4-9ca8-78a63d663036 2026-05-18 urn:nbn:nl:ui:32-0a95eb34-3f22-4bc4-9ca8-78a63d663036/mods The role of earthworms in enhanced mineral weathering : Understanding their impact on carbon dynamics and sustainable fertilisation Wageningen University dgg Calogiuri Tullia 0000000529581707 aut J.W. van Groenigen opn A. Vidal opn M. Hagens opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 238 10.18174/681649 en Actively removing carbon dioxide (CO₂) from the atmosphere is urgently needed, in addition to reducing emissions, to meet the Paris Agreement target of limiting global warming to 1.5°C. Carbon Dioxide Removal technologies, such as Enhanced Mineral Weathering (EMW), offer a promising solution by speeding up the natural breakdown of silicate rocks to store CO₂ as inorganic carbon. EMW can also improve organic carbon stabilisation and enhance plant fertilisation. This technique can be applied to soils using different rock types and grain sizes and has the potential to remove up to 4 gigatonnes of CO₂ per year. However, this remains below the approximately 10 gigatonnes required annually to meet climate goals. Although reactor-based EMW can increase efficiency, it is expensive and energy-intensive, leading to growing interest in bio-based systems that use soil organisms to enhance weathering in a more sustainable way. Earthworms are particularly promising because their digestion processes and soil mixing activities can potentially increase weathering rates.This PhD research was part of the European Horizon2020 BAM project, which aimed to explore biologically enhanced EMW. The main objective of this thesis was to understand how earthworms influence carbon dynamics and plant fertilisation through mineral weathering. The two main research goals were: first, to identify optimal conditions for earthworm survival in artificial organo-mineral systems and to understand how earthworms affect carbon stabilisation and sequestration; second, to test whether earthworm-processed material could improve soil carbon sequestration and plant fertilisation in grasslands.To achieve these goals, a controlled experimental setup was developed, consisting of 200 microcosms filled with an artificial organo-mineral mixture. This system allowed the manipulation of abiotic and biotic factors, such as watering frequency, rock type and size, organic matter type, and earthworm species and density. Results showed that the structure of the system strongly influenced earthworm survival and activity. Coarser grains and straw improved water flow and prevented low-oxygen conditions, creating better living conditions for earthworms.This research also revealed that living and dead earthworms affected mineral weathering differently. Living earthworms had limited short-term effects on inorganic carbon sequestration but likely contributed more to organic carbon stabilisation through physical and chemical soil processes. In contrast, dead earthworms significantly enhanced carbon capture, mainly through increased microbial activity. Further experiments using carbon isotopes confirmed that dead earthworms promoted inorganic carbon formation over time, while both living and dead earthworms increased organic carbon stabilisation through different pathways.In a greenhouse experiment, two organo-mineral mixtures, processed and unprocessed by earthworms, were applied to potassium-poor sandy soil sown with grass. Results showed that grass enhanced mineral weathering through respiration and nutrient uptake. Both mixtures improved grass growth and reduced potassium deficiency, although no significant difference was observed between them.Finally, this thesis highlighted the need for standardised indicators to measure mineral weathering and carbon sequestration. It also introduced the concept of “dead earthworm-mediated stimulation” and discussed the complex feedback between plant growth and mineral weathering. Overall, the research emphasizes the importance of biological processes in developing effective carbon removal strategies. PE&RC Soil Biology Soil Biology Operations Manager Soil Chemistry PE&RC Bodembiologie Soil Biology Operations Manager Soil Chemistry urn:nbn:nl:ui:32-0a95eb34-3f22-4bc4-9ca8-78a63d663036/obj 2026-05-18 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/7d8775a9-65e4-496b-b5e0-fa5fe7274a1b 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-7d8775a9-65e4-496b-b5e0-fa5fe7274a1b 2026-04-02 urn:nbn:nl:ui:32-7d8775a9-65e4-496b-b5e0-fa5fe7274a1b/mods From windows of threat to windows of opportunity : Housing management and nutritional interventions in early life toimprove pig health by shaping the gut microbiota, immune status and welfare Wageningen University dgg Wen Caifang 0000000529702572 aut H. Smidt opn H.A. Schols opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 239 10.18174/680908 en Weaning-associated environmental, psychological, and nutritional stressors can disrupt piglets’ gastrointestinal health and thus compromise their growth performance. Antimicrobials are used to sustain herd health during this stage. A multifaceted integrated approach is required to minimized reliance on antimicrobials usage for the development of more sustainable livestock production systems. In this thesis we aimed to evaluate effects of two such approaches. First, we investigated the effects of two housing conditions, i.e., conventional housing: (CH) versus enriched housing (EH), on welfare, immune status and gut microbiota from birth to 61 days. Our findings confirmed that EH pigs exhibited better welfare and immune status compared to CH pigs. EH pigs demonstrated increased percentages of T cells and cytotoxic T cells in peripheral blood, and higher ex vivo secretion of IL1ß and TNF-alpha after lipopolysaccharide stimulation. Additionally, the enriched house accelerated the maturation of pre-weaning gut microbiota, leading to increased relative abundance of bacterial groups involved in fibre degradation, such as Prevotella_2, Christensenellaceae_R_7_group and Ruminococcus gauvreauii group. Second, we evaluated the effects of supplementation of a potential postbiotic, rye overgrown with mycelium (ROM) of mushroom Agaricus subrufescens, on intestinal microbiota colonization and immune system development. Piglets received ROM or a tap water placebo every other day from day 2 to day 44. Eight animals per treatment were dissected on days 27, 44 and 70. Our findings revealed that pre-weaning faecal microbiota was more homologous in ROM pigs, with a prolonged effect on jejunal/caecal microbiota composition post-intervention. ROM supplementation primarily influenced the pig intestinal immune development. For instance, in the ileum, only a few genes were regulated in the control group from day 27 to day 44 post-weaning. In contrast, ROM pigs exhibited upregulated genes related to Toll-like receptor signaling, inflammatory responses, redox signaling, and apoptosis pathways. Moreover, ROM animals showed higher NK cell activation in blood and enhanced IL-10 production in ex vivo stimulated MLN cells before weaning. Lastly, we investigated bioactive carbohydrate-related compounds in ROM, using cytokine induction in chicken immune cells. Fractionation of rye and ROM and subsequent testing fractions on macrophage cell line HD11 showed that IL-12p40 production was mainly induced by hot water-soluble solids (HWSS) with ROM-HWSS more active than rye-HWSS. Stimulation of chicken splenocytes further confirmed their immunomodulatory capacity. Rye- and ROM-HWSS > 10 kDa (bioactive polymers) mainly consisted of arabinoxylan and glucan with smaller and variable amounts of protein and ferulic acid. NaOH treatment (0.1M) substantially reduced IL-12p40 induction by HWSS fractions and removed some ferulic ester groups, suggesting that feruloylated arabinoxylan structures contribute to IL-12p40 induction. Degradation of arabinoxylan, glucan and fructan in the HWSS fractions with specific enzymes did not affect IL-12p40 induction. Protease, chitosanase and Driselase treatments reduced IL-12p40 induction in ROM-HWSS, suggesting that mycelial compounds (e.g., protein, chitosan and galactan/mannan) may (also) contribute to the bioactivity. Overall, the findings of this thesis indicate that timely interventions through enriched housing and functional nutrition based on Agaricus subrufescens after birth can promote healthier, more resilient pigs, and thus better prepare them for the weaning transition. VLAG Microbiology Food Chemistry VLAG Microbiology Levensmiddelenchemie urn:nbn:nl:ui:32-7d8775a9-65e4-496b-b5e0-fa5fe7274a1b/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/4387c1f4-508d-408b-969e-4b80988bc3c0 2026-04-02 thesis

urn:nbn:nl:ui:32-4387c1f4-508d-408b-969e-4b80988bc3c0 2026-04-02 urn:nbn:nl:ui:32-4387c1f4-508d-408b-969e-4b80988bc3c0/mods From bite to system : How grazing management shapes dairy production Wageningen University dgg Menegazzi Conceição Gabriel 0000000529625095 aut J. Dijkstra opn W.J.J. Gerrits opn P. Chilibroste opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 301 10.18174/681787 en The overarching objective of this thesis was to elucidate how post-grazing sward height modulates the contribution of grazed forage to dairy cow diets, the associated grazing behaviour strategies, and the downstream consequences for intake, milk production, methane emissions, and system performance at both animal and land-use scales. In addition, the thesis evaluated whether the infrastructure used for supplementation in mixed feeding systems influences productive and economic outcomes. Chapters 2 and 4 examined how dairy cows behaviour respond to contrasting post-grazing sward heights when grazing tall fescue pastures. Chapter 2 focused on unsupplemented, late-lactation cows with low milk yield, whereas Chapter 4 addressed supplemented cows producing at medium to high levels across early and mid-lactation. Despite these contrasts in physiological state and supplementation level, the responses to residual sward height were remarkably consistent. Daily grazing time was primarily driven by supplementation level and pasture access time, and only marginally affected by residual height. In contrast, the structure of grazing activity within the day differed: cows grazing taller residuals adopted a pattern of shorter but more frequent meals, whereas cows grazing shorter residuals compensated with fewer but longer meals. At the spatial scale, cows managed on taller residuals exhibited a distinct “rapid sampling” strategy, characterized by higher feeding station turnover and fewer bites per station. This strategy enabled higher grazed forage intake, reflecting both improved sward structure and enhanced selectivity for higher-quality forage. Across production levels, these behavioural adjustments translated into higher milk yield and improved body condition when taller post-grazing sward heights were maintained. Chapter 3 expanded the inference from short-term responses to a near full-lactation perspective, integrating animal performance with pasture dynamics over 215 days. Although cows managed under taller residuals produced more milk per cow and recovered body condition earlier, these individual-level gains did not fully offset the lower stocking rate associated with laxer grazing. As a result, milk production per hectare tended to be lower. Nevertheless, grazed forage intake per hectare remained similar between treatments, while supplementary feed input per hectare was reduced under taller residual management, leading to comparable income over feed costs at the land-use scale. Chapter 5 demonstrated that higher post-grazing sward height improved whole-animal energy utilization and reduced methane emission intensity without increasing absolute methane production. Greater intake of higher-quality forage enhanced feed efficiency and diluted maintenance energy requirements, allowing a larger proportion of metabolizable energy to be retained as milk and body tissue. Although higher dietary crude protein increased nitrogen losses, cumulative methane emissions per hectare were lower under taller residual management. Finally, Chapter 6 addressed the role of supplementation infrastructure. While fully confined systems achieved the highest milk yields, differences between compost-barn and outdoor soil-bedded systems within mixed feeding were modest. Environmental exposure did not consistently affect cow performance, although compost barns offered episodic advantages under heat stress. Overall, this thesis shows that integrating grazing management, supplementation, and infrastructure design can enhance nutrient capture and use efficiency, reduce methane intensity, and sustain competitive milk yields. WIAS Animal Breeding and Genomics Animal Nutrition WIAS Animal Breeding and Genomics Diervoeding urn:nbn:nl:ui:32-4387c1f4-508d-408b-969e-4b80988bc3c0/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/0491d994-9792-4d7b-aa12-fed26639282e 2026-04-02 thesis

urn:nbn:nl:ui:32-0491d994-9792-4d7b-aa12-fed26639282e 2026-04-02 urn:nbn:nl:ui:32-0491d994-9792-4d7b-aa12-fed26639282e/mods A behaviour-based approach to improving food hygiene practices : Application to the street food sector in Ecuador Wageningen University dgg Pilamala Rosales Araceli A. 0000000529622214 aut P. A. Luning opn A.R. Linnemann opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 312 10.18174/680949 en Street food consumption is a global public health concern due to the risks of foodborne illness. Approximately 2.5 billion people consume street food daily, highlighting its importance as both a nutritional source and an employment opportunity, particularly in low- and middle-income countries. In Ecuador, street food is culturally and economically significant, yet frequently associated with unsafe practices. Despite governmental efforts to improve safety, challenges persist.This thesis investigates the causes of food safety issues in Ecuador’s street food sector through structured surveys and in-depth interviews assessing vendors’ knowledge, hygiene practices, and perceptions of services. Results showed that while vendors generally possessed adequate knowledge and complied with hygiene requirements, gaps remained in personal hygiene and the simultaneous handling of food and money. Vendors also reported deficiencies in waste management and pest control. These findings underscore the need for targeted training and improved resource provision.The Theory of Planned Behaviour (TPB) was applied to identify predictors of hygiene practices. Subjective norms emerged as the strongest predictor, influencing intentions to perform handwashing, food protection, waste disposal, and cleaning. Perceived behavioural control was linked only to maintaining cleanliness in food handling areas. Observations revealed a gap between intentions and actual practices, social, attitudinal, and resource-related factors.A training program based on TPB, combining theoretical, reflective, and practical components, improved vendors’ knowledge, attitudes, subjective norms, and perceived behavioural control. While effective, sustaining behavioural change requires institutional and environmental support. Stakeholder analysis using the Net-Map method revealed fragmented collaboration, with municipalities playing a central role but overlapping responsibilities limiting efficiency.The study concludes that multi-phase training, clearer stakeholder roles, and coordinated governance are essential to enhance street food safety. A multi-layered approach integrating education, infrastructure, and enforcement is advocated to protect public health while preserving the socio-economic value of street food vending. VLAG Food Quality and Design VLAG Food Quality and Design urn:nbn:nl:ui:32-0491d994-9792-4d7b-aa12-fed26639282e/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/68c1e931-d4be-4783-b755-ba605d05052a 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-68c1e931-d4be-4783-b755-ba605d05052a 2026-04-02 urn:nbn:nl:ui:32-68c1e931-d4be-4783-b755-ba605d05052a/mods Methane-oxidizing bacteria; “the gatekeepers of methane” : Insights into their niche differentiation in freshwater systems Wageningen University dgg Pérez Pesamosca Germán 0000000529622142 aut P.L.E. Bodelier opn Paul Bodelier opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 262 10.18174/680925 en Methane (CH₄) is a potent greenhouse gas whose atmospheric concentration continues to rise, strongly influencing Earth’s climate. As the end product of archaeal metabolism, methane is mainly produced under anoxic conditions, making freshwater systems an important natural source of biogenic CH₄. Lakes, ponds, rivers, and agricultural drainage systems are now recognized as significant contributors to global methane emissions. Because these ecosystems are highly vulnerable to anthropogenic pressures such as eutrophication, their methane emissions are expected to increase in the future.A major natural process counteracting methane emissions is performed by methane-oxidizing bacteria (MOB). These bacteria use methane as a source of carbon and energy and can prevent up to 80% of sediment-produced methane from reaching the atmosphere. Despite their importance, the ecology of freshwater MOB has received limited attention, largely because the contribution of freshwater systems to the global methane budget has only recently been acknowledged. Understanding the abiotic and biotic factors shaping MOB diversity, distribution, and activity is therefore essential for predicting methane emissions from freshwater ecosystems.In this thesis, I investigated freshwater MOB using a combination of field surveys and experimental approaches. The overall aim was to describe MOB abundance, activity, and diversity, and to identify the abiotic and biotic drivers underlying MOB niche differentiation in freshwater environments.Chapter 2 examined MOB niche differentiation in the upper sediment layer (~1 cm) of 50 agricultural drainage ditches across 10 regions in the Netherlands. MOB Type Ib dominated most sites, and nitrogen-related variables emerged as the main drivers of MOB distribution. Clear niche differentiation among closely related species suggested trait divergence at the species level. MOB interactions were strongly context dependent, potentially shifting from facilitation to competition under different environmental conditions. MOB accounted for 3–7% of the total bacterial community and showed strong associations with other microbial taxa.Chapter 3 explored whether methane-derived carbon provided by MOB could support cyanobacterial carbon demands. Highly negative delta¹³C signatures in phytoplankton indicated the use of methane-derived carbon. Co-culturing experiments confirmed syntrophic interactions between MOB and cyanobacteria, and activity assays revealed active MOB on cyanobacterial filaments in stratified lakes, pointing to bidirectional interactions affecting methane emissions.Chapter 4 investigated interactions between methane-cycling microorganisms and cyanobacteria as a potential methane mitigation strategy in rice paddies. Microcosm experiments using two indigenous cyanobacterial isolates showed methane emissions decreased up to 20-fold, depending on cyanobacterial identity and soil depth.Chapter 5 assessed the effects of fish-mediated bioturbation on methane dynamics in shallow systems. Fish activity increased methane ebullition but reduced CO₂ emissions. Although planktonic MOB abundance increased due to trophic cascading effects, methane oxidation rates remained unchanged.Overall, this thesis demonstrates that MOB niche differentiation in freshwater systems is shaped by a complex interplay of abiotic and biotic drivers. These interactions link MOB to multiple trophic levels and strongly influence methane cycling, emphasizing the need for a polyphasic approach to studying freshwater methane dynamics. PE&RC Soil Biology PE&RC Bodembiologie urn:nbn:nl:ui:32-68c1e931-d4be-4783-b755-ba605d05052a/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/e79092f4-8f47-4877-9bed-136f9c478ff3 2026-04-02 thesis

urn:nbn:nl:ui:32-e79092f4-8f47-4877-9bed-136f9c478ff3 2026-04-02 urn:nbn:nl:ui:32-e79092f4-8f47-4877-9bed-136f9c478ff3/mods Socio-technical fertiliser interventions to enhance on-farm productivity Wageningen University dgg Setsoafia Eugene Dela 0000000529622265 aut P.C. Struik opn H. Maat opn C. Freeman opn M. El Gharous opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 179 10.18174/681624 en This thesis explored how smallholder farmers perceive and manage soil fertility, focusing on their use of mulch, manure, and mineral fertilisers, and how these practices are shaped by agronomic, socio-economic, and institutional factors. This thesis shows that farmers have real perceptions of soil fertility decline, especially in intensively cultivated areas with identified causes including continuous cropping without fallow and without the adequate use of mineral and organic fertilisers, bush burning, overgrazing, and soil compaction. The thesis shows that beyond farmers′ coping mechanisms, which is their improvisation and adaptation skills in the face of declining soil fertility, addressing low productivity and declining soil fertility requires context-specific, integrated soil fertility management approaches that align with farmers′ needs and opportunities, and local agroecological conditions. This is particularly important because not all farmers are equally placed to achieve enhanced productivity. Many farmers are lagging economically, not least because they lack resources to purchase mineral fertilisers, but also because they often lack resources even to successfully implement their coping strategies, for example procuring tractor services early enough to enable early planting. PE&RC Centre for Crop Systems Analysis (CSA) PE&RC Centre for Crop Systems Analysis (CSA) urn:nbn:nl:ui:32-e79092f4-8f47-4877-9bed-136f9c478ff3/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/a324eca4-a633-421d-8821-cda673a6be66 2026-04-02 thesis

urn:nbn:nl:ui:32-a324eca4-a633-421d-8821-cda673a6be66 2026-04-02 urn:nbn:nl:ui:32-a324eca4-a633-421d-8821-cda673a6be66/mods Microbial wood degradation in a composting environment : influencing factors and improvement strategies Wageningen University dgg Li Anran 0000000529594014 aut C.J.N. Buisman opn W.-S. Chen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 224 10.18174/681677 en Space heating is a major contributor to energy demand in temperate regions. Although wood is a widely available renewable fuel, conventional combustion causes severe air pollution and has short-term climate impacts. Biological wood oxidation (BWO) offers an alternative approach to decentralized heat production by harnessing microbial activity to oxidize wood in a composting environment, releasing low-temperature heat (typically 40–50°C) in a slow and controllable manner. This thesis investigates how key composting parameters and intervention strategies influence microbial wood degradation at the particle scale, focusing on wood particle size, nutrient availability (specifically nitrogen and phosphorus), environmental pH, oxygen availability, and bioactive organic additives. The work provides fundamental insights and practical guidance for enhancing microbial wood degradation in wood-dominated compost heat recovery systems (CHRSs). It also advances understanding of microbial decomposition of lignocellulosic materials and contributes to the development of sustainable resource management within a circular bioeconomy. WIMEK Biological Recovery & Re-use Technology Environmental Technology WIMEK Biological Recovery & Re-use Technology Milieutechnologie urn:nbn:nl:ui:32-a324eca4-a633-421d-8821-cda673a6be66/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/090fe062-6ab1-4cb6-bc7d-76837c6a819d 2026-04-02 thesis

urn:nbn:nl:ui:32-090fe062-6ab1-4cb6-bc7d-76837c6a819d 2026-04-02 urn:nbn:nl:ui:32-090fe062-6ab1-4cb6-bc7d-76837c6a819d/mods Species sorting and community-level functionality in a natural microbial community: experiments using a traditional fermented dairy ecosystem model from Zambia Wageningen University dgg Nehanda Shepherd 0000000529636173 aut B.J. Zwaan opn E.J. Smid opn S.E. Schoustra opn J. Chileshe opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 178 10.18174/681164 en Microbial communities are continuously faced with environmental changes, leading to unpredictable states in their structure and functioning. Species sorting has been one of the important concepts pursued to understand the microbial community assembly process, which views member species as being driven by their differential fitness traits in response to selection. Several model systems have been applied regarding the study of species sorting, yet the complexity of field-based models often attracts rigorous and costly procedures during data capture, and often overlooks sampling over long temporal scales, while rarely providing community-functional relationships. This motivates the use of traditional fermented milks as simple model systems, given that they constitute self-assembled microbial communities through spontaneous fermentation, therefore representative of natural systems, yet are culturable even under laboratory conditions, and their community-level functionality can be tracked over a prolonged period. This study explored species sorting and community functionality using mabisi, a traditional fermented milk found in Zambia. Specifically, we tracked how microbial community structure shifts following exposure to novel substrates (Chapter 2 and 3) and processor location (Chapter 4) as different ecological selective factors through 16S rDNA sequencing. Alongside, we tracked community-level functionality through proxy analysis of volatile organic compounds (VOC), pH, consistency, and B-group vitamins. We found that the microbial community shifted with variation in novel substrate treatments and processor location. This shift was also time-dependent, conforming to early and late phases of propagation. However, the overall functionality was redundant, although it occurred to varying degrees. For instance, microbial communities from Mongu outperformed those from Kaoma for the acidification process and B-group vitamin production, manifesting as relatively lower median pH, and contributing more Vitamin B9 and B1 through PCA analysis. The findings in this thesis provide a broad significance spanning the microbial ecology and biotechnology interface. Firstly, it illustrates species sorting and prediction of community-level functionality through the interaction of substrate, time, and geographical location. Secondly, novel milk substrates can be used for mabisi processing, given mabisi microbial communities have adapted and exhibited functions similar to mabisi from raw cow milk based substrates. As such, mabisi microbial communities can be a bio-enrichment source for prebiotic and probiotic properties for infant formula, and we highlight the feasibility and effectiveness of the current practice of its use in treating malnourished children. PE&RC Genetics (GEN) PE&RC Genetics (GEN) urn:nbn:nl:ui:32-090fe062-6ab1-4cb6-bc7d-76837c6a819d/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/d734f3e1-b448-4d49-b7dd-ee21295e3f75 2026-04-02 thesis

urn:nbn:nl:ui:32-d734f3e1-b448-4d49-b7dd-ee21295e3f75 2026-04-02 urn:nbn:nl:ui:32-d734f3e1-b448-4d49-b7dd-ee21295e3f75/mods Global multi-pollutant modelling: uncovering new perspectives for river exports of nutrients, plastics, and chemicals Wageningen University dgg Micella Ilaria 0000000529581723 aut M. Strokal opn T. Tang opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 283 10.18174/681683 en This thesis assesses river exports of nutrients, plastics, and chemicals to coastal waters worldwide across sub-basins in the 21st century under socio-economic disparities and climate-driven hydrological changes. Using the new MARINA-Multi model, results show that in 2010, diffuse sources contributed by >95% to river exports of nitrogen and macroplastics, while point sources contributed by about 40% to river exports of phosphorus and microplastics globally. Future multi-pollutant scenarios indicate that 56%–78% of the global population is expected to live in more polluted river sub-basins by 2100, with the Indian Ocean receiving alarming pollutant levels. Income-based disparities further shape 2050 water quality: high-income sub-basins experience plastic pollution pressures from urbanisation, while low-income sub-basins in Africa and South Asia face the highest exposure to multiple river pollutants. Many African sub-basins show greater variation in river exports of multiple pollutants due to future climate-driven hydrological uncertainties. Therefore, new perspectives for advancing multi-pollutant modelling widen the scope of models, link sectors, and address uncertainties. WIMEK Earth Systems and Global Change WIMEK Earth Systems and Global Change urn:nbn:nl:ui:32-d734f3e1-b448-4d49-b7dd-ee21295e3f75/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/be46b4f1-74b1-48c4-a58e-7df8f13e2681 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-be46b4f1-74b1-48c4-a58e-7df8f13e2681 2026-04-02 urn:nbn:nl:ui:32-be46b4f1-74b1-48c4-a58e-7df8f13e2681/mods Unraveling the plant cell wall integrity mechanisms in nematode feeding structures (using spatial transcriptomics) Wageningen University dgg Pijnacker Anna 0000000529566005 aut G. Smant opn J.L. Lozano Torres opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 166 10.18174/681818 en Cyst and root-knot nematodes are destructive plant-parasites that threaten global food security by inducing permanent feeding structures in host roots. These feeding structures serve as the sole nutrient source for the nematodes. Therefore, preventing feeding structure formation is a key target for crop improvement. In this thesis, we propose a novel strategy to enhance plant immunity exploiting the plant’s own cell wall integrity (CWI) mechanism. We hypothesize that plant CWI receptors perceive the cell wall modifications required for nematode feeding structure formation and subsequently activate immune responses.We focused on a putative CWI receptor family, the Proline-rich Extensin-like Receptor Kinases (PERKs), in the model plant Arabidopsis thaliana. We demonstrate that Arabidopsis plants overexpressing PERK13 display almost complete resistance to the cyst nematode Heterodera schachtii, while perk13 knockout plants become hyper-susceptible. Transcriptome and reporter gene expression analyses indicate that the increased susceptibility of perk13 mutants involves the upregulation of DMR6-LIKE OXYGENASE1 (DLO1), a suppressor of salicylic acid-mediated immunity. Furthermore, we show that recombinant PERK13 binds pectin in vitro, confirming its function as a CWI receptor that regulates host immunity during early H. schachtii infection.To resolve the spatial complexity of host-parasite interactions, we introduced RNA tomography, a spatial transcriptomics technology, for use in plant tissues. By generating high-resolution spatial gene expression maps of both host and parasite simultaneously in H. schachtii-infected Arabidopsis roots, we offer novel insights into the early stages of plant-nematode interaction that would not have been possible with traditional bulk transcriptomics.Finally, we investigated the role of Arabidopsis PERKs in infection by the root-knot nematode Meloidogyne incognita. Nine perk knockout mutants were more susceptible to the root-knot nematode than wild-type Arabidopsis plants. Of these nine, six perk knockouts displayed similar relative susceptibility to H. schachtii. Remarkably, PERK13 overexpression plants displayed increased susceptibility to M. incognita, in contrast to the near complete resistance to H. schachtii. RNA tomography revealed that PERK13 is irregularly expressed across root tissues; thus, its expression is not restricted to feeding structures or surrounding tissue. Transcriptome analysis showed that differentially expressed genes in M. incognita-infected plants overexpressing PERK13 were associated with cell wall biogenesis and restructuring, indicating that PERK13 regulates plant susceptibility through distinct cell wall modifications during feeding structure formation.Altogether, this thesis elucidates the multifaceted role of CWI receptors during nematode infection, highlighting specific trade-offs that must be considered when engineering CWI-based nematode-resistant crops. EPS Nematology (NEM) EPS Nematology (NEM) urn:nbn:nl:ui:32-be46b4f1-74b1-48c4-a58e-7df8f13e2681/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/e7d95dc2-78e2-429e-a661-c4d2f25bea0d 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-e7d95dc2-78e2-429e-a661-c4d2f25bea0d 2026-04-02 urn:nbn:nl:ui:32-e7d95dc2-78e2-429e-a661-c4d2f25bea0d/mods Globalising fields: precision agriculture and agrarian change in the global production network : A case of Cederberg Valley, South Africa Wageningen University dgg Shahid Ramsha 0000000529622230 aut P. Hellegers opn G. van Halsema opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 169 10.18174/681544 en In today’s context of widespread precision agriculture(PA) technology adoption and enthusiasm across policy, media, development and technology circles, this thesis examines the impact of PA technology in shaping agrarian change. Specifically, it investigates how PA technologies reshape existing social relations of production and lead to the emergence of new relations, actors, and dynamics. The main research question is: How do PA technologies shape agrarian change? Agrarian change is conceptualised as a process driven by local-global interactions within commodity production networks, in which PA technology is both a constituting and mediating actor. Empirically, the thesis focuses on global citrus production network and one of its production nodes, the Cederberg Valley in South Africa. The main conclusions drawn about the impact of PA technologies on agrarian change are that PA technologies enhance the competitive dynamics of global trade centred on issue of quality. They also play a mediating role in the processes of exclusion and inclusion of regions and regional actors in global production networks. Library WASS Water Resources Management Library WASS Water Resources Management urn:nbn:nl:ui:32-e7d95dc2-78e2-429e-a661-c4d2f25bea0d/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/47e70e6b-0d3d-419a-804a-100d9f821c71 2026-04-02 thesis

urn:nbn:nl:ui:32-47e70e6b-0d3d-419a-804a-100d9f821c71 2026-04-02 urn:nbn:nl:ui:32-47e70e6b-0d3d-419a-804a-100d9f821c71/mods Lighting strategies to enhance crop quality in controlled environment agriculture Wageningen University dgg Min Qianxixi 0000000529588327 aut E.J. Woltering opn L.F.M. Marcelis opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 202 10.18174/680863 en Fresh fruit and vegetables are essential components of a healthy diet, yet their health benefits depend not only on availability but also on nutritional quality, sensory appeal, and postharvest storability. Controlled environment agriculture (CEA), including high-tech greenhouses and vertical farms, enables precise regulation of environmental conditions and thus can be used to improve crop quality while maintaining yield. This thesis aimed to investigate how preharvest strategies shape quality at harvest and during postharvest, with a particular focus on lighting strategies—from short-term End-of-Production (EoP) treatments to long-term light management in combination with nutrient solution electrical conductivity (EC). Lettuce and dwarf tomato were used as model crops, representing leafy vegetables with short shelf life and fruit crops whose market value is strongly linked to flavor.The work is built on the central hypothesis that establishing a high quality status before harvest enhances resistance to postharvest deterioration. Crop quality is approached as a multidimensional concept, integrating nutritional value, flavor, visual attributes, and shelf life. Special attention is given to carbohydrates, vitamin C, and sensory quality as key determinants of both consumer acceptance and postharvest performance.In lettuce, short-term EoP lighting was shown to be an effective strategy to rapidly enhance quality without affecting earlier growth. High-intensity EoP lighting increased dry matter, carbohydrates, and total ascorbic acid at harvest, and these improvements persisted during dark storage. Lettuce exposed to high EoP light retained superior sensory quality and exhibited more than double the shelf life compared with low-light treatments. Importantly, carbohydrate and vitamin C levels at harvest were positively correlated with subsequent shelf life, demonstrating that postharvest resilience depends on enhanced energy and antioxidant reserves established before harvest.Further experiments disentangled the roles of light intensity, photoperiod, daily light integral (DLI), and treatment duration during EoP. Quality enhancement was primarily driven by DLI rather than light intensity alone. At a given DLI, longer photoperiods with lower light intensity resulted in higher carbohydrate and vitamin C accumulation than shorter photoperiods with higher intensity, whereas extending treatment duration at low DLI provided no measurable benefit. These results identify extended photoperiod EoP lighting as an efficient strategy to improve lettuce quality.In dwarf tomato, increasing EC improved fruit flavor and nutritional quality but reduced yield. By combining higher EC with increased DLI, it was possible to mitigate yield losses while further enhancing quality compare to higher EC applied alone. Higher light promoted fruit biomass allocation while maintaining or improving flavor and nutritional traits, without compromising shelf life. These responses were supported by physiological adjustments, including changes in leaf morphology and stomatal conductance.Overall, this thesis demonstrates that preharvest lighting strategies can be deliberately designed to elevate initial quality and thereby enhance postharvest performance. Since quality traits differ in their sensitivity and temporal dynamics, effective interventions require developmentally timed and trait-specific strategies. Looking forward, integrating dynamic preharvest lighting with postharvest management, supported by emerging sensing and predictive modeling approaches, offers promising opportunities to translate physiological insights into robust, quality-driven management strategies for modern and future food supply chains. Horticulture and Product Physiology (HPP) PE&RC Horticulture and Product Physiology (HPP) PE&RC urn:nbn:nl:ui:32-47e70e6b-0d3d-419a-804a-100d9f821c71/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/3e2faa06-b51c-4d72-8340-8b6a121ab488 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-3e2faa06-b51c-4d72-8340-8b6a121ab488 2026-04-02 urn:nbn:nl:ui:32-3e2faa06-b51c-4d72-8340-8b6a121ab488/mods Fields2Cover : Transparent and efficient coverage paths for autonomous agricultural vehicles Wageningen University dgg Mier Gonzalo 0000-0002-7588-9911 0000000529566013 aut S. de Bruin opn J. Valente opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 10.18174/681452 en By mid century agriculture must feed a larger population with fewer workers while preserving soil function. Mechanization has raised yields but growing machine weight compacts soil reduces water flow and restricts roots. This thesis argues that lighter robots combined with smarter motion planning can raise output without harming the ground. Controlled Traffic Farming offers a path forward by confining vehicles to fixed swaths and limiting compaction to narrow strips. To exploit those swaths a planner must generate routes that cover the full field. This task defines the Agricultural Coverage Path Planning problem.Most existing planners seek short routes or low energy use and focus on the inner field. They often ignore headlands where machines turn and where damage concentrates. They also treat path length as a proxy of soil compaction and rarely expose code or data. These limits slow progress and weaken trust in results. This thesis aims to raise efficiency and transparency in coverage path planning through open tools and new algorithms that address swaths and headlands coverage and soil response directly.The work pursues four objectives. It integrates planning methods into a unified framework. It improves scientific transparency through open source release and benchmarking. It develops planners that fully cover headlands while respecting vehicle kinematics. It reduces soil compaction by embedding a physical soil model into the optimization.The thesis introduces Fields2Cover an open source library for agricultural coverage path planning. The library structures the problem into modules that generate headlands, create swaths, sort routes, and smooth paths. This design lets researchers swap components and test ideas without rebuilding full pipelines. Implementations in C++, Python, and ROS support use in simulation and on real robots. Early versions focused on convex fields and straight swaths.The framework then expands into a benchmark that supports non convex fields with obstacles and flexible execution order. A shared dataset of field geometries and a configuration system enable fair comparison across methods. Use cases demonstrate how users adapt the workflow to diverse needs.A new headland planner follows. It handles convex and concave corners and accounts for robot and implement size curvature limits and curvature change rates. Multiple corner strategies allow a tradeoff between short paths and full area coverage. Curve concatenation enables effective headland treatment.Finally the thesis optimizes routes to reduce soil compaction by coupling planning with the SoilFlex model. Experiments across repeated passes and intercropping scenarios show clear divergence from length-based optimization and lower predicted damage.By releasing Fields2Cover and its benchmarks this work opens coverage path planning to the community. The modular workflow accelerates research enables reuse and supports integration into larger systems. The proposed planners improve coverage quality and protect soil health. Information Technology PE&RC Geo-information Science and Remote Sensing Toegepaste Informatiekunde PE&RC Geo-information Science and Remote Sensing urn:nbn:nl:ui:32-3e2faa06-b51c-4d72-8340-8b6a121ab488/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/c1f2ebb5-bfb0-4762-b13c-f274b4241dbf 2026-04-02 thesis

urn:nbn:nl:ui:32-c1f2ebb5-bfb0-4762-b13c-f274b4241dbf 2026-04-02 urn:nbn:nl:ui:32-c1f2ebb5-bfb0-4762-b13c-f274b4241dbf/mods Levelling up tempeh: enhancing the antidiarrheal potential of fermented soy with bacterial exopolysaccharides Wageningen University dgg Pramudito Theodorus Eko 0000-0001-8547-267X 0000000529097552 aut H.A. Schols opn E.J. Smid opn C.E. Klostermann opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 235 10.18174/681747 en Lactic acid bacteria (LAB) can produce exopolysaccharides (EPS) that can inhibit enterotoxigenic Escherichia coli (ETEC) adhesion to the mammalian intestinal surface, thus mitigating ETEC-mediated diarrhea. LAB are present in tempeh, a Rhizopus-fermented food product made from soybean. We investigated the anti-adhesion bioactivity against ETEC of EPS from tempeh-associated LAB strain isolates to explore their possible application as adjunct culture in tempeh production to develop tempeh with stronger anti-adhesion functionality against ETEC.Four EPS-producing LAB strains were isolated from tempeh-related environments: Pediococcus pentosaceus TL (PpTL), Leuconostoc citreum TR (LcTR), Leuconostoc mesenteroides WA (LmWA) and L. mesenteroides WN (LmWN). PpTL, LmWA and LmWN each produced a mixture of dextran (alpha-1,6-linked glucan) and levan (beta-2,6-linked fructan) in a 2:3, 1:4 and 4:1 ratio for each respective strain, while LcTR produced mixed-linkage dextran-type EPS. All EPSs had a molecular weight (Mw) >500 kDa and can bind to ETEC cells. When grown on soy dough (SoyD), only LcTR, LmWA and LmWN retained their EPS-producing capabilities. LmWA and LmWN produced EPS with diverse Mw (~20–1000 kDa) when grown on SoyD. Water extract from LAB-fermented SoyD can inhibit ETEC F4 adhesion to porcine gastric mucin, while water extract from non-treated SoyD did not show inhibition. To investigate the optimal structural feature for anti-adhesion bioactivity, LmWN dextran was partially hydrolyzed and tested. It was found that alpha-1,6 glucan structure with Mw ~14–35 kDa showed the highest anti-adhesion bioactivity. Native and partially hydrolyzed EPS from LcTR did not result in anti-adhesion bioactivity, likely due to its mixed-linkage structure. LmWA and LmWN were chosen for application as adjunct culture in tempeh production. The strains could persist through fermentation and were present in the product. Water extract from LAB-supplemented tempeh showed stronger anti-adhesion bioactivity against ETEC F4 compared to non-supplemented tempeh. When the tempeh extract was treated with dextranase, the bioactivity decreased thus indicating the effect of dextran on the bioactivity.We have shown that supplementation of EPS-producing LAB in tempeh production can improve the antidiarrheal potential of the product. This increase in bioactivity is due to the presence of EPS in the product. VLAG Food Chemistry Food Microbiology VLAG Levensmiddelenchemie Levensmiddelenmicrobiologie urn:nbn:nl:ui:32-c1f2ebb5-bfb0-4762-b13c-f274b4241dbf/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/abdf2dcb-cd1d-4a67-8236-96b85fa15eeb 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-abdf2dcb-cd1d-4a67-8236-96b85fa15eeb 2026-04-02 urn:nbn:nl:ui:32-abdf2dcb-cd1d-4a67-8236-96b85fa15eeb/mods Machine learning for fertilizer recommendation in Ghana Wageningen University dgg Asamoah Eric 0000000529560869 aut G.B.M. Heuvelink opn V. Logah opn P.S. Bindraban opn I. Chairi opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 181 10.18174/681431 en Maize is a major staple crop in Ghana and across Sub-Saharan Africa (SSA), yet yields remain far below their potential due to persistent soil fertility constraints, inefficient fertilizer use, and reliance on blanket recommendations that fail to capture site-specific variability. Mechanistic models such as QUEFTS have advanced understanding of crop–nutrient relationships, but their application in SSA is limited by high data requirements and weak consideration of farmer risk and socioeconomic realities. Recent advances in machine learning (ML) provide new opportunities to generate data-driven, site-specific, and adaptive fertilizer recommendations, but questions remain regarding model reliability under data-scarce conditions, uncertainty quantification, and alignment with smallholder decision-making. This thesis evaluates the potential of ML to support maize fertilizer recommendations in Ghana by addressing yield prediction, agronomic efficiency, uncertainty, and farmer risk preferences. Using large, multi-season, multi-location datasets of maize field trials, Random Forest (RF) and other ML models were trained and rigorously validated. Results showed that RF explained up to 81% of yield variation and moderately predicted agronomic efficiency, with nitrogen fertilizer, rainfall, temperature, soil organic carbon, and bulk density emerging as key drivers. Comparative analysis of ML algorithms demonstrated that tree-based models (RF and XGBoost) outperformed other approaches under heterogeneous and data-scarce conditions. Field validation experiments across major agroecological zones revealed that ML-derived fertilizer recommendations were generally more site-specific and cost-effective than conventional approaches, particularly in the Guinea Savanna and Forest–Savanna Transition zones. While mechanistic models performed well in some environments, ML approaches often achieved comparable or higher yields with improved net profit margins. Importantly, integrating predictive uncertainty and farmer risk preferences through a utility-based framework showed that risk-averse farmers prefer lower fertilizer rates than technically optimal recommendations, especially in marginal environments. Overall, the thesis demonstrates that ML can complement mechanistic models by providing flexible, data-driven, and risk-aware decision support. By explicitly accounting for uncertainty, data limitations, and farmer behaviour, this research lays the foundation for farmer-centered agronomic decision-support systems that enhance productivity, profitability, and resilience in smallholder maize systems in SSA. PE&RC Soil Geography and Landscape ISRIC - World Soil Information PE&RC Bodemgeografie en Landschap ISRIC - World Soil Information urn:nbn:nl:ui:32-abdf2dcb-cd1d-4a67-8236-96b85fa15eeb/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/7f572f20-f218-4e9d-9a1b-a17992cd612b 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-7f572f20-f218-4e9d-9a1b-a17992cd612b 2026-04-02 urn:nbn:nl:ui:32-7f572f20-f218-4e9d-9a1b-a17992cd612b/mods Nudges, integrated pest management, and livelihoods : Experimental evidence from rural Ethiopia Wageningen University dgg Deffersha Solomon Balew 0000000529101726 aut E.H. Bulte opn M. Kassie opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 184 10.18174/681005 en The thesis looks at how small changes in how we present information or rewards can help farmers and communities adopt better farming and health practices. I focused on rural Ethiopia, studying ways to encourage farmers to use new technologies that can boost crop yields and reduce pests, as well as ways to prevent malaria through house improvements. I found that using social recognition and highlighting risks of not acting (loss framing) are powerful tools to motivate change. These small nudges, combined with support and active participation, can lead to lasting improvements in livelihoods and health. This research shows that understanding local social dynamics and emotions is key to designing effective programs that are sustainable and truly help communities improve their lives. WASS Development Economics WASS Ontwikkelingseconomie urn:nbn:nl:ui:32-7f572f20-f218-4e9d-9a1b-a17992cd612b/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/352236a2-c7ab-4587-bc77-1d351185c8c6 2026-04-02 thesis

urn:nbn:nl:ui:32-352236a2-c7ab-4587-bc77-1d351185c8c6 2026-04-02 urn:nbn:nl:ui:32-352236a2-c7ab-4587-bc77-1d351185c8c6/mods Microalga as a sustainable oil crop Wageningen University dgg Abdelkarim Omnia H. 0000-0002-9149-1209 0000000529561175 aut M.J. Barbosa opn R.H. Wijffels opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 314 10.18174/681731 en Microalgae represent promising sustainable platforms for producing high-value lipid compounds, yet our understanding of how environmental factors regulate carbon partitioning between fatty acid and sterol biosynthesis remains limited. This thesis investigates how nitrogen availability, light intensity, temperature, and salinity affect carbon allocation between fatty acid and sterol across multiple microalgal species, with particular focus on Nannochloropsis oceanica.Our research revealed distinct strain-specific responses to environmental conditions. Under nitrogen starvation, N. oceanica achieved a maximum triacylglycerol (TAG) content of 37% dry weight (DW) at high biomass-specific photon supply rates (BSPSR), representing a 1.3-fold increase compared to low BSPSR. Temperature shifts enhanced membrane lipid and eicosapentaenoic acid (EPA) synthesis. Additionally, N. oceanica exhibited diurnal cholesterol oscillations, varying 26% between day and night, under salinity stress. High salinity conditions (50 g/L NaCl) increased cholesterol accumulation to 4% DW while simultaneously enhancing TAG synthesis.The research demonstrates that environmental stresses induce specific carbon partitioning patterns, with nitrogen starvation primarily driving TAG accumulation, salinity stress promoting both sterol and fatty acid synthesis, and temperature shifts influencing membrane lipid composition. These findings advance understanding of microalgal lipid metabolism regulation and provide cultivation strategies for optimizing high-value lipid production in biotechnological applications. Bio Process Engineering VLAG Bio Process Engineering VLAG urn:nbn:nl:ui:32-352236a2-c7ab-4587-bc77-1d351185c8c6/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/caa3cf55-c651-4b51-80bb-f8f730426f3f 2026-04-02 thesis

urn:nbn:nl:ui:32-caa3cf55-c651-4b51-80bb-f8f730426f3f 2026-04-02 urn:nbn:nl:ui:32-caa3cf55-c651-4b51-80bb-f8f730426f3f/mods Towards a sustainable food system in China : insights from an integrated environmental-economic modelling approach Wageningen University dgg Long Weitong 0000000529465861 aut X. Zhu opn H.-P. Weikard opn O. Oenema opn Y. Hou opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 274 10.18174/681315 en Feeding a growing global population in a healthy manner while reducing environmental degradation is one of the most pressing challenges of the 21st century. Addressing this challenge calls for a transition from the current food system towards a system that is not only resilient but also equitable and environmentally sustainable. Although numerous studies have examined the environmental benefits of various food system transformation options, many of them neglect the economic interactions. Using an integrated environmental-economic applied general equilibrium modelling approach, this thesis contributes to the assessment of the environmental and economic impacts of various food system transformation options. It focuses on China, the world’s largest agricultural producer and importer, and the largest annual emitter of greenhouse gases. The thesis captures both the domestic impacts of transformation options in China and the cross-border impacts on its main food and feed trading partners (MTP, including Brazil, the United States, and Canada) due to the involved international trade.The thesis starts with an introduction to general equilibrium theory, the core economic theory that this thesis is based on. It also introduces some literature on applications of general equilibrium models in the environmental economics field. Then the thesis presents three particular empirical modelling applications to assess the environmental and economic impacts of various food transformation options in China. First, it explores options for mitigating the negative environmental spillovers from international trade between trading partners and China and assesses the environmental and economic impacts of a dietary shift from pork to novel soy-based food, the adoption of cleaner cereals production technology, and a unilateral environmental policy in China. Second, it assesses the environmental and economic impacts of upcycling food waste and food processing by-products as feed for China’s monogastric livestock and explores strategies to absorb the rebound effects of this upcycling while safeguarding food security. Third, it assesses the environmental and economic impacts of China’s transition towards a healthier diet and an afforestation policy. It also analyses how China’s unilateral emission mitigation measures interact with a stringent global climate mitigation policy. Overall, the thesis contributes to policy design aimed at achieving the dual dividend of environmental sustainability and food security and provides insights into minimising trade-offs and exploiting synergies in China’s food system transformation. Environmental Economics and Natural Resources WASS Sustainable Soil Use Milieueconomie en Natuurlijke Hulpbronnen WASS Duurzaam Bodemgebruik urn:nbn:nl:ui:32-caa3cf55-c651-4b51-80bb-f8f730426f3f/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/b8619ca1-dd4e-4e9a-9e41-6a9dc04c442f 2026-04-02 thesis

urn:nbn:nl:ui:32-b8619ca1-dd4e-4e9a-9e41-6a9dc04c442f 2026-04-02 urn:nbn:nl:ui:32-b8619ca1-dd4e-4e9a-9e41-6a9dc04c442f/mods Application of trait-based plant-soil feedback for agroecosystem optimization Wageningen University dgg Bin Zhaoqi 0000-0003-0192-3846 000000052954632X aut W.H. van der Putten opn J. Zhang opn G.F. Veen opn G. Wang opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 243 10.18174/681532 en The Green Revolution increased global food production, but intensive agriculture now relies heavily on fertilizers and pesticides, resulting in soil degradation, pollution, resource depletion, and biodiversity loss. Sustainable agriculture therefore requires not only maintaining crop yields but also supporting multiple soil functions, such as biomass production, nutrient cycling, carbon storage, and disease suppressiveness, simultaneously, a concept known as soil multifunctionality. These functions are shaped by interactions between plants and soil biotic and abiotic properties, commonly described as plant–soil feedbacks (PSFs). Although PSF theory is increasingly applied to agriculture, its predictability remains limited, and its relationship with soil multifunctionality is poorly understood.In this thesis, I investigated whether plant traits can predict PSFs of crop species and how crops influence individual soil functions and overall soil multifunctionality. While trait-based PSF approaches have been widely studied in natural ecosystems, their application to agricultural crops remains rare. By combining a quantitative synthesis (Chapter 2), a greenhouse PSF experiment (Chapter 3), and a soil multifunctionality assessment (Chapter 4), I evaluated the potential of trait-based PSF approaches to inform crop rotation design that balances productivity and soil health.In Chapter 2, I synthesized published studies reporting both PSF and plant traits, supplemented with trait values from the TRY database. Across a wide range of species, trait–PSF relationships were generally weak, with root length showed the strongest association with PSF. Relationships were stronger within functional groups than across all species, indicating strong context dependence. Traits measured in situ explained more variation than database-derived traits, suggesting that local environmental conditions strongly influence trait expression relevant to PSF. Combining data sources did not improve predictions, highlighting the limited and context-dependent nature of trait-based PSF inference.In Chapter 3, I experimentally tested PSFs of twelve major crops under controlled greenhouse conditions and assessed whether root traits could predict crop PSFs. Results showed clear species-specific PSF: broad bean generally enhanced subsequent crop growth, whereas wheat had inhibitory effects. Root traits such as projected root area, root tip number, and root tissue density were the best PSF predictors, but their predictive power depended on whether traits were measured in sterilized or conspecific-conditioned soils. Moreover, crops differed in both their ability to condition soils and their responsiveness to soils conditioned by others, limiting the practical value of trait-based PSF predictions for crop rotation design.In Chapter 4, I extended the analysis beyond PSF to assess how the same twelve crops affected four soil functions and overall soil multifunctionality. No single crop consistently enhanced all functions. Instead, crops contributed in complementary ways: legumes promoted biomass production and nutrient cycling, while crucifers enhanced disease suppressiveness and carbon storage. Soil multifunctionality increased with functional evenness, indicating that crop diversity can enhance multiple soil functions simultaneously.Overall, this thesis shows that while PSFs are strong and species specific, trait-based PSF predictions are limited and highly context dependent. Sustainable crop rotation design therefore requires moving beyond yield-centered strategies toward functional complementarity among crops to support long-term soil multifunctionality and agricultural resilience. PE&RC Nematology (NEM) PE&RC Nematology (NEM) urn:nbn:nl:ui:32-b8619ca1-dd4e-4e9a-9e41-6a9dc04c442f/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/e68c18c1-3c50-442d-a763-9e5116f769c1 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-e68c18c1-3c50-442d-a763-9e5116f769c1 2026-04-02 urn:nbn:nl:ui:32-e68c18c1-3c50-442d-a763-9e5116f769c1/mods Inclusive business beyond borders: the role of innovation intermediaries in market integration for the Base-of-the-Pyramid Wageningen University dgg Danse Myrtille G. 303487860 0000000388423894 aut L.W.A. Klerkx opn R. Lie opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 254 10.18174/681029 en This dissertation examines how business models aimed at improving food security in Base-of-the-Pyramid (BOP) markets can be effectively developed and socially embedded to generate mutual economic and social value. Addressing a central dilemma in international development, the study examines how multinational enterprises (MNEs) pursue commercial objectives while contributing to social outcomes in contexts characterized by poverty, institutional voids, and fragmented value chains. The research focuses in particular on the role of innovation intermediaries in cross-border, cross-sector development partnerships (CSDPs) and their contribution to collaboration, institutional bridging, local embeddedness, and long-term social value creation in low-income markets.Positioned within the evolution of the BOP paradigm, the dissertation builds on critiques of early BOP approaches that emphasized affordability and market access while insufficiently addressing structural development outcomes. It aligns with the BOP 3.0 perspective, which foregrounds systemic change, environmental sustainability, and local ownership. Within this perspective, the study addresses four interrelated research questions: how MNEs select international markets for inclusive innovation; which business strategies are deployed to address food and nutrition security; what roles and functions innovation intermediaries perform in cross-border CSDPs; and how these intermediaries enable social value creation in BOP markets.Methodologically, the research adopts a mixed-methods design combining literature review, international database analysis, surveys, and in-depth qualitative case studies. The empirical core consists of four cross-border CSDPs in Kenya and Nigeria, supported by 55 semi-structured interviews with MNE managers, innovation intermediaries, local partners, farmers, and public-sector actors. Additional data include a survey of 25 innovation intermediaries and participatory validation workshops conducted in both Africa and the Netherlands, enabling triangulation across data sources and stakeholder perspectives.The findings yield several key insights. First, private sector representatives often apply cognitive criteria based on relations and familiarity during early-stage country screening. While existing databases enable more refined assessments of BOP market attractiveness, particularly regarding institutional and infrastructural conditions, such data are typically consulted only once firms engage in CSDPs and collaborate with locally embedded intermediaries. Second, inclusive business success depends not only on affordability but on product and service quality and on embedding business models within local ecosystems. Innovation intermediaries play a key role in this process by linking value chain actors through coordinated marketing and distribution strategies and by supporting training and coalition-building to bridge institutional and cultural gaps and strengthen nutrition and food security outcomes. Third, the study develops a typology of innovation intermediary roles, identifying intermediaries as conveners, mediators, co-creators, and learning catalysts. These roles are dynamic rather than static, shifting in response to contextual volatility, donor pressures, and local needs. Finally, the research shows that social outcomes remain contingent on the extent to which cross-border CSDPs embed local ownership, shared risk management, and long-term financial sustainability beyond initial grant funding, highlighting the need to align inclusive business model design with adaptive intermediation practices.The dissertation contributes theoretically to international business, inclusive business model, and innovation intermediation literatures, and offers practical guidance for policymakers and donors seeking to strengthen governance mechanisms that safeguard social value creation over time. WASS Knowledge Technology and Innovation WASS Kennis, Technologie and Innovatie urn:nbn:nl:ui:32-e68c18c1-3c50-442d-a763-9e5116f769c1/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/fdb652d7-534c-4155-a9a6-1394ab4666ed 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-fdb652d7-534c-4155-a9a6-1394ab4666ed 2026-04-02 urn:nbn:nl:ui:32-fdb652d7-534c-4155-a9a6-1394ab4666ed/mods The fate and removal of micropollutants and antibiotic resistance in aerobic granular sludge systems Wageningen University dgg Feng Zhaolu 0000000529546354 aut N.B. Sutton opn H. Schmitt opn M.C.M. van Loosdrecht opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 296 10.18174/681635 en Emerging contaminants, including micropollutants (OMPs), antibiotic resistant bacteria (ARB), and their genes (ARGs), are frequently detected in municipal wastewater and are only partially removed by conventional activated sludge systems. Aerobic granular sludge (AGS) process offers a promising alternative, but its granule size distribution and batch-fed operation lead to different treatment dynamics. To date, the fate and removal of these contaminants in full-scale AGS systems, especially regarding granule size fractions and wet-weather impacts, remain poorly understood. This thesis investigates OMP removal via sorption and biotransformation, and ARB (Escherichia coli) elimination through protozoan predation or other mechanisms across six AGS size fractions. Larger granules enhanced OMP sorption and E. coli predation, while smaller fractions contributed more to OMP biotransformation and ARG dissemination. Full-scale monitoring showed reduced OMP and ARG removal during wet weather due to operational adjustments. Overall, this thesis assesses the potential of AGS process for controlling emerging contaminants and proposes strategies to enhance their removal by optimising granule size distribution and operational parameters. WIMEK Environmental Technology WIMEK Milieutechnologie urn:nbn:nl:ui:32-fdb652d7-534c-4155-a9a6-1394ab4666ed/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/ed207692-b444-4fe9-a04e-81f515427b68 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-ed207692-b444-4fe9-a04e-81f515427b68 2026-04-02 urn:nbn:nl:ui:32-ed207692-b444-4fe9-a04e-81f515427b68/mods Assessment of micro and nanoplastic toxicity and their protein corona using in vitro and in silico new approach methodologies Wageningen University dgg Brouwer Hugo 0000000529453131 aut H. Bouwmeester opn M. Busch opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 291 10.18174/681575 en The invention of plastic has revolutionized our world by providing a readily available, moldable material which is light, strong and durable. However, excessive use of plastics has led to universal pollution of our planet. Over time plastic waste and products can degrade, leading to release of microscopic particles called microplastics and nanoplastics (MNPs). MNPs are abundant in our food, the water we drink and the air we breathe and in turn human exposure is unavoidable. Oral ingestion is the biggest source of MNP exposure for humans and amidst all human organs the intestine faces the largest MNP exposure which potentially affects intestinal health. In animals, MNP exposure can cause inflammatory effects and barrier disruption in the intestine, however it is unknown if these effects occur in humans. Given the diversity of MNPs found in nature, exhaustive safety testing through animal studies is undesirable and instead In vitro and in silico methods (collectively called New Approach Methodologies (NAMs)) can aid MNP toxicity assessment. Current MNP research with NAMs has limited ability to predict toxicity in humans due to lack of assessment of true-to-life secondary MNPs, aberrant phenotype of in vitro cell lines and a lack of understanding of mechanisms like protein-corona formation and biokinetic processes. The aim of this thesis was to improve in vitro and in silico NAMs for MNP toxicity assessment and to improve understanding of the formation and effects of the protein corona on MNPs. This thesis demonstrated that commonly used micro and nanoplastic models are not predictive of true microplastic toxicity to the intestine or resident immune cells. We show that this discrepancy is in part due to the overreliance on polystyrene materials and due to effects of a bound layer of proteins, called the protein corona, on toxicity and bioavailability. Finally we build one of the first in silico models that predict tissue concentrations after oral ingestion of micro and nanoplastics. Overall our results show that specific proteins of the protein corona increase immunogenicity, generation of reactive oxygen species and barrier disruption as well as particle uptake through phagocytosis. Our in silico model predicts that at the moment microplastic toxicity to humans is of low risk, however the differences between model microplastics and true-microplastics need to be considered as micro- and nanoplastic risk assessment matures. Overall the studies described in this thesis indicate that the gut is one of the target organs of environmental microplastics which may be harmful to the human intestine, and that a realistic protein corona composition needs to be considered for both toxicokinetic and toxicodynamic assessment of microplastics. VLAG Toxicology VLAG Toxicologie urn:nbn:nl:ui:32-ed207692-b444-4fe9-a04e-81f515427b68/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/4c58aa0e-1951-4c72-9b44-09cb27dd47b0 2026-04-02 thesis

urn:nbn:nl:ui:32-4c58aa0e-1951-4c72-9b44-09cb27dd47b0 2026-04-02 urn:nbn:nl:ui:32-4c58aa0e-1951-4c72-9b44-09cb27dd47b0/mods Beyond land restoration: learning from successful smallholder communities Wageningen University dgg Asresehegn Tewodros G. 0000000529560842 aut R.P.O. Schulte opn S. Schulz opn V. Valencia opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 201 10.18174/681598 en Land degradation remains a pervasive global challenge, undermining ecosystem functions and threatening rural livelihoods. Its impacts are particularly severe for smallholder farmers, who account for nearly one-third of global food production and provide the primary source of food calories in many low-income countries. Addressing both the current and anticipated land degradation is therefore not only a local imperative but also a global priority, situating land restoration at the core of sustainable development agendas, including national strategies, international commitments such as the UN Decade on Ecosystem Restoration, and initiatives like the Bonn Challenge. Ethiopia exemplifies this challenge, as its highland agricultural landscapes continue to experience significant land degradation—combined with recurrent natural and human-induced shocks— threatening the productivity and resilience of smallholder systems that form the backbone of the national economy. Despite decades of restoration interventions implemented by government agencies, development partners, and community programs, restoration outcomes remain highly variable, with some communities achieving substantial high restoration outcomes while others require additional resources and time to achieve the same. To investigate the drivers of this variability, this study employed a transdisciplinary approach, examining 72 communities across the Ethiopian Highlands with high-, medium-, and low-performance in land restoration. The analysis reveals that social and institutional factors, including strong local leadership, robust self-organization, inclusive decision-making, and active community participation throughout the design, implementation and progress monitoring of restoration programs, are critical determinants of success. Communities exhibiting these attributes not only restore degraded landscapes more effectively but also demonstrate greater capacity to innovate, adopt adaptive land management practices, and transform their farming systems in response to biotic, abiotic, and socio-polictical. In contrast, communities with weaker local leadership capacity, organizational structures or limited engagement often require additional resources and time to achieve comparable results. These findings underscore that technical interventions alone are insufficient for sustainable restoration; instead, targeted investment in building the social, institutional, and adaptive capacities of local communities provides the foundation for lasting restoration outcomes, enhanced resilience, and sustainable smallholder livelihoods. By highlighting the interplay between social dynamics, institutional support, and ecological restoration, this study contributes to a deeper understanding of how sustainable landscape restoration can be effectively scaled across degraded agricultural systems, particularly in regions vulnerable to multiple shocks and stresses. PE&RC Farming Systems Ecology (FSE) PE&RC Farming Systems Ecology (FSE) urn:nbn:nl:ui:32-4c58aa0e-1951-4c72-9b44-09cb27dd47b0/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/cbbd6511-83bc-4679-8a6d-f1ea793d160d 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-cbbd6511-83bc-4679-8a6d-f1ea793d160d 2026-04-02 urn:nbn:nl:ui:32-cbbd6511-83bc-4679-8a6d-f1ea793d160d/mods Finding the Achilles’ heel of Streptococcus suis : molecular mechanisms of adaptation to host-like environments Wageningen University dgg Juanpere-Borràs Maria 0000000529180815 aut J.M. Wells opn P. van Baarlen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 205 10.18174/681597 en This thesis investigates how Streptococcus suis adapts to host environments and identifies vulnerabilities that could inform new antimicrobial strategies. Using transposon mutagenesis and host-derived fluids, we uncovered conditionally essential genes that support growth in activated porcine serum and cerebrospinal fluid, highlighting key roles for purine biosynthesis, membrane homeostasis, and amino acid transport. We then dissected membrane-stress responses and revealed a coordinated regulatory network involving the LiaFSR and two LytTR systems that controls envelope integrity, competence, biofilm formation, and viability in host-like conditions. Epigenetic regulation was explored through two type I restriction–modification systems, showing that interactions between two different methylation systems influence carbohydrate acquisition, central metabolism, and growth, particularly in disease-associated lineages. We also benchmarked Nanopore sequencing for applications requiring precise taxonomic and genetic resolution, improving long-read workflows for microbiome and mutagenesis studies. Together, these findings expose metabolic and regulatory bottlenecks that shape S. suis survival in host niches and provide entry points for antimicrobial discovery. WIAS Host-Microbe Interactomics WIAS Host-Microbe Interactomics urn:nbn:nl:ui:32-cbbd6511-83bc-4679-8a6d-f1ea793d160d/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/8d41f3cc-3ac7-4baa-86d4-b140cb0c6db8 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-8d41f3cc-3ac7-4baa-86d4-b140cb0c6db8 2026-04-02 urn:nbn:nl:ui:32-8d41f3cc-3ac7-4baa-86d4-b140cb0c6db8/mods Disease suppression in intercropping systems: a mechanistic perspective Wageningen University dgg Homulle Zohralyn 0000-0002-0075-5812 0000000529546338 aut N.P.R. Anten opn J.C. Douma opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 272 10.18174/681554 en The mechanisation, specialisation and intensification of agriculture have resulted in highly efficient and productive agricultural systems. However, this mode of agriculture also comes at a cost; it contributes to numerous forms of environmental degradation, biodiversity loss, and land and water pollution. Monocultures - (large-scale) fields where a single crop type is grown - are a key element of such agricultural systems, and relatively vulnerable to pests and diseases. Intercropping, the simultaneous cultivation of multiple crop species within the same field, offers a promising strategy to enhance agroecosystem diversity and suppress plant diseases. Although numerous studies demonstrate disease-suppressive effects of intercropping, the relative importance of underlying mechanisms and the influence of management practices, crop traits, and pathogen characteristics remain poorly understood, especially in strip cropping systems compatible with modern machinery.This thesis investigated the drivers and mechanisms of disease suppression in intercropping using a two-fold approach. First, a meta-analysis across diverse crop–pathogen systems assessed general patterns of disease suppression and factors influencing them. Second, detailed field experiments and modelling focused on potato late blight, caused by Phytophthora infestans, within a strip cropping context.The meta-analysis demonstrated that intercropping consistently reduced plant disease compared with monocropping by lowering both initial disease incidence and subsequent infection rates. These effects were robust across crop combinations and planting patterns. Species that were taller than the focal crop significantly suppressed vectored plant pathogens in the focal crop more than companions of similar or shorter height, suggesting a potentially important role of the barrier effect. However, high variability among systems and experimental designs limited the ability to disentangle specific causal mechanisms.To examine mechanisms in detail, three years of field experiments in the Netherlands evaluated potato strip cropping with companion crops differing in stature. Strip cropping with grass or maize significantly reduced late blight severity relative to monoculture, whereas faba bean had no significant effect. Measurements of microclimate, spore dispersal, and host resistance revealed that disease suppression arose from multiple interacting mechanisms. Grass reduced relative humidity within potato strips, while maize primarily acted as a barrier to spore dispersal but could also increase humidity later in the season, creating time-dependent trade-offs.A simulation model integrating host dilution, microclimate modification, and barrier effects showed that no single mechanism fully explained disease suppression. Instead, combined effects best predicted observed disease dynamics, with mechanisms varying in strength and occasionally counteracting one another while remaining overall suppressive.In the final chapter, I discuss the usefulness of meta-analysis for studying disease suppression, discuss challenges in designing and implementing strip-cropping systems in conventional agriculture, and consider their potential to reduce chemical inputs. Lastly, I stress the importance of looking beyond optimisation and (short-term) techno-fixes, advocating instead for a radical transformation of the food system and a change in power structures to actually address the negative side effects of modern agriculture. PE&RC Centre for Crop Systems Analysis (CSA) PE&RC Centre for Crop Systems Analysis (CSA) urn:nbn:nl:ui:32-8d41f3cc-3ac7-4baa-86d4-b140cb0c6db8/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/68473b7c-e638-4860-acb4-b99f269325cb 2026-04-02 thesis

urn:nbn:nl:ui:32-68473b7c-e638-4860-acb4-b99f269325cb 2026-04-02 urn:nbn:nl:ui:32-68473b7c-e638-4860-acb4-b99f269325cb/mods Towards understanding uncertainties in the measurement of microplastic concentrations in river systems Wageningen University dgg Wang Siting 000000052946587X aut A.A. Koelmans opn Jing Wu opn S.M. Mintenig opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 140 10.18174/681522 en This thesis investigates how methodological choices and regional context shape freshwater microplastic monitoring and risk assessment. It first evaluates key analytical parameters, showing that higher-resolution micro-FTIR objectives greatly increase detected particle numbers, while a 20 micro-m sieve can be sufficient for routine work. It then quantifies abundances, size spectra and polymer types in the Yangtze–Huangpu system and the Rhine–Meuse delta, revealing high contamination and region-specific polymer profiles. A systematic review of Yangtze studies, scored against updated QA/QC criteria, exposes substantial methodological gaps and likely underestimation of small particles, yet indicates that ecological thresholds are often exceeded. Finally, a detailed uncertainty analysis identifies sediment sampling, blank correction, and particle-to-mass conversion (including polymer density assumptions) as dominant error sources. Together, these components provide harmonized datasets, an uncertainty framework, and clear recommendations for standardized, quality-controlled monitoring to support more reliable freshwater microplastic risk assessments and management. WIMEK Aquatic Ecology and Water Quality Management WIMEK Aquatische Ecologie en Waterkwaliteitsbeheer urn:nbn:nl:ui:32-68473b7c-e638-4860-acb4-b99f269325cb/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/38f99750-d9c1-4c43-bff0-dc5ba25a974c 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-38f99750-d9c1-4c43-bff0-dc5ba25a974c 2026-04-02 urn:nbn:nl:ui:32-38f99750-d9c1-4c43-bff0-dc5ba25a974c/mods Envisage phenotyping : integrating artificial intelligence in image analysis for selective breeding in aquaculture Wageningen University dgg Xue Yuanxu 0000000529546303 aut H. Bovenhuis opn J.W.M. Bastiaansen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 189 10.18174/681487 en Automated phenotyping is a rapidly evolving interdisciplinary field focused on high-throughput, non-invasive phenotype collection to support breeding and management decisions in aquaculture. Current development primarily targets production traits, leaving a gap in traits linked with metabolism, health and physiological well-being. These traits are complex and difficult to measure, but advancements in AI-based prediction models combined with imaging technologies provide opportunities. This thesis used fish image data collected in breeding facilities, to broaden the scope of predicted phenotypes that contribute to the breeding goals for these species.For production traits, a structural framework was introduced to determine optimal image-based prediction strategies, demonstrated in gilthead seabream (Sparus aurata). The framework captures both simple and high-dimensional relationships between images and target traits. Interpretation of the model was provided by visualizing predictive imaginal features.To dissect the genetic basis of swimming performance in rainbow trout (Oncorhynchus mykiss), a novel workflow identified accessible and heritable morphological indicators. Among fish of the same weight, relatively larger and broader epaxial muscles, larger heads, and smaller caudal fins were associated with poorer swimming performance. This study illustrates how images and AI can be interpreted physiologically using Explainable AI.Individual re-identification is essential for longitudinal traits. Although image-based re-identification is promising, it remains infeasible for Atlantic salmon (Salmo salar) under realistic aquaculture conditions due to variation in the phenotyping environment, especially lighting, and limited phenotypic stability. In search for solutions, a review was conducted on the current state of vision-based re-identification in aquaculture. Limitations in data acquisition, data analysis, and practical implementation were identified. Without high-tech data acquisition, multi-dimensional data quality frameworks, and benchmarking methods, vision-based re-identification is found too immature to replace PIT tags. Future progress depends on dataset standardization, methodological refinement, and strong alignment with aquaculture systems.The objectivity of qualitative phenotypic measurements using images was improved and applied to body shape in gilthead seabream (Sparus aurata). Two moderately heritable traits, “Distance to the Best” (DtB) and “Distance to the Worst” (DtW), were derived for the deviation of each fish from an ideal or undesirable shape. This approach is objective, automated, visually intuitive, and flexible for updating target shapes.This thesis emphasizes that successful integration of AI and image analysis requires an understanding of the entire breeding program, not just phenotypic data collection and analysis. This thesis contributes advanced phenotyping and decision-support AI tools to the ongoing integration of emerging AI trends to improve animal production, health, and welfare. WIAS Animal Breeding and Genomics WIAS Animal Breeding and Genomics urn:nbn:nl:ui:32-38f99750-d9c1-4c43-bff0-dc5ba25a974c/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/0fb2aca9-600d-4864-b492-3aad1892efa5 2026-04-02 thesis

urn:nbn:nl:ui:32-0fb2aca9-600d-4864-b492-3aad1892efa5 2026-04-02 urn:nbn:nl:ui:32-0fb2aca9-600d-4864-b492-3aad1892efa5/mods Flows on the edge : Boundary interactions and local heterogeneities in complex fluid flows Wageningen University dgg Majhi Akankshya 0000000529546274 aut J. van der Gucht opn J.A. Dijksman opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 176 10.18174/681076 en From toothpaste to face creams, complex fluids are ubiquitous. Their flow behaviour depends not only on intrinsic material properties but also on interactions with confining boundaries and local flow heterogeneities. Understanding these effects is critical for linking microscopic interactions to macroscopic rheology in fundamental and applied contexts. This thesis addresses the influence of boundary roughness, multi-directional flows, and local heterogeneities on the flow behaviour of Newtonian and non-Newtonian fluids. Through a combination of rheological and imaging studies, it highlights how local flow dynamics connect to global rheological responses.Chapter 2 investigates laminar Newtonian flow near rough boundaries using custom-designed Couette geometries, patterned with horizontal, vertical, and angled ridges. Fluid penetration into surface asperities is quantified as penetration depth delta, which captures the spatially averaged behaviour of the decaying fluid velocity profile between the roughness patterns. Experiments and numerical simulations demonstrate that delta depends on ridge depth, spacing, and orientation. For horizontal ridges, delta collapses onto a simple exponential master curve, while vertical ridges show reduced penetration, and angled ridges exhibit intermediate penetration. This coarse-graining approach enables wall roughness to be modelled as a modified no-slip boundary condition, providing a generalised length scale for rough surfaces.Chapter 3 builds on this analysis by directly measuring penetration depth from local flow fields using rheo-MRI in angled ridged Couette geometries. Such wall patterning induces an axial flow, in addition to primary azimuthal flow, even in the laminar regime. The effect of roughness directionality on the flow behaviour of Newtonian and yield stress fluids is quantified through spatially resolved velocity profiles. A clear correlation is found between penetration depth and axial flow, both increasing with ridge angle and rotation rate. A critical rotation rate is identified for yield stress fluids, below which axial flow is suppressed. This finding demonstrates that yielding behaviour influences both primary and secondary flows, thereby controlling flow penetration.Chapter 4 introduces rheo-LSI, a technique combining rheology with laser speckle imaging, to resolve local flow heterogeneities in complex fluids. This technique maps heterogeneities at wall boundaries, with high sensitivity across a large field of view, by incorporating a deformable elastomer slab, whose deformation relates to local wall stress. The technique is validated with Newtonian fluids of different viscosities, and subsequently applied to a shear thickening cornstarch suspension. Spatially resolved stress maps reveal regions of flow heterogeneity that correspond directly to the macroscopic rheological response. Rheo‑LSI thus offers a tool to relate local spatio‑temporal stresses with bulk flow.Chapter 5 applies rheo-LSI to visualise the spatio-temporal evolution of local heterogeneities in dense cornstarch suspensions under oscillatory shear. These suspensions exhibit discontinuous shear thickening (DST) at high concentrations. Three regimes of local dynamics are identified, featuring a jamming front propagating radially inwards with increasing strain. At intermediate and high strain amplitudes, dynamic localised regions emerge, correlating with macroscopic DST. These observations elucidate the pivotal role of heterogeneous microstructural dynamics in governing bulk rheology.Overall, this thesis establishes the importance of boundary interactions and local heterogeneities in linking microscopic flow dynamics to macroscopic rheology. Physical Chemistry and Soft Matter VLAG Fysische Chemie en Zachte Materie VLAG urn:nbn:nl:ui:32-0fb2aca9-600d-4864-b492-3aad1892efa5/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/cffb1236-d98c-4211-b31f-eae1a00095c1 2026-04-02 thesis

urn:nbn:nl:ui:32-cffb1236-d98c-4211-b31f-eae1a00095c1 2026-04-02 urn:nbn:nl:ui:32-cffb1236-d98c-4211-b31f-eae1a00095c1/mods Decoding tropical forest change at fine scale with multi-sensor satellite data and artificial intelligence Wageningen University dgg Slagter Bart 0000000492249670 aut M. Herold opn J. Reiche opn M. Peña-Claros opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 167 10.18174/681455 en Tropical forests are of crucial importance but are seriously threatened by human-driven deforestation and forest degradation. To better manage and protect tropical forests, we need fast and precise satellite-derived information on forest change, its causes, and its impacts. Current remote sensing-based monitoring systems commonly focus on generic detections of tree cover loss only, without thematic distinction of direct drivers, and often have a critical blind spot for selective logging activities, which are widespread across the tropics. This limits our understanding of the ecological and climate impacts of forest changes, and hampers the options to avert illegal or unsustainable activities in a timely manner. In this thesis, deep learning methods were developed based on multi-sensor Sentinel-1 radar and Sentinel-2 optical imagery for driver-specific tree cover loss monitoring across the pantropics, and for detailed monitoring of road development and associated logging activities in the Congo Basin forest. Beyond method development, these approaches were applied wall-to-wall to obtain a deeper understanding and assessment of recent forest changes.The results revealed that tree cover loss is driven by a wide range of processes across the tropics, with local-scale complexities, spatiotemporal interactions, and strong seasonality. While large-scale agriculture and wildfire were confirmed as the dominant drivers of tree cover loss, the fine-scale monitoring approach brought a novel perspective on the critical role of road development, selective logging, mining, small-scale agriculture, and natural disturbances. Furthermore, the near real-time delivery of these driver attributions to tree cover loss detections presents a critical step forward to advance the actionability of alerting systems as tools for rapid responses against illegal or unsustainable forest activities. A deeper look specifically into road development and associated timber harvests revealed the extent and impact of selective logging activities in the Congo Basin forest. The results showed that up to 10,000 km of new roads are opened up annually in the region. The majority is located inside concessions and built for logging purposes, with notable encroachment into intact forests. Based on the lengths of logging roads and surrounding satellite-detected canopy disturbances, it was estimated that approximately 14.7 million m³ of timber is harvested annually. This results in estimated emissions of 88.2 TgCO₂, of which 31.1 TgCO₂ can potentially be avoided with the adoption of reduced-impact logging for climate change mitigation practices (RIL-C).In conclusion, this thesis presents timely and detailed satellite-based monitoring, characterizing, and assessing of tropical forest changes to enable a better understanding of the causes and impacts of deforestation, forest degradation, and logging activities. This aids the implementation of climate change mitigation initiatives and policies, and can assist local forest management, forest conservation, and law enforcement to avert illegal or unsustainable activities. PE&RC Geo-information Science and Remote Sensing Cum laude PE&RC Geo-information Science and Remote Sensing urn:nbn:nl:ui:32-cffb1236-d98c-4211-b31f-eae1a00095c1/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/ff86fecc-4c79-474f-8be1-f16c7821085c 2026-04-02 thesis

urn:nbn:nl:ui:32-ff86fecc-4c79-474f-8be1-f16c7821085c 2026-04-02 urn:nbn:nl:ui:32-ff86fecc-4c79-474f-8be1-f16c7821085c/mods Multifunctional and stakeholder-informed agricultural : Landscape redesign in the north China plain Wageningen University dgg Cheng Jiali 0000000529532630 aut Jeroen C.J. Groot opn Wopke van der Werf Werf opn Andries Richter opn Wenfeng Cong opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 219 10.18174/681106 en Agricultural landscapes support the provisioning of ecosystem services (ESs), such as food production, pest control, and nutrient cycling, while agricultural land use also generates disservices, including biodiversity loss, nutrient runoff, and greenhouse gas emissions. In the simplified landscapes of the North China Plain (NCP), intensive double cropping of winter wheat and summer maize sustains a high production of cereal grains, but the system relies heavily on artificial fertilizer and groundwater, leading to environmental degradation and reduced regulating and supporting services. Landscape diversification—through diverse cropping systems and semi-natural habitats—has been proposed as a means to better balance agricultural productivity with the provisioning of ESs and to achieve improved multifunctionality. However, little information is available on the perspective of stakeholders with regard to ESs.In this thesis, I describe a case study on Quzhou County, a typical county in the NCP and a demonstration area for China’s National Agriculture Green Development Strategy. The study pursues three main objectives: (1) assessing the current state and trends of ESs and disservices, (2) integrating stakeholder perspectives in the prioritization of ESs, and (3) redesigning agricultural landscapes to enhance multifunctionality.Stakeholders perceived provisioning services as high, while regulating and supporting services were considered scarce, with low scores for natural enemies, earthworms, and semi-natural habitats. Despite documented evidence, most farmers did not recognize agricultural disservices. Differences in perception among villages with different socio-economic and biophysical conditions suggest room for locally adapted policies.I used Q methodology to analyze the priorities of seven different stakeholder groups, including farmers, companies, citizens, academics, and government officials, for different ESs. The analysis revealed 2–3 distinct perspectives on 20 ESs within each stakeholder group. Across all perspectives, most prioritize provisioning services, while the least prioritize supporting services. Academics attached high priority to regulating and supporting services, whereas companies primarily valued provisioning services. Farmers’ perspectives varied by age and education, with older farmers prioritizing provisioning services and younger generations showing greater preference for non-provisioning services.Building on the stakeholder insights, a multi-objective optimization model (Landscape IMAGES) was adapted to explore diversified agricultural landscapes that balance multiple ESs while considering stakeholder priorities. The model was applied to two landscapes in Quzhou County, each consisting of five villages with different land-use intensity. Results showed strong trade-offs between crop production-derived income and non-provisioning ESs, reflecting a trade-off between private and public benefits. The model generated landscapes tailored to stakeholders with different perspectives. A profit-oriented scenario included more wheat-millet and vegetable production, while an environment-oriented scenario resulted in the inclusion of more tuber and oil crops. No single landscape can simultaneously maximize all ESs or meet the preferences of all stakeholders.Overall, the thesis presents an integrated methodological framework that links perception-based surveys, Q-sorting, crop and soil databases, and multi-objective optimization models to guide the redesign of agricultural landscapes. The integrated framework has the potential to be broadly applicable to other intensively cultivated landscapes and supports more effective decision-making in future landscape co-design efforts. Crop and Weed Ecology PE&RC Plant Production Systems (PPS) Farming Systems Ecology (FSE) Centre for Crop Systems Analysis (CSA) Crop and Weed Ecology PE&RC Plant Production Systems (PPS) Farming Systems Ecology (FSE) Centre for Crop Systems Analysis (CSA) urn:nbn:nl:ui:32-ff86fecc-4c79-474f-8be1-f16c7821085c/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/5788c090-5d7b-46f3-882f-0a11ebc61b5b 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-5788c090-5d7b-46f3-882f-0a11ebc61b5b 2026-04-02 urn:nbn:nl:ui:32-5788c090-5d7b-46f3-882f-0a11ebc61b5b/mods Pathways to perception : sexual differentiation and pheromone communication in parasitoid wasps Wageningen University dgg Williams Aidan Thomas 0000-0001-5997-8001 0000000529532622 aut M. Dicke opn Eveline C. Verhulst opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 229 10.18174/681123 en Insects have evolved genetic pathways that determine whether they develop as a male or female. These pathways also shape physical and behavioural differences in their pheromone communication systems to facilitate how they share and process information. Research into how these pathways regulate these differences has primarily been limited to the fruit fly Drosophila melanogaster, which utilizes a so-called dedicated labelled-line system to perceive and process pheromones. Hymenoptera – ants, bees and wasps – have developed a combinatorial coding system, where a single chemical can trigger various sensory neurons to enable these insects to perceive complex pheromones. However, it is not yet fully understood how the sex-determination pathway actually regulates this pheromone-processing mechanism.The aim of my thesis was to elucidate the genetic mechanisms by which sex determination regulates pheromone communication in parasitoid wasps by investigating how key sex-determination genes influence pheromone production and perception in the parasitoid model species Nasonia vitripennis.In Chapter 2, I provide a detailed review of current scientific literature and focus on the distinct olfactory systems insects have evolved to detect and process pheromones. A comparison is made between Diptera, Lepidoptera and Hymenoptera. Conclusions are drawn on how their unique antennal lobes and glomeruli develop to process odours as well as on the causal effects of genes of the sex-determination pathway.Chapters 3 and 4 focus on differences between males and females in the olfactory system of N. vitripennis and how two sex-determination genes, Transformer and Doublesex, influence these differences. I analysed how males and females develop different sensilla on their antennae and how their glomeruli are organized in the antennal lobe. I conclude that these male-female differences arise from modifications in sensory neurons in the antennae. Antennal sensory neurons express the olfactory receptor co-receptor, Orco, a conserved chemosensory gene known to play an important role in forming the glomeruli in other Hymenoptera. My experiments confirm that Orco is required for adult glomerular formation in N. vitripennis.In Chapters 5 and 6, I look at how the sex-determination pathway regulates differences between male and female pheromones. My experiments show that, in females, Transformer is crucial for producing the unique mix of specific pheromones called cuticular hydrocarbons, CHCs. These sex-specific differences in CHCs are driven by the regulation of genes responsible for pheromone production. I analysed a group of these genes that are regulated by Doublesex, called fatty acyl-CoA reductases. My experiments show that these genes play a crucial role in the chemical pathway that creates CHCs and are essential for producing sex-specific pheromone profiles.In Chapter 7, I interpret the key findings of my thesis and contextualize them within the existing body of knowledge on insect sexual differentiation. I explain how the sex-determination pathway shapes complex pheromone systems and highlight the importance that sex-determining genes have in producing the extensive range of pheromones seen in parasitoid wasps. I elaborate on the implications and future directions of my research within the areas of evolutionary biology, neuroethology and biological control. PE&RC Entomology (ENT) PE&RC Entomology (ENT) urn:nbn:nl:ui:32-5788c090-5d7b-46f3-882f-0a11ebc61b5b/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/ba1aa7e9-cd34-4601-b0d3-fdac5ed95a8e 2026-04-02 thesis

urn:nbn:nl:ui:32-ba1aa7e9-cd34-4601-b0d3-fdac5ed95a8e 2026-04-02 urn:nbn:nl:ui:32-ba1aa7e9-cd34-4601-b0d3-fdac5ed95a8e/mods Sugared proteins, unsweet outcomes : Glycation, RAGE signaling, and their relation to diabetes and Alzheimer’s Disease Wageningen University dgg Croes Cresci-Anne C.C. 0000000529546290 aut H. Savelkoul opn J. Keijer opn M. Teodorowicz opn D. Vorselen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 208 10.18174/681310 en Protein glycation is a non-enzymatic reaction between reducing sugars and amino groups in proteins, resulting in the formation of advanced glycation end-products (AGEs). These modifications accumulate during aging and are accelerated under hyperglycemic conditions such as type 2 diabetes. Although the chemistry of glycation and the Maillard reaction is well characterized, the biological consequences of distinct glycation chemistries remain incompletely understood. In particular, it is unclear how dietary and endogenous glycation products engage AGE receptors, drive inflammation, and influence disease-related protein interactions. This thesis aimed to elucidate how protein glycation affects structure, receptor binding, immune activation, and functional outcomes in both nutritional and pathological contexts. Dietary glycation was investigated using soy proteins heated with glucose as a controlled Maillard reaction model. Progression of glycation chemistry closely tracked biological activity. Early-stage reaction products already showed measurable binding to AGE receptors, including the receptor for advanced glycation end-products (RAGE), galectin-3, and scavenger receptors. Prolonged heating increased aggregation, receptor affinity, and low-grade inflammatory responses in monocytes and macrophages, characterized by enhanced secretion of IL-1beta, IL-8, and TNFalpha. These findings demonstrate that dietary Maillard products are biologically active and that heating duration is a key predictor of immunogenicity. Endogenous glycation was examined using human serum albumin (HSA), a highly abundant and glycation-prone plasma protein. Glycation induced by methylglyoxal (MGO) caused greater structural disruption and stronger receptor engagement than glucose-mediated glycation. MGO-glycated HSA elicited pronounced inflammatory responses in macrophages, whereas carboxymethyl-lysine (CML)-modified HSA was the strongest activator in primary human monocytes. These results highlight the pro-inflammatory potential of both dicarbonyl stress and CML formation, with RAGE emerging as a central signaling hub. The impact of glycation on HSA’s interaction with amyloid-beta (Abeta) peptides was examined to explore potential links between metabolic disease and neuroinflammation. Native HSA reduced Abeta-induced inflammation and aggregation, whereas glucose-glycated HSA lost this protective capacity and accelerated Abeta fibrillization. Glycated HSA readily formed complexes with Abeta that exhibited enhanced RAGE binding and provoked stronger inflammatory responses than complexes with non-glycated HSA, identifying these complexes as highly bioactive ligands at the metabolic–cognitive interface. Finally, the role of AGE receptors in phagocytosis was investigated. Direct RAGE engagement was sufficient to promote uptake in macrophages; however, glycation chemistry modulated effective clearance. Glucose- and CML-modified proteins impaired phagocytosis compared to native protein, whereas MGO-modified proteins preserved uptake capacity, suggesting that certain AGE structures may interfere with inflammatory resolution. Together, these findings demonstrate that glycation chemistry and molecular presentation, rather than protein origin alone, determine biological activity. They underscore the importance of dietary processing control, mitigation of dicarbonyl stress, and modulation of RAGE signaling as strategies to limit glycation-driven inflammation and its contribution to metabolic and neurodegenerative disease. WIAS Cell Biology and Immunology WIAS Celbiologie en immunologie urn:nbn:nl:ui:32-ba1aa7e9-cd34-4601-b0d3-fdac5ed95a8e/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/0825ec6a-0a8e-43a3-afdd-fb6df1e08cd9 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-0825ec6a-0a8e-43a3-afdd-fb6df1e08cd9 2026-04-02 urn:nbn:nl:ui:32-0825ec6a-0a8e-43a3-afdd-fb6df1e08cd9/mods Developing integrated strategies to reduce the disease burden of mycotoxin contamina-tion in Ethiopia Wageningen University dgg Awol Sadik Jemal 0000000529546362 aut H.J. van der Fels-Klerx opn I.D. Brouwer opn N. Fentahun opn M. Tessema opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2026 178 10.18174/681663 en Smallholder farmers in Ethiopia have limited resources and inadequate knowledge of good agricultural and storage practices, resulting in frequent mycotoxin contamination of staple crops. Information on the health impacts of mycotoxins and the relationships between farming practices and contamination remains fragmented. Generating evidence on contamination levels, associated health burdens, and management practices is therefore essential to inform policies that protect public health and support international trade.This PhD research investigated pre- and post-harvest practices related to mycotoxin contamination in maize and sorghum. A systematic literature review revealed that several traditional maize pre-harvest practices-including shallow ploughing, suboptimal fertilizer and pesticide use, subjective harvesting decisions, prolonged sun drying, and kernel damage during shelling-are positively associated with mycotoxin contamination. In addition, improper indoor and outdoor storage practices are also positively associated with mycotoxin contamination due to moisture ingress, elevated temperatures, and insect infestation. Although improved technologies such as solar bubble dryers and PICS sacks show potential to reduce contamination, their adoption remains limited due to supply chain constraints.For sorghum, field studies were conducted to assess the relationships between both pre-harvest and storage practices and mycotoxin contamination. Freshly harvested sorghum samples were collected from 120 smallholder households. Mycotoxin analysis showed that 75% of the sorghum samples contained at least one mycotoxin, with 23 of the 33 tested mycotoxins detected. Most regulated mycotoxins were below European Union (EU) limits, except for ochratoxin A, which exceeded the limit in 4% of samples. Significant associations were identified between mycotoxin contamination and pre-harvest practices, including sowing method, fertilizer type, crop rotation, and seed treatment. After six months of storage, 88% of the sorghum samples were contaminated, with a small proportion exceeding EU limits for aflatoxins, ochratoxin A, and zearalenone. Storage practices such as the type and placement of storage structures, insecticide use, and the knowledge and experience of the person responsible for storage were significantly associated with mycotoxin contamination. Health risk assessment indicated that exposure to fumonisin through sorghum consumption was well below international safety limits. However, aflatoxin exposure suggested a potential public health concern based on margin of exposure values, although the estimated liver cancer risk and disease burden (DALYs) were relatively low. WASS Business Economics WASS Bedrijfseconomie urn:nbn:nl:ui:32-0825ec6a-0a8e-43a3-afdd-fb6df1e08cd9/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/654248 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-654248 2026-04-02 urn:nbn:nl:ui:32-654248/mods Essays on innovation and sustainability in the food industry Wageningen University dgg Uhlemann Jan-Philip Rado 0000-0002-9871-0849 000000052945314X aut A.G.J.M. Oude Lansink opn T. Dalhaus opn J.J. Leahy opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 150 10.18174/681808 en Technological innovation has the potential to address sustainability challenges in the food industry. This thesis focused on nutrient recycling, digital technologies, and advanced automation technology, such as artificial intelligence, automated machines, and robotics. We used data from a literature review, commodity price data, and firm-level microdata on technology and production. We find that commodity price risk in natural gas and phosphorus markets lead to a decrease of the investment profitability of phosphorus recycling. Moreover, artificial intelligence in the food industry increases productivity, but has no effect on output, employment, and energy intensity. As most of the impacts of technology are on economic variables, policy makers have a responsibility to guide technology in a sustainable direction. WASS Business Economics WASS Bedrijfseconomie urn:nbn:nl:ui:32-654248/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/653798 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-653798 2026-04-02 urn:nbn:nl:ui:32-653798/mods The power of variation : Novel methods to use genetic variance in breeding programs Wageningen University dgg Niehoff Tobias A.M. 0000000529180874 aut M.P.L. Calus opn J. ten Napel opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 328 10.18174/681749 en The availability of genomic data enables using new methods of selection in animal breed. Traditionally, selection focuses on the estimated genetic performance of animals. Genomics data has improved this by improving the accuracy of selection but the focus on the estimated genetic value remains. Some studies have suggested to also consider the expected genetic variation in the offspring of animals in selection decisions as more genetic gain can be made in families that show high genetic variation. In this thesis, I tested this proposed method and extended it. The extensionis by multiple future generation. For this, I developed equations to predict the expected variance beyond the the offspring generation, i.e., in the grand-offspring generation, great-grand-offspring generation etc.. I test the consequences of these new selection methods in simulated swine breeding programs. I show that the benefits of the new proposed selection criteria are higher the further ahead into the future they look. However, effects on genetic improvement are relatively small, but never negative relatively to traditional selection on estimated genetic performance. As a side product, the new criteria also keep more variation in the population. To improve the long-term sustainability of breeding programs, I tested the effects of introduction of external diversity into the breeding program. This resulted in loosing less genetic variation but came at the cost of reduced genetic improvement. No big difference between different indicators of diversity used for selecting external donors of diversity were found. As a countermeasure for the reduced gain, I proposed assortative mating to improve the genetic level of animals whose semen is sold to production farms. I show that improved commercial genetic gain can only be sustainably achieved if genetic diversity is considered in selection since inbreeding is accelerated otherwise. Assortative mating could not fully help recovering lower genetic gain when the population size is reduced to introduce external diversity. Lastly, ideas for future development of new methods using of SNP based variance prediction are discussed. Overall, the findings of this thesis improve our understanding of genetics and utilizing trait-specific diversity for genetic improvement of livestock. WIAS Animal Breeding & Genomics Animal Breeding and Genomics Cum laude WIAS Fokkerij & Genomica Animal Breeding and Genomics urn:nbn:nl:ui:32-653798/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/653778 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-653778 2026-04-02 urn:nbn:nl:ui:32-653778/mods More-than-human care : Weaving flourishing futures for biodiversity conservation in Brazil Wageningen University dgg Ressiore Adriana 0000000529101734 aut D. Ludwig opn E. Turnhout opn Charbel Niño El-Hani opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 311 10.18174/681370 en The accelerating loss of biodiversity is one of the most urgent and complex crises of our time—not only ecological, but also an ontological, epistemic, and relational one, with significant economic, social, and cultural consequences that threaten human survival. Often framed as species loss or ecosystem collapse, this thesis argues that biodiversity loss is a crisis of care. This crisis manifests not only in the destruction of biodiversity but also in how biodiversity is studied, governed, and conserved. Dominant conservation and governance frameworks remain rooted in modernist, technocratic, and extractive rationalities that marginalize relational, plural, and situated ways of knowing and caring.This research is situated in Brazil, where biodiversity exists in tension with deep structural violence—including deforestation, land-use change, extractive industries, and the historical legacies and ongoing impacts of colonialism. This contradiction makes Brazil a critical site to investigate how more-than-human care is materialized, denied, or negotiated in biodiversity conservation and governance. This thesis’s objective is to investigate how more-than-human care can challenge dominant models and contribute to more just, plural, and flourishing conservation futures. The research is grounded in feminist theories and methodologies, as well as Participatory Action Research. Methods include semi-structured interviews, participant observation, arts-based and participatory methods, autoethnography, and document analysis, among others. The conceptual understanding of more-than-human care informed fieldwork, relationships, and data collection and analysis—centering responsibility, reciprocity, and relationality.The thesis examines more-than-human care across four interwoven threads. Chapter 2 anchors the thesis conceptually and empirically. In Siribinha, more-than-human care unfolds in everyday practices—fishing, listening, living with—and emerges as vital, relational, reciprocal, and fostering flourishing for as many as possible. Chapter 3 presents the Council of Care, an arts-based, transdisciplinary method that invites humans and non-humans to participate in a mock decision-making process, fostering inclusive dialogue that challenges dominant and human-centric governance logics toward more caring and collaborative futures. Chapter 4 focuses on the Interstate Movement of Babassu Coconut Breakers (MIQCB), where care is both a political and interspecies force resisting extractive development. Here, care and conflict coexist. Chapter 5 investigates care within the realm of policy-relevant knowledge production by focusing on the Brazilian Platform for Biodiversity and Ecosystem Services (BPBES). Care is present in collaboration but limited by institutional constraints shaped by neutrality, efficiency, and metrics. The chapter insists that care must remain a situated, embodied, and political practice to inform more responsive knowledge-making.This study shows that more-than-human care is not only a concept—it is a commitment, a practice, a method, a political force, and an epistemic stance. It emerges as mainly daily, embodied, relational, reciprocal, situated, material, and shaped by tensions and inequalities. More-than-human care resists extractive, individualistic, and technocratic logics, offering instead plural, relational, and situated alternatives. To conclude, more-than-human care in the realm of biodiversity conservation aims toward flourishing futures not as an endpoint, but as a continuous, everyday struggle to relate otherwise. Flourishing futures, as proposed here, are about daily acts of care, reciprocity, and resistance—gestures that keep life going even in the face of despair or precarity. WASS Knowledge Technology and Innovation WASS Kennis, Technologie and Innovatie urn:nbn:nl:ui:32-653778/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/653776 2026-04-02 thesis

urn:nbn:nl:ui:32-653776 2026-04-02 urn:nbn:nl:ui:32-653776/mods Spotting opportunities in human milk composition research Wageningen University dgg Wang Peiheng 0000000529101769 aut K.A. Hettinga opn E. Bijl opn E.M. Brouwer-Brolsma opn G.IJ. Salentijn opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 148 10.18174/681583 en Human milk composition varies considerably between mothers and within an individual mother, potentially influencing infant development. Maternal diet is a modifiable factor contributing to some of this variation, offering opportunities to optimize milk composition through dietary adjustments. Understanding how maternal diet influences human milk composition is therefore essential, yet previous research has been limited by methodological constraints. This thesis identified methodological opportunities to advance human milk research, focusing on refined dietary data analyses, refined milk compositional analyses, optimized sampling strategies, and the development of innovative dried milk spot (DMS) sampling methods.In Chapter 2, associations between maternal dietary protein quality and milk protein composition were examined, demonstrating the value of refined dietary and milk compositional analyses. Dietary protein intake was evaluated using the Protein Quality Score, a dietary metric incorporating the quantity of protein intake and the adequacy of essential amino acids relative to nutritional requirements. Milk protein composition was analyzed at the individual protein level instead of aggregated total protein measurements. With these refined methodologies, associations emerged between maternal dietary protein quality and milk caseins, which were previously undetectable by conventional total protein measurements. These findings illustrate the potential of refined dietary and milk compositional analysis approaches, exemplified here by dietary protein quality and detailed milk protein analysis.In Chapter 3, day-to-day and within-feed variations in milk proteins and fatty acids were characterized, and their implications for sampling strategies were examined. Results from samples collected over five consecutive days revealed that, to obtain reliable estimates of an individual's average milk composition, at least two consecutive sampling days were necessary for individual milk proteins due to day-to-day variation. Fatty acids exhibited greater daily variation, requiring at least four consecutive sampling days. These findings highlight risks associated with the commonly used practice of single-day sampling and underscore the importance of adopting higher-frequency sampling strategies.In Chapters 4 and 5, innovative dried milk spot (DMS) methodologies were developed to simplify milk sample collection, storage, and handling. A DMS method optimized for milk protein analysis was developed and validated (Chapter 4). Initial protein losses due to interactions between milk proteins and the paper substrate were resolved through a specialized wax-coated paper combined with an ethanol pre-wetting step. The optimized method provided accurate and reliable measurement of the two most abundant milk proteins, alpha-lactalbumin and beta-casein. This wax-coated DMS technique was expanded by developing a dual-purpose extraction protocol enabling simultaneous analysis of milk proteins and fatty acids from a single dried milk spot (Chapter 5). Despite methodological trade-offs, this combined protocol effectively captured major variations in both protein and fatty acid composition from minimal milk volumes, enhancing feasibility in studies with limited milk availability.Overall, this thesis presents methodological advancements that enhance the accuracy, reliability, and practicality of research investigating maternal diet and human milk composition. Refined dietary data analyses and milk compositional analyses (Chapter 2), increased sampling frequency (Chapter 3), and innovative dried milk spot sampling methods (Chapters 4 and 5) collectively offer valuable strategies for future research. VLAG Global Nutrition Team Bioassays & Biosensors Food Quality and Design VLAG Wereldvoeding Team Bioassays & Biosensors Food Quality and Design urn:nbn:nl:ui:32-653776/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/653768 2026-04-02 thesis

urn:nbn:nl:ui:32-653768 2026-04-02 urn:nbn:nl:ui:32-653768/mods Swimming in unsteady flows: physiological assessments of salmonid exercise performance Wageningen University dgg Agbeti Wisdom 0000000529101742 aut M.P.L. Calus opn A.P. Palstra opn L.J. Magnoni opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 180 10.18174/681541 en As climate change and environmental pressures increase, salmon farming is expanding from sheltered coastal waters into more exposed offshore locations. These areas experience stronger and constantly changing water currents, which may affect how farmed fish swim, use energy, and cope with their environment. Understanding how salmon respond to these changing conditions is important for designing offshore cages, improving feeding strategies, and ensuring good fish welfare. My research investigated how Atlantic and Chinook salmon handle unsteady flow conditions (where water speed changes over time) that resemble those found offshore. This was compared with how they handle steady flow conditions where water speed does not change with time. I used a combination of swim-tunnel experiments and tank trials, some with fish carrying surgically implanted sensors that measured their heart rate and movement. These tools allowed me to study how fish adjust their swimming, how hard their hearts work, and how much energy they use under different flow conditions.I found that salmon use more energy when swimming under unsteady flow compared to steady flow conditions at the same speeds. Despite this, their heart rate did not always rise accordingly. In many cases, heart rate remained high but relatively stable, even when the fish were working harder. This suggests that heart rate alone is not a reliable indicator of energy use for salmon, especially in unsteady flow conditions. Movement-based measurements, such as acceleration, proved to be stronger and more consistent indicators of how much effort the fish were exerting. I also examined the long-term effects of exercise in different flow conditions. Salmon trained under unsteady flow conditions grew just as well as those trained under steady flow conditions, and both groups outperformed fish kept in low-flow conditions. This shows that salmon can adapt to changing water movement without compromising growth. In free-swimming Chinook salmon, heart rate and movement followed daily patterns and were higher under unsteady flow conditions compared to steady flow conditions. These findings suggest that offshore environments may influence activity and energy use throughout the day and night. Overall, my work highlights that movement sensors offer a more accurate way to monitor salmon energy use than heart rate alone. These insights can help guide offshore aquaculture towards better site selection, cage design, and monitoring technologies, ultimately supporting more sustainable and welfare-focused fish farming as the industry moves into the open ocean. WIAS Animal Breeding and Genomics WIAS Animal Breeding and Genomics urn:nbn:nl:ui:32-653768/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/653754 2026-04-02 thesis

urn:nbn:nl:ui:32-653754 2026-04-02 urn:nbn:nl:ui:32-653754/mods Unlocking regeneration: an induced pluripotency stem cell tool for plants Wageningen University dgg Wittmer Jana 000000052912053X aut B.J.G. Scheres opn R. Heidstra opn W. Kohlen opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 234 10.18174/681351 en Plants have an incredible ability to regrow entire organs or even whole bodies from a few cells—a process called regeneration. However, not all plants can do this easily, and scientists have long relied on plant hormones to trigger this process. In my research, I discovered that two natural plant stem cell genes, called PLT and WOX5, can together reprogram mature plant cells to start growing again—without the need for added hormones. By turning these genes on in specific ways, I could make cells lose their original identity and form new shoots or even embryos from for example roots. These findings not only deepen our understanding of how plants regenerate but also open new possibilities for sustainable crop improvement and biotechnology applications where regeneration is a major bottleneck. EPS Molecular Biology (MOB) Cell Biology (CBL) EPS Molecular Biology (MOB) Cell Biology (CBL) urn:nbn:nl:ui:32-653754/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/653755 2026-04-02 thesis

urn:nbn:nl:ui:32-653755 2026-04-02 urn:nbn:nl:ui:32-653755/mods Engendering river : The politics of future-making for the Meuse and Magdalena Rivers Wageningen University dgg de Jong Lotte 438189523 0000000509840919 aut R. Boelens opn L.A. Melsen opn G.J. Veldwisch opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 186 10.18174/681885 en Through ethnographic methods, this thesis investigates how adaptation projects for the Meuse (Netherlands) and Magdalena (Colombia) Rivers shape, legitimise, and contest dominant river futures. Chapter 2 conceptualises river imaginaries and shows how modern, market-driven, and eco-centric visions coalesce into an ecomodernist imaginary that consolidates truth regimes about river futures. Chapter 3 analyses the performative authority of the Dutch Maasmodel, demonstrating how modelling practices co-produce territorial transformations, reinforce dominant configurations, and constrain alternative imaginaries despite moments of counterperformativity or counter-modelling. Chapter 4 explores future-making in the Lower Magdalena, revealing how ecomodernist adaptation logics rely on manufactured ignorance that silences rooted, amphibian imaginaries. Chapter 5 shows how ecohydrological modelling naturalises river futures, rendering only calculable and codable futures legitimate while downplaying community concerns. The conclusion synthesises how ecomodernist norms shape adaptation governance, how models consolidate truth regimes, and how contestation emerges—highlighting the need for diverse onto-epistemic mediums capable of representing plural river imaginaries and enabling more just, representative river futures. WASS Water Resources Management WASS Water Resources Management urn:nbn:nl:ui:32-653755/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/653466 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-653466 2026-04-02 urn:nbn:nl:ui:32-653466/mods Why water works : Shaping durable pellets in biomass agglomeration Wageningen University dgg Benders Richard T. 0000-0003-3069-2266 aut J. van der Gucht opn J.A. Dijksman opn M. Thomas opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 161 10.18174/681306 en Every year, nearly a billion tons of biomass—such as animal feed ingredients and wood residues—are compressed into pellets. Although pelleting looks simple, turning loose powders into strong, durable pellets is surprisingly complex. The mixture needs to flow smoothly through the machine, yet it must also form strong bonds so the final pellets do not crumble. My PhD research set out to explain how this transformation happens and how we can better control it.A central finding of this work is the major role of water, especially when added as steam. Using advanced imaging techniques—such as X-ray scans, surface profiling, and electron microscopy—I studied what happens to ingredients inside the narrow metal die of a pellet press. We discovered that part of the added water forms a very thin water layer between the material and the die wall. This layer reduces friction. When the water layer is too thin, friction is high and the press uses excessive energy. When it becomes too thick, excess energy is consumed during production. This explains why small changes in steam addition or ingredient composition can drastically affect pellet quality and energy consumption.The research also introduces the concept of a stickiness temperature: the minimum temperature at which a material begins to bond and pellets can form. Each ingredient mixture has its own stickiness temperature depending on its chemical makeup. Once this temperature is reached, the energy absorbed by the material no longer just raises its temperature. Instead, it drives physical transitions and chemical reactions that create the internal bonds needed for strong pellets. This means pellet production is not just mechanical compression—it is a form of reactive extrusion, where heat, time, and composition determine the final pellet strength.These insights lead to a new perspective on efficiency in pellet production. Beyond considering the machine’s overall energy use, we can evaluate how effectively ingredients absorb the heat required for bonding. This helps explain why certain technologies—such as expanders or small recipe adjustments—increase production capacity and pellet durability. It also offers practical strategies for improving feed mill performance while lowering energy costs.Finally, the research proposes two new ideas. First, making powders more uniform in particle size may increase pellet durability by improving how particles interact during compression. Second, for some mixtures, pellet strength may depend more on aging after production than on the exact processing conditions. This means that storage conditions—especially in the first hours to days—can play an essential role in determining final pellet quality.Overall, this thesis provides a clearer picture of what happens inside a pellet press. By uncovering how water, temperature, friction, and ingredient chemistry interact, it offers new ways to improve pellet quality, reduce energy use, and avoid production problems. Physical Chemistry and Soft Matter VLAG Animal Nutrition Fysische Chemie en Zachte Materie VLAG Diervoeding urn:nbn:nl:ui:32-653466/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/653465 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-653465 2026-04-02 urn:nbn:nl:ui:32-653465/mods Toward sustainable development of livestock production: the role of dairy standards Wageningen University dgg McGarr-O'Brien Keeley aut I.J.M. de Boer opn E.M. de Olde opn J. Herron opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 155 10.18174/681340 en Livestock production represents an important component of global agricultural production, yet is currently faced with mounting environmental, economic, and social sustainability challenges including greenhouse gas emissions, biodiversity loss, animal welfare concerns, and farm viability concerns. In response to rising societal and political pressure to address these challenges, market-based sustainability standards have emerged as a prominent governance mechanism that establishes criteria beyond legal norms to guide livestock farming practices toward more sustainable outcomes, while also serving as marketing tools. There has been a rapid increase in the number of such standards in the dairy sector. Yet, more understanding is required regarding how standards operationalise sustainability across environmental, social, and economic dimensions and navigate inherent trade-offs between credibility, accessibility, and continuous improvement (the Devil’s Triangle). This thesis addresses this gap by evaluating the contribution of market-based standards to the sustainable development of livestock production, specifically considering the case of the dairy sector. This aim was achieved through a multi-lens approach that examined standard documents, analysed perceptions of both farmer participants and standard organisers, positioned dairy standards along a sustainable transformation pathway, and revealed the balance of inherent standard trade-offs. The research discovered significant heterogeneity among dairy standards, with organisations varying widely in their objectives, scope, operations, and governance approaches and inconsistently addressing environmental, social, and economic sustainability dimensions. Using the Devil's Triangle framework, the research found that standards were also variable in their balancing of accessibility, credibility, and continuous improvement. Notably, the majority of standards lacked sufficient focus on continuous improvement despite its importance for sustainable development. The analysis revealed that standards serve as private governance mechanisms for sustainability, operating without external oversight. Standards face challenges in proving measurable impact and thereby risk functioning more as marketing tools than transformative instruments. Yet, illustrating impact is not equally possible for all sustainability themes. Standards are currently situated mainly within two phases of a sustainable transformation pathway, focusing on either competition or coherence. The linear nature of most standards conflicts with the non-linear, interconnected nature of sustainable development. To address this tension, different approaches to standards may be required to incorporate systems approaches and co-create visions which actors can work toward in context-relevant ways. This thesis concluded that for standards to meaningfully contribute to the sustainability of livestock production, they require greater transparency, increased farmer participation in design and governance, enhanced focus on continuous improvement, and recognition that they function as one component within a broader ecosystem of sustainability efforts rather than standalone solutions to complex agricultural sustainability challenges. WIAS Animal Production Systems WIAS Dierlijke productiesystemen urn:nbn:nl:ui:32-653465/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/653464 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-653464 2026-04-02 urn:nbn:nl:ui:32-653464/mods Versatile FRUITFULL : Redundancy and specificity in tomato Wageningen University dgg Wang Xiaowei 0000000529072216 aut G.C. Angenent opn R.A. de Maagd opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 193 10.18174/681685 en Fruit development and ripening in tomatoes involve the coordination and tight regulation of gene expression. MADS-domain transcription factors, which are gene expression-regulating proteins, play a crucial role in various biological processes of plants, and interactions between MADS-domain proteins, which are transcription factors are essential for their functions. In tomato, several MADS-domain proteins, such as FUL1, FUL2, MADS-RIN, TAGL1, and MADS1, playing a role in fruit development and ripening have been identified, but an in-depth characterization of their unique and (partially) redundant functions in these processes is lacking. In this project, I aimed to elucidate further the regulatory functions exerted by MADS-box proteins and the interactions among them and with other proteins, particularly for FUL1, FUL2, and TAGL1. First, I have used CRISPR/Cas to generate single mutants and combinations thereof to reveal any redundant functions or cooperativity among these proteins during fruit development and ripening. Second, I also analyzed the detailed temporal and spatial expression of the FULs, to identify specific targets and co-factors. Third, I used the results to develop a refined regulatory model of tomato fruit ripening, incorporating mutagenesis, expression profiles, and interaction data. Altogether, this study will elucidate the molecular regulatory network of MADS-BOX proteins, particularly FUL1/2, in fruit development and ripening. EPS Molecular Biology (MOB) Plant Developmental Biology BIOS Plant Development Systems EPS Molecular Biology (MOB) Plant Developmental Biology BIOS Plant Development Systems urn:nbn:nl:ui:32-653464/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/653463 2026-04-02 thesis

urn:nbn:nl:ui:32-653463 2026-04-02 urn:nbn:nl:ui:32-653463/mods LETS Sport! : Life Experience Through Sports and its impact on adults in socially vulnerable positions Wageningen University dgg Alarslan Güven 0000000529092196 aut M.A.E. Wagemakers opn K.T. Verkooijen opn I.M. van Hilvoorde opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 235 10.18174/681171 en Sport is widely recognized for a range of benefits to physical, mental, and social health outcomes. Participating in sports can also facilitate the development and transfer of life skills, such as discipline, teamwork, and coping skills. One group that can benefit from these positive outcomes is adults who find themselves in socially vulnerable positions. These adults may face challenges such as homelessness, unemployment, social isolation, addiction, or mental health difficulties. To make sports accessible for these adults, community sports programs have been developed that offer low-threshold, inclusive, and supportive environments. This PhD thesis examines what adults in socially vulnerable positions gain from community sports programs, with a particular focus on the development and transfer of life skills.The research was carried out in collaboration with the Life Goals Foundation in the Netherlands. The thesis integrates a systematic literature review, in-depth interviews, focus groups, and a Group Concept Mapping study to understand which life skills are developed and transferred, the mechanisms that facilitate the development and transfer of life skills, and the elements that are necessary for sports programs to be successful.Chapter 2 presents what is currently known in the literature about life skills development and transfer. Chapter 3 provides a detailed overview of the life skills that were developed and transferred by adults in socially vulnerable positions who participated in the Life Goals activities. In Chapter 4, the mechanisms that facilitate the development and transfer of these life skills are identified. Chapter 5 shows which elements of community sports programs are necessary for their success.This thesis concludes that community sports programs can contribute meaningfully to improving the well-being of adults in socially vulnerable positions through the development and transfer of life skills. Importantly, participants do not necessarily learn these skills from scratch, but rather rediscover or refine existing skills that had been overshadowed by difficult life circumstances. Sports participation offers structure, social connection, and a context in which life skills can be practiced. The findings underline the value of integrating community sports into broader social and health policies and provide guidance for practitioners and policymakers seeking to strengthen the role of sport in promoting inclusion and personal development. Health and Society WASS Gezondheid en Maatschappij WASS urn:nbn:nl:ui:32-653463/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/653441 2026-04-02 thesis

urn:nbn:nl:ui:32-653441 2026-04-02 urn:nbn:nl:ui:32-653441/mods Poo matters : Determinants of faecal quality in salmonids Wageningen University dgg Prakash Satya 0000000529083767 aut J. Schrama opn Ø. Sæle opn R.M. Maas opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 214 10.18174/681516 en Fish culture, like all animal production systems, generates waste. In aquaculture, waste is broadly classified into solid and dissolved waste. The major source of solid waste is undigested feed, excreted as faeces. Removal success of faeces from production system depends on characteristics like size, stability and density of faecal pellets. Vast amount of knowledge is available on factors determining faecal quantity in various fish species. Therefore, this thesis focused on the less explored area of faecal quality. The impact of the dietary (ingredient and nutrient composition of diet), environmental (salinity) and fish-specific (species) factors in determining faecal quality were investigated and as a secondary aim the impact on faecal quantity was taken along. Salmonids were selected as the model group due to their high economic importance, widespread culture in RAS and euryhaline nature. Since there were no standard methods available for determining faecal stability, a simplified and standardized protocol for measuring faecal stability was developed and used across different chapters of this thesis. First, the impact of a diverse set of ingredients (incl. novel) was evaluated regarding the quantity and quality of faecal waste produced by rainbow trout (Oncorhnychus mykiss). Results showed that ingredients in the diet determine the amount of faecal waste produced, sedimentation based removal efficiency, and the amount of non-removed faeces accumulating in the system. Findings suggested that the high dietary carbohydrate content impaired faecal quality, whereas high dietary ash content improved it. Building on these leads, the impact of dietary starch levels and dietary ash content on faecal quality in rainbow trout was investigated. It was also evaluated if exogenous supplementation of amylase could mitigate the potential adverse impacts of starch on faecal quality. Elevated starch levels decreased faecal removal efficiency by sedimentation and increased the quantity of non-removed faeces. Amylase supplementation improved starch digestibility, but did not alter the faecal waste production, removal efficiency, size, and stability of faeces. As hypothesized, increasing dietary ash enhanced faeces' density and sinking velocity but did not result in a measurable improvement in faecal removal efficiency. A species comparison trial revealed that even closely related salmonids produce faeces with markedly different sizes and stability, even when fed the same diet and reared under the same conditions (same systems). Arctic charr (Salvelinus alpinus) produced faeces dominated by particles of smaller size and lower stability compared to rainbow trout and Atlantic salmon (Salmo salar). No consistent trends were observed regarding how salinity affected faecal size and stability. Finally, I demonstrated that rainbow trout reared in saline water produce faeces of diverse types and that faecal pellets have a dual mucoidal coating. It was also shown that coating is an important factor determining the faeces size and stability. A generalized conceptual framework integrating these findings was developed and system design and water flow management were identified as critical factors determining the efficacy of dietary interventions in determining faecal quality. To conclude this thesis demonstrates that, faecal quality is governed by complex interplay of dietary, environmental, species-specific, and system-level factors. WIAS Aquaculture biology and Fisheries ecology Cum laude WIAS Aquaculture biology and Fisheries ecology urn:nbn:nl:ui:32-653441/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/653442 2026-04-02 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-653442 2026-04-02 urn:nbn:nl:ui:32-653442/mods Entrepreneurial pathways : Identity, behavioural heterogeneity and sustainable agriculture among smallholders in the Philippines Wageningen University dgg van Luijn Donny 000000052909217X aut W.A. Dolfsma opn V.C. Materia opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 125 10.18174/681128 en Entrepreneurial Identity (EntID) offers a behavioural framework for analysing variation in Sustainable Agricultural Practices (SAP) adoption, income outcomes and participation in sustainability-oriented contract farming (CF) among smallholder farmers. This thesis investigates how identity-linked behavioural orientations, formalised through EntID, shape SAP adoption heterogeneity, the income effects associated with adoption and participation in CF in the Philippines. EntID is defined as a multidimensional behavioural orientation that integrates the cognitive traits of Entrepreneurial Orientation (EO), namely innovativeness, proactiveness and risk-taking, with Collective Environmental Attitude (CEA), which captures environmentally oriented values and group based commitments to ecological stewardship. EntID provides a behavioural lens for interpreting differentiated responses to sustainability interventions.The empirical analysis draws on survey data from 2,541 farming households in the Municipality of Carmen in North Cotabato and applies a multi method econometric strategy across three studies. First, latent class analysis (LCA) identifies distinct latent adopter classes based on SAP adoption patterns. Post classification multinomial regression assesses how EntID traits and contextual variables shape the probability of belonging to each class. The findings identify three EntID configurations and show that behavioural differentiation linked to EntID is a significant determinant of latent class membership. The configurations correspond to limited, selective and broad SAP adoption and reflect systematic variation in behavioural, structural and contextual characteristics.Second, ordinary least squares moderation models examine whether behavioural traits condition the income effects of SAP adoption. The results show that income gains from SAP adoption occur when adoption is accompanied by higher CEA. This indicates that normative environmental orientation strengthens the economic realisation of SAP benefits by supporting coordinated implementation of practices. The moderating effect indicates that behavioural dispositions shape income outcomes, and structural variables including market access, asset endowments and exposure to climatic variability account for distinct sources of income variation. Third, an instrumental variable probit model evaluates participation in CF schemes that promote SAP. The estimates indicate that innovativeness and proactiveness increase participation, indicating alignment between forward oriented dispositions and the requirements of contractual engagement. Risk-taking and CEA reduce participation, suggesting limited compatibility between these traits and the risk structure and normative expectations embedded in the CF schemes. These behavioural effects persist after accounting for contractual attributes. Structural factors such as credit reliance, market orientation and local environmental conditions display associations with CF participation.The thesis contributes to adoption research by applying behavioural constructs within an econometric framework to explain heterogeneity in SAP adoption, income outcomes and participation in sustainability oriented institutional arrangements. EntID provides explanatory value for interpreting how cognitive and normative orientations shape these outcomes, and the findings support the development and refinement of institutional arrangements aimed at promoting SAP adoption, enhancing farmer inclusion and strengthening rural development policy in smallholder agricultural systems. Business Management and Organisation WASS Bedrijfsvoering en Organisatie WASS urn:nbn:nl:ui:32-653442/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/653204 2026-05-18 thesis edurep openaire public publickb

urn:nbn:nl:ui:32-653204 2026-05-18 urn:nbn:nl:ui:32-653204/mods Exploring competencies and learning for sustainable agriculture : Towards a competence-based sustainability approach for agricultural education in Burundi Wageningen University dgg Nyamweru Jean Claude 0000000529008871 aut H. Biemans opn A. Kessler opn W.-M. Ndayitwayeko opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 188 10.18174/681154 en The PhD research explored how vocational agricultural education in Burundi can foster sustainability competencies among students to prepare them as effective change agents. Conducted within the Project to Improve the Coherence of Agricultural Education in Burundi (PACEA), the research focused on the curricula of vocational agricultural education (ITAB) in the context of environmental degradation, food insecurity, and post-conflict recovery. Four studies were carried out: identifying key sustainability competencies, assessing their integration in the ITAB curriculum, evaluating student learning via a Participatory Integrated Planning (PIP) module, and analysing teacher self-efficacy and professional development for sustainable agriculture education. Findings highlighted eleven key competencies, with a strong emphasis on attitudinal dimensions such as facilitation, creativity, and systems thinking. The PIP module significantly enhanced both student and teacher capacities. The research underscores the need for flexible, competence-based curricula and authentic, participatory learning environments. The research contributed theoretically to sustainability education and practically to curriculum reform, with implications for scaling sustainable agriculture learning programmes across similar educational contexts. WIMEK Soil Physics and Land Management WIMEK Bodemfysica en Landbeheer urn:nbn:nl:ui:32-653204/obj 2026-05-18 http://purl.org/eprint/accessRights/OpenAccess

oai:library.wur.nl:wurpubs/653203 2026-04-02 thesis

urn:nbn:nl:ui:32-653203 2026-04-02 urn:nbn:nl:ui:32-653203/mods Perceptions of justice in food system transitions Wageningen University dgg de Bruin Annemarieke 0000-0001-8316-5975 0000000517858262 aut I.J.M. de Boer opn C.J.A.M. Termeer opn E.M. de Olde opn N.R. Faber opn text info:eu-repo/semantics/doctoralThesis Wageningen University Wageningen 2025 244 10.18174/681261 en A transition is ongoing towards more sustainable and just food systems in response to environmental and social injustices. However, food system actors, including researchers, risk reproducing existing injustices and/or creating new ones as part of the transition process. To support a just food system transition, we need to understand whether and how food system actors contribute to making the food system and the transition more just, but what is just depends on who is asked. Perceptions of justice are not universal but contextual and situated in relationships that are relative to time and place.This thesis aimed to understand how justice is perceived in the context of ongoing food system transitions and more specifically within the regional case study of the North of the Netherlands. We developed a conceptual framework that structures conversations about, and the analysis of, perceptions of justice in the context of food system transitions. We then reviewed the literature to understand how researchers write about justice implications of food-related initiatives. In the regional case study, we ran a workshop series and held in-depth interviews with actors from across the food system and with people who may have had experiences of marginalisation.We identified a number of food system situations that participants judged from a justice perspective. These included (a lack of) changes in production practices, food aid, the capacity to participate in the transition, and supply chain power dynamics. We found that participants’ role(s) in the food system and their experiences with injustices influenced their perceptions of justice. We also found that systemic (income) inequalities currently undermine a just (Dutch) food system transition. To ensure a just food system transition, we conclude that justice has to become part of the political and societal debates about the ongoing food system transition and potential food system futures. WIAS Animal Production Systems WIAS Dierlijke productiesystemen urn:nbn:nl:ui:32-653203/obj 2026-04-02 http://purl.org/eprint/accessRights/OpenAccess 200:::nl_didl:thesis: