Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Flavor Retention and Release from Beverages : A Kinetic and Thermodynamic Perspective
Ammari, Ali ; Schroen, Karin - \ 2018
Journal of Agricultural and Food Chemistry (2018). - ISSN 0021-8561 - p. 9869 - 9881.
aqueous food - experimental method - flavor release - modeling

For the investigation of retention and release of flavor components, various methods are available, which are mostly used on a case-to-case basis depending on the raw material. These effects that originate from kinetics and thermodynamics could be put in a much wider perspective if these fields were taken as a starting point of investigation in combination with rigorous data analysis. In this Review, we give an overview of experimental techniques and data analysis methods, and predictive methods using mass transfer techniques are also discussed in detail. We use this as a foundation to discuss the interactions between volatile flavors and the matrix of liquid foods/beverages. Lipids present in the form of an emulsion are the strongest volatile retainers due to the lipophilic nature of most of the volatile flavors. Proteins also have flavor retention properties, whereas carbohydrates hardly have a retention effect in beverages. Smaller components, such as sugars and salts, can change the water activity, thereby facilitating flavor release. Alternatively, salts can also indirectly affect binding sites of proteins leading to release (e.g., NaCl and Na2SO4) or retention (NaCSN and Cl3CCOONa) of flavors. Furthermore, the effects of temperature and pH are discussed. The Review concludes with a critical section on determination of parameters relevant to flavor release. We highlight the importance of accurate determination of low concentrations when using linearization methods and also show that there is an intrinsic preference for nonlinear regression methods that are much less sensitive to measurement error.

Multi-objective decision-making for dietray assessment and advice
Lemmen - Gerdessen, J.C. van - \ 2017
University. Promotor(en): Jack van der Vorst; P. van 't Veer, co-promotor(en): Frits Claassen. - Wageningen : Wageningen University - ISBN 9789463437073 - 136
questionnaires - food - fractionation - modeling - diet - food intake - decision making - diet counseling - vragenlijsten - voedsel - fractionering - modelleren - dieet - voedselopname - besluitvorming - dieetadvisering

Unhealthy diets contribute substantially to the worldwide burden of non-communicable diseases, such as cardiovascular diseases, cancers, and diabetes. Globally, non-communicable diseases are the leading cause of death, and numbers are still rising, which makes healthy diets a global priority. In Nutrition Research, two fields are particularly relevant for formulating healthier diets: dietary assessment, which assesses food and nutrient intake in order to investigate the relation between diet and disease, and dietary advice, which translates food and nutrient recommendations into realistic food choices. Both fields face complex decision problems: which foods to include in dietary assessment or advice in order to pursue the multiple objectives of the researcher or fulfil the requirements of the consumer. This thesis connects the disciplines of Nutrition Research and Operations Research in order to contribute to formulating healthier diets.

In the context of dietary assessment, the thesis proposes a MILP model for the selection of food items for food frequency questionnaires (a crucial tool in dietary assessment) that speeds up the selection process and increases standardisation, transparency, and reproducibility. An extension of this model gives rise to a 0-1 fractional programming problem with more than 200 fractional terms, of which in every feasible solution only a subset is actually defined. The thesis shows how this problem can be reformulated in order to eliminate the undefined fractional terms. The resulting MILP model can solved with standard software.

In the context of dietary advice, the thesis proposes a diet model in which food and nutrient requirements are formulated via fuzzy sets. With this model, the impact of various achievement functions is demonstrated. The preference structures modelled via these achievement functions represent various ways in which multiple nutritional characteristics of a diet can be aggregated into an overall indicator for diet quality. Furthermore, for Operations Research the thesis provides new insights into a novel preference structure from literature, that combines equity and utilitarianism in a single model.

Finally, the thesis presents conclusions of the research and a general discussion, which discusses, amongst others, the main modelling choices encountered when using MODM methods for optimising diet quality.

Summarising, this thesis explores the use of MODM approaches to improve decision-making for dietary assessment and advice. It provides opportunities for better decision-making in research on dietary assessment and advice, and it contributes to model building and solving in Operations Research. Considering the added value for Nutrition Research and the new models and solutions generated, we conclude that the combination of both fields has resulted in synergy between Nutrition Research and Operations Research.

Using yield gap analysis to give sustainable intensification local meaning
Silva, João Vasco - \ 2017
University. Promotor(en): Martin van Ittersum, co-promotor(en): Ken Giller; Pytrik Reidsma. - Wageningen : Wageningen University - ISBN 9789463437141 - 361
crops - yields - crop yield - modeling - simulation models - cereals - farming systems - yield losses - gewassen - opbrengsten - gewasopbrengst - modelleren - simulatiemodellen - graansoorten - bedrijfssystemen - oogstverliezen

Yield gap analysis is useful to understand the relative contribution of growth-defining, -limiting and -reducing factors to actual yields. This is traditionally performed at the field level using mechanistic crop growth simulation models, and directly up-scaled to the regional and global levels without considering a range of factors intersecting at farm and farming system levels. As an example, these may include farmers' objectives and resource constraints, farm(er) characteristics, rotational effects between subsequent crops or decisions on resource allocation and prioritization of crop management. The objective of this thesis is to gain insights into yield gaps from a farm(ing) systems perspective in order to identify opportunities for sustainable intensification at local level.

Three contrasting case studies representing a gradient of intensification and capturing a diversity of agricultural systems were selected for this purpose, namely mixed crop-livestock systems in Southern Ethiopia, rice based-farming systems in Central Luzon (Philippines) and arable farming systems in the Netherlands. A theoretical framework combining concepts of production ecology and methods of frontier analysis was developed to decompose yield gaps into efficiency, resource and technology yield gaps. This framework was applied and tested for the major crops in each case study using crop-specific input-output data for a large number of individual farms. In addition, different statistical methods and data analyses techniques were used in each case study to understand the contribution of farmers' objectives, farm(er) characteristics, cropping frequency and resource constraints to yield gaps and management practices at crop level.

Yield gaps were largest for maize and wheat in Southern Ethiopia (ca. 80\\\\% of the water-limited yield), intermediate for rice in Central Luzon (ca. 50\\\\% of the climatic potential yield) and smallest for the major arable crops in the Netherlands (ca. 30\\\\% of the climatic potential yield). The underlying causes of these yield gaps also differed per case study. The technology yield gap explained most of the yield gap observed in Southern Ethiopia, which points to a lack of adoption of technologies able to reach the water-limited yield. The efficiency yield gap was most important for different arable crops in the Netherlands, which suggests a sub-optimal timing, space and form of the inputs applied. The three intermediate yield gaps contributed similarly to the rice yield gap in Central Luzon meaning that sub-optimal quantities of inputs used are as important in this case study as the causes mentioned for the other case studies.

Narrowing the yield gap of the major crops does not seem to entail trade-offs with gross margin per unit land in each case study. However, the opposite seems to be true for N use efficiency and labour productivity particularly in Southern Ethiopia and Central Luzon, and to a less extent in the Netherlands. This means that (sustainable) intensification of smallholder agriculture in the tropics needs to go hand-in-hand with agronomic interventions that increase land productivity while ensuring high resource use efficiency and with labour-saving technologies that can reduce the drudgery of farming without compromising crop yields.

Other insights at farm(ing) system level were clearer in Southern Ethiopia than in Central Luzon or in the Netherlands. For example, alleviating capital constraints was positively associated with intensification of maize-based farming systems around Hawassa and increases in oxen ownership (an indicator of farm power) was associated with extensification of wheat-based farming systems around Asella. In Central Luzon, farm and regional factors did not lead to different levels of intensification within the variation of rice farms investigated and the most striking effect was that direct-seeding (and thus slightly lower rice yields) was mostly adopted in larger farms, and used lower amounts of hired labour, compared to transplanting. In the Netherlands, the analysis of rotational effects on crop yields provided inconclusive results but confounding effects with e.g. rented land do not allow to conclude that these are not at stake in this farming system.

This thesis broadens the discussion on yield gaps by moving from the technical aspects underlying their estimation towards the broader farm level opportunities and constraints undermining their closure. Overall, insights from contrasting case studies support conventional wisdom that intensification of agriculture needs to occur in the 'developing South', where yield gaps are large and resource use efficiency low, while a focus on improving sustainability based on sustainable intensification (or even extensification) is more appropriate in the 'developed North', where yield gaps are small and resource use efficiency high.

Keeping humans in the ecosystem
Link, Jason S. ; Thébaud, Olivier ; Smith, David C. ; Smith, Anthony D.M. ; Schmidt, Jorn ; Rice, Jake ; Poos, J.J. ; Pita, Cristina ; Lipton, Doug ; Kraan, M.L. ; Frusher, Stewart ; Doyen, Luc ; Cudennec, Annie ; Criddle, Keith ; Bailly, Denis - \ 2017
ICES Journal of Marine Science 74 (2017)7. - ISSN 1054-3139 - p. 1947 - 1956.
ecosystem-based management - governance - indicators - integrated ecosystem assessment - marine socio-ecological systems - modeling - scenario analysis - stakeholder engagement
The World Ocean presents many opportunities, with the blue economy projected to at least double in the next two decades. However, capitalizing on these opportunities presents significant challenges and a multi-sectoral, integrated approach to managing marine socio-ecological systems will be required to achieve the full benefits projected for the blue economy. Integrated ecosystem assessments have been identified as the best means of delivering the information upon which marine resource management decisions can be made. By their nature, these assessments are inter-disciplinary, but to date have mostly focused on the natural sciences. Inclusion of human dimensions into integrated ecosystem assessments has been lagging, but is fundamental. Here we report on a Symposium, and the articles emmanating from it that are included in this Theme Set, that address how to more effectively include human dimensions into integrated ecosystem assessments. We provide an introduction to each of the main symposium topics (governance, scenarios, indicators, participatory processes, and case studies), highlight the works that emerged from the symposium, and identify key areas in which more work is required. There is still a long way to go before we see end-to-end integrated ecosystem assessments inclusive of all the major current and potential ocean use sectors that also encompass multiple aspects of human dimensions. Nonetheless, it is also clear that progress is being made and we are developing tools and approaches, including the human dimension, that can inform management and position us to take advantage of the multi-sectoral opportunities of sustainable blue growth.
What determines plant species diversity in Central Africa?
Proosdij, Andreas S.J. van - \ 2017
University. Promotor(en): Marc Sosef, co-promotor(en): Jan Wieringa. - Wageningen : Wageningen University - ISBN 9789463436618 - 161
plants - biodiversity - species diversity - species - distribution - biogeography - central africa - biosystematics - tropical rain forests - modeling - planten - biodiversiteit - soortendiversiteit - soorten - distributie - biogeografie - centraal-afrika - biosystematiek - tropische regenbossen - modelleren

Planet Earth hosts an incredible biological diversity. Estimated numbers of species occurring on Earth range from 5 to 11 million eukaryotic species including 400,000-450,000 species of plants. Much of this biodiversity remains poorly known and many species have not yet been named or even been discovered. This is not surprising, as the majority of species is known to be rare and ecosystems are generally dominated by a limited number of common species.

Tropical rainforests are the most species-rich terrestrial ecosystems on Earth. The general higher level of species richness is often explained by higher levels of energy near the Equator (latitudinal diversity gradient). However, when comparing tropical rainforest biomes, African rainforests host fewer plant species than either South American or Asian ones. The Central African country of Gabon is situated in the Lower Guinean phytochorical region. It is largely covered by what is considered to be the most species-rich lowland rainforest in Africa while the government supports an active conservation program. As such, Gabon is a perfect study area to address that enigmatic question that has triggered many researchers before: “What determines botanical species richness?”.

In the past 2.5 million years, tropical rainforests have experienced 21 cycles of global glaciations. They responded to this by contracting during drier and cooler glacials into larger montane and smaller riverine forest refugia and expanding again during warmer and wetter interglacials. The current rapid global climate change coupled with change of land use poses new threats to the survival of many rainforest species. The limited availability of resources for conservation forces governments and NGOs to set priorities. Unfortunately, for many plant species, lack of data on their distribution hampers well-informed decision making in conservation.

Species distribution models (SDMs) offer opportunities to bridge at least partly this knowledge gap. SDMs are correlative models that infer the spatial distribution of species using only a limited set of known species occurrence records coupled with high resolution environmental data. SDMs are widely applied to study the past, present and future distribution of species, assess the risk of invasive species, infer patterns of species richness and identify hotspots, as well as to assess the impact of climate change. The currently available methods form a pipeline, with which data are selected and cleaned, models selected, parameterized, evaluated and projected to other areas and climatic scenarios, and biodiversity patterns are computed from these SDMs. In this thesis, SDMs of all Gabonese plant species were generated and patterns of species richness and of weighted endemism were computed (chapter 4 & 5).

Although this pipeline enables the rapid generation of SDMs and inferring of biodiversity patterns, its effective use is limited by several matters of which three are specifically addressed in this thesis. Not knowing the true distribution limits the opportunities to assess the accuracy of models and assess the impact of assumptions and limitations of SDMs. The use of simulated species has been advocated as a method to systematically assess the impact of specific matters of SDMs (virtual ecologist). Following this approach, in chapter 2, I present a novel method to simulate large numbers of species that each have their own unique niche.

One matter of SDMs that is usually ignored but has been shown to be of great impact on model accuracy is the number of species occurrence records used to train a model. In chapter 2, I quantify the effect of sample size on model accuracy for species of different range size classes. The results show that the minimum number of records required to generate accurate SDMs is not uniform for species of every range size class and that larger sample sizes are required for more widespread species. By applying a uniform minimum number of records, SDMs of narrow-ranged species are incorrectly rejected and SDMs of widespread species are incorrectly accepted. Instead, I recommend to identify and apply the unique minimum numbers of required records for each individual species. The method presented here to identify the minimum number of records for species of particular range size classes is applicable to any species group and study area.

The range size or prevalence is an important plant feature that is used in IUCN Red List classifications. It is commonly computed as the Extent Of Occurrence (EOO) and Area Of Occupancy (AOO). Currently, these metrics are computed using methods based on the spatial distribution of the known species occurrences. In chapter 3, using simulated species again, I show that methods based on the distribution of species occurrences in environmental parameter space clearly outperform those based on spatial data. In this chapter, I present a novel method that estimates the range size of a species as the fraction of raster cells within the minimum convex hull of the species occurrences, when all cells from the study area are plotted in environmental parameter space. This novel method outperforms all ten other assessed methods. Therefore, the current use of EOO and AOO based on spatial data alone for the purpose of IUCN Red List classification should be reconsidered. I recommend to use the novel method presented here to estimate the AOO and to estimate the EOO from the predicted distribution based on a thresholded SDM.

In chapter 4, I apply the currently best possible methods to generate accurate SDMs and estimate the range size of species to the large dataset of Gabonese plant species records. All significant SDMs are used here to assess the unique contribution of narrow-ranged, widespread, and randomly selected species to patterns of species richness and weighted endemism. When range sizes of species are defined based on their full range in tropical Africa, random subsets of species best represent the pattern of species richness, followed by narrow-ranged species. Narrow-ranged species best represent the weighted endemism pattern. Moreover, the results show that the applied criterion of widespread and narrow-ranged is crucial. Too often, range sizes of species are computed on their distribution within a study area defined by political borders. I recommend to use the full range size of species instead. Secondly, the use of widespread species, of which often more data are available, as an indicator of diversity patterns should be reconsidered.

The effect of global climate change on the distribution patterns of Gabonese plant species is assed in chapter 5 using SDMs projected to the year 2085 for two climate change scenarios assuming either full or no dispersal. In Gabon, predicted loss of plant species ranges from 5% assuming full dispersal to 10% assuming no dispersal. However, these numbers are likely to be substantially higher, as for many rare, narrow-ranged species no significant SDMs could be generated. Predicted species turnover is as high as 75% and species-rich areas are predicted to loose many species. The explanatory power of individual future climate anomalies to predicted future species richness patterns is quantified. Species loss is best explained by increased precipitation in the dry season. Species gain and species turnover are correlated with a shift from extreme to average values of annual temperature range.

In the final chapter, the results are placed in a wider scientific context. First, the results on the methodological aspects of SDMs and their implications of the SDM pipeline are discussed. The method presented in this thesis to simulate large numbers of species offers opportunities to systematically investigate other matters of the pipeline, some of which are discussed here. Secondly, the factors that shape the current and predicted future patterns of plant species richness in Gabon are discussed including the location of centres of species richness and of weighted endemism in relation to the hypothesized location of glacial forest refugia. Factors that may contribute to the lower species richness of African rainforests compared with South American and Asian forests are discussed. I conclude by reflecting on the conservation of the Gabonese rainforest and its plant species as well as on the opportunities SDMs offer for this in the wider socio-economic context of a changing world with growing demand for food and other ecosystem services.

Modeling spatial pattern formation in plant development
Adibi, Milad - \ 2017
University. Promotor(en): Vitor Martins dos Santos, co-promotor(en): Christian Fleck. - Wageningen : Wageningen University - ISBN 9789462956896 - 209
plant development - mathematical models - patterns - arabidopsis thaliana - vascular system - xylem - auxins - modeling - systems biology - plantenontwikkeling - wiskundige modellen - patronen - vaatsysteem - xyleem - auxinen - modelleren - systeembiologie

Modern biological research is accumulating an ever-increasing amount of information on genes and their functions. It is apparent that biological functions can very rarely be attributed to a single genes, but rather arise from complex interaction within networks that comprise many genes. A fundamentally important challenge in contemporary biology is to extract mechanistic understanding about the complex behavior of genetic networks from the available data. The interactions within a genetic network are often exceedingly complex and no-linear in nature, and thus are not open to intuitive understanding. This situation has given rise to a host of mathematical and computational approaches aimed at in-depth analysis of genetic network topologies and dynamics. In particular these approaches focus on system level proprieties of these networks, not directly derivable from their constituent components. To a large extent the power of these theoretical approaches rely on meaningful reduction in complexity by utilizing justified simplifications and abstractions. The underlying principle is that in order to comprehend a mechanism, it is not necessary to take into account all the available information about the mechanism. Given this, Computational models that follow this approach focus on incorporating core components that are essential in answering a specific biological question, while simplifying/omitting the less relevant processes. A fundamental question is this regard is what simplifying concept should be employed when developing a theoretical model of a genetic network.

A successful approach to address this question is the notion of network motif analysis. This approach is based on the core idea that most genetic networks are not arbitrary nor unique, instead they can be categorized into common network dynamics and topologies that perform core functions. Analogous to components of an electric circuit (resistors, capacitor, etc.) these network motifs have distinct properties that are independent of the network that they are embedded in. Therefore analysis of genetic networks in terms of their constituent motifs can potentially be an effective mean in obtaining mechanistic understanding about them.

In this thesis the network motif approach is utilized to study two instances of pattern formation in plant tissues. The first study focuses on organization of stem cells within the shoot apical meristem of the model plant, Arabidopsis thaliana. The results demonstrate that three interconnected network motifs can account for a range of experimental observations regarding this system. Furthermore through an exhaustive exploration of the available data, candidate genes and interactions corresponding to these motifs are outlined, thus paving the way for future interdisciplinary investigations.

The second study explores the development of vasculature during arabidopsis embryogenesis. In contrast to shoot apical mersitem in mature plant, the cell number and arrangement of vasculature in highly dynamic during its embryonic development. To account for this feature, a computational framework was utilized that is capable of capturing the interplay between genes and cell growth and division. The outcome revealed that two interlocking networks motifs dynamically control both patterning and growth of the vascular tissue. The study revealed novel spatial features of a motif previously studies exclusively in non-spatial settings. Furthermore the study resulted in a compelling example of model-driven discovery, where theoretical analysis predicted a specific cellular arrangement to be crucial for the correct development of vasculature. Subsequent analysis of experimental data confirmed the existence of this cellular arrangement in the embryo.

The projects presented in this thesis exemplify successful applications of the network motif approach in studying spatial genetic network. In both cases the networks were successfully examined in terms of their constituent motifs, which subsequently lead to increased mechanistic understanding of them. Ultimately the work presented in this thesis demonstrates the effectiveness of studying genetic networks by a combination of careful examination of available biological data and a reductionist modeling approach guided by the concept of network motifs.

Modelling the dynamic interactions between food production and ecosystem services : a case study in Benin
Duku, C. - \ 2017
University. Promotor(en): Lars Hein, co-promotor(en): S.J. Zwart. - Wageningen : Wageningen University - ISBN 9789463431613 - 141
ecosystem services - modeling - food production - case studies - hydrology - irrigation - forests - woodlands - climatic change - nature conservation - food security - benin - ecosysteemdiensten - modelleren - voedselproductie - gevalsanalyse - hydrologie - irrigatie - bossen - bosgebieden - klimaatverandering - natuurbescherming - voedselzekerheid

Given the high levels of food insecurity and the loss of vital ecosystem services associated with deforestation, countries in sub-Saharan Africa (SSA) face a major dilemma. How can they produce enough food in a changing climate to feed an increasing population while protecting natural forests and woodlands that provide a wide array of ecosystem services beneficial to livelihoods? Thus, the objectives of this thesis are twofold. First, to further enhance the understanding of the dynamic interactions between food production, and natural and semi-natural ecosystems with a case study in Benin. Second, to further enhance the understanding of how hydrological ecosystem services can be captured in an accounting framework. Understanding hydrological ecosystem services is key to understanding the multi-directional relationship between food production and ecosystem services supply from natural and semi-natural ecosystems. First, I examine how a spatially explicit ecohydrological model can be used to analyse multiple hydrological ecosystem services in line with the ecosystem accounting framework. The hydrological ecosystem services include crop water supply for rainfed agriculture, household water supply (both groundwater supply and surface water supply), water purification, and soil erosion control. Second, I develop a general modelling approach for analysing the effects of deforestation on the availability of water for irrigation at the watershed level, and I apply the approach to the Upper Oueme watershed in Benin. Third, I analyse the impact of climate change on agricultural intensification options. Finally, I quantify trade-offs between per capita food availability and protecting forests and woodlands at different levels of yield increases taking into account climate change, population growth. This thesis shows that the integration of hydrological ecosystem services into an accounting framework can provide relevant information at appropriate scales suitable for decision-making. It is empirically feasible to distinguish between service capacity and service flow of hydrological ecosystem services. This requires appropriate decisions regarding physical and mathematical representation of ecohydrological processes, spatial heterogeneity of ecosystems, temporal resolution, and required model accuracy. This thesis also shows that opportunities for irrigation expansion depend on conservation of forests and woodlands in the headwaters of the rivers feeding the irrigation scheme. Opportunities for agricultural intensification in SSA are likely to diminish with climate change, hence increasing pressure to expand cultivated areas in order to meet increasing food demand. Climate change will lead to substantial reductions in; exploitable yield gaps for major food crops, rainfed cropland areas that can support the cultivation of two or more crops per year, and water availability for irrigation expansion. Furthermore, in the far future crop yields will have to increase at a faster rate than has been recorded over the past two and half decades in order to maintain current levels of per capita food availability. Failure to achieve the required levels of yield increases is likely to lead to the conversion of substantial areas of forests and woodlands for crop cultivation. Based on the results of this thesis, four main recommendations to help address the dual challenge of food security and ecosystem protection in Benin and the larger SSA region are made: (i) promote a precautionary approach to forest and woodland conservation, (ii) promote cross-sectoral policy coherence and consultations, (iii) promote the development of satellite ecosystem accounts consistent with national accounts, and (iv) identify, evaluate and implement adaptation and resilience measures to reduce agricultural vulnerability to climate change.

Metabolic modeling to understand and redesign microbial systems
Heck, Ruben G.A. van - \ 2017
University. Promotor(en): Vitor Martins dos Santos, co-promotor(en): Maria Suarez Diez. - Wageningen : Wageningen University - ISBN 9789463434553 - 239
micro-organismen - modelleren - kooldioxide - biotechnologie - algen - metabolisme - pseudomonas - microorganisms - modeling - carbon dioxide - biotechnology - algae - metabolism

The goals of this thesis are to increase the understanding of microbial metabolism and to functionally (re-)design microbial systems using Genome- Scale Metabolic models (GSMs). GSMs are species-specific knowledge repositories that can be used to predict metabolic activities for wildtype and genetically modified organisms. Chapter 1 describes the assumptions associated with GSMs, the GSM generation process, common GSM analysis methods, and GSM-driven strain design methods. Thereby, chapter 1 provides a background for all other chapters. In this work, there is a focus on the metabolically versatile bacterium Pseudomonas putida (chapters 2,3,4,5,6), but also other model microbes and biotechnologically or societally relevant microbes are considered (chapters 3,4,6,7,8).

GSMs are reflections of the genome annotation of the corresponding organism. For P. putida, the genome annotation that GSMs have been built on is more than ten years old. In chapter 2, this genome annotation was updated both on a structural and functional level using state-of-the-art annotation tools. A crucial part of the functional annotation relied on the most comprehensive P. putida GSM to date. This GSM was used to identify knowledge gaps in P. putida metabolism by determining the inconsistencies between its growth predictions and experimental measurements. Inconsistencies were found for 120 compounds that could be degraded by P. putida in vitro but not in silico. These compounds formed the basis for a targeted manual annotation process. Ultimately, suitable degradation pathways were identified for 86/120 as part of the functional reannotation of the P. putida genome.

For P. putida there are 3 independently generated GSMs, which is not uncommon for model organisms. These GSMs differ in generation procedure and represent different and complementary subsets of the knowledge on the metabolism of the organism. However, the differing generation procedures also makes it extremely cumbersome to compare their contents, let alone to combine them into a single consensus GSM. Chapter 3 addresses this issue through the introduction of a computational tool for COnsensus Metabolic Model GENeration (COMMGEN). COMMGEN automatically identifies inconsistencies between independently generated GSMs and semi-automatically resolves them. Thereby, it greatly facilitates a detailed comparison of independently generated GSMs as well as the construction of consensus GSMs that more comprehensively describe the knowledge on the modeled organism.

GSMs can predict whether or not the corresponding organism and derived mutants can grow in a large variety of different growth conditions. In comparison, experimental data is extremely limited. For example, BIOLOG data describes growth phenotypes for one strain in a few hundred different media, and genome-wide gene essentially data is typically limited to a single growth medium. In chapter 4 GSMs of multiple Pseudomonas species were used to predict growth phenotypes for all possible single-gene-deletion mutants in all possible minimal growth media to determine conditionally and unconditionally essential genes. This simulated data was integrated with genomic data on 432 sequenced Pseudomonas species, which revealed a clear link between the essentiality of a gene function and the persistence of the gene within the Pseudomonas genus.

Chapters 5 and 6 describe the use of GSMs to (re-)design microbial systems. P. putida is, despite its acknowledged versatile metabolism, an obligate aerobe. As the oxygen-requirement limits the potential applications of P. putida, there have been several experimental attempts to enable it to grow anaerobically, which have so far not succeeded. Chapter 5 describes an in silico effort to determine why P. putida cannot grow anaerobically using a combination of GSM analyses and comparative genomics. These analyses resulted in a shortlist of several essential and oxygen-dependent processes in P. putida. The identification of these processes has enabled the design of P. putida strains that can grow anaerobically based on the current understanding of P. putida metabolism as represented in GSMs.

Efficient microbial CO2 fixation is a requirement for the biobased community, but the natural CO2 fixation pathways are rather inefficient, while the synthetic CO2 fixation pathways have been designed without considering the metabolic context of a target organism. Chapter 6 introduces a computational tool, CO2FIX, that designs species-specific CO2 fixation pathways based on GSMs and biochemical reaction databases. The designed pathways are evaluated for their ATP efficiency, thermodynamic feasibility, and kinetic rates. CO2FIX is applied to eight different organisms, which has led to the identification of both species-specific and general CO2 fixation pathways that have promising features while requiring surprisingly few non-native reactions. Three of these pathways are described in detail.

In all previous chapters GSMs of relatively well-understood microbes have been used to gain further insight into their metabolism and to functionally (re-)design them. For complex microbial systems, such as algae (chapter 7) and gut microbial communities (chapter 8), GSMs are similarly useful, but substantially more difficult to create and analyze. Algae are widely considered as potential centerpieces of a biobased economy. Chapter 7 reviews the current challenges in algal genome annotation, modeling and synthetic biology. The gut microbiota is an incredibly complex microbial system that is crucial to our well-being. Chapter 8 reviews the ongoing developments in the modeling of both single gut microbes and gut microbial communities, and discusses how these developments will enable the move from studying correlation to causation, and ultimately the rational steering of gut microbial activity.

Chapter 9 discusses how the previous chapters contribute to the research goals of this thesis. In addition, it provides an extensive discussion on current GSM practices, the issues associated therewith, and how these issues can be tackled. In particular, the discussion focuses on issues related to: (i) The inability to distinguish between biological difference and GSM generation artifacts when using multiple GSMs, (ii) The lack of continuous GSM updates, (iii) The mismatch between what GSM predictions and experimental data represent, (iv) The need for standardization in GSM evaluation, and (v) The lack of experimental validation of GSM-driven strain design for metabolic engineering.

Preserving Urmia Lake in a changing world : reconciling anthropogenic and climate drivers by hydrological modelling and policy assessment
Shadkam, Somayeh - \ 2017
University. Promotor(en): Pavel Kabat, co-promotor(en): Fulco Ludwig; Pieter van Oel. - Wageningen : Wageningen University - ISBN 9789463431866 - 140
lakes - hydrology - climatic change - modeling - water resources - water management - environmental protection - iran - meren - hydrologie - klimaatverandering - modelleren - watervoorraden - waterbeheer - milieubescherming

Urmia Lake, in north-western Iran, is an important internationally recognized natural area designated as a RAMSAR site and UNESCO Biosphere Reserve. Over the last 20 years, the surface area of Urmia Lake has declined by 80%. As a result, the salinity of the lake has sharply increased which is disturbing the ecosystems, local agriculture and livelihoods, regional health, as well as tourism, which could amplify economic, political and ethnic tensions in this already volatile region. In response to that, Iranian government established the ten-year “Urmia Lake Restoration Program (ULRP)” proposing six approaches in terms of controlling, protecting, surveying, studying and supplying water from other sources. This study first assessed the main reasons for the decreased inflow using the Variable Infiltration Capacity (VIC) hydrological model, including reservoirs and irrigation modules. The results showed that climate change was the main contributor to this inflow reduction. However, water resources development, particularly water use for irrigation, has played a substantial role as well. In the second step assessed Urmia lake inflow under future climate change and irrigation scenarios. Then, the (VIC) model was forced with bias-corrected climate model outputs for both the lowest (RCP2.6) and highest (RCP8.5) greenhouse-gas concentration scenarios to estimate future water availability. The results showed that the water resources plans are not robust to changes in climate. In other words, if future climate change is limited due to rapid mitigation measures (RCP2.6) the new strategy of reduction of irrigation water use can contribute to preserve Urmia Lake.

The next step of this study assessed the quantitative impacts of ULRP by introducing a constructive framework. The framework depicts real water saving by distinguishing between water withdrawals, depletion, and demand in the context of uncertainties in future demand and supply. The results showed that although the ULRP helps to increase inflow by up to 57% it is unlikely to fully reach its target for three main reasons. The first reason is decreasing return flows due to increasing irrigation efficiency. The second reason is increased depletion which is due to neglecting the fact that agricultural water demand is currently higher than available water for agriculture. The third reason is ignoring the potential impact of climate change. However, there still can be some additional none-quantifiable barriers and challenges that may cause the failure of the restoration plan. Therefore, in the last step, this study used two types of qualitative data to explore these aspects: first, the opinions from 40 experts and the in-situ observation of some of the ULRP implementation practices. The results indicate a number of challenges for the ULRP implementation including the water use regulations and the agricultural measures. In addition, (water) demand-side measures such as crop pattern changes were more supported, as opposed to supply-side measures.

This thesis showed that the sustainable approach to preserve Urmia Lake should incorporate both demand management (considering socioeconomic complexity) and flexible supply management strategies (to deal with uncertainties in climate variability and change) in a participatory approach. To be prepared for the future, also scenarios with reduced inflow into Urmia Lake, either due to climate change or water resources development, need to be considered to deal with considerable amounts of variability in the current system and with future changes in climate and socioeconomic conditions.

The Mekong’s future flows : quantifying hydrological changes and developing adaptation options
Hoang, Long Phi - \ 2017
University. Promotor(en): Pavel Kabat; Rik Leemans, co-promotor(en): Fulco Ludwig; Michelle van Vliet. - Wageningen : Wageningen University - ISBN 9789463431088 - 159
hydrology - mekong river - modeling - climatic change - socioeconomics - water resources - water use - south east asia - hydrologie - mekong - modelleren - klimaatverandering - sociale economie - watervoorraden - watergebruik - zuidoost-azië

This multidisciplinary study focuses on projecting and adapting to future hydrological changes in the Mekong – an international river of global significance in terms of rapidly increasing human pressures and climate-change vulnerability. A modelling framework was developed to project future changes in both the river flow regime and hydrological extremes (i.e. high/low flows and floods), under multiple scenarios of climate change, irrigation and hydropower developments. Furthermore, we developed a combined quantitative-qualitative approach to develop suitable adaptation measures and strategies to future floods in the Mekong Delta being a key vulnerability hotspot.

Results show that the Mekong’s future flow regime is subjected to substantial changes under climate change and human developments. Climate change will intensify the hydrological cycle, resulting in increasing average river flows (between +5 % and +16%, annually), and more frequent and extreme high flows during the wet season. Flow regime shows substantial alterations in the seasonal flow distributions under the combined impacts of climate change, irrigation expansions and hydropower developments. While dry season flows increase strongly (monthly changes up to +150%), wet season flows show contrasting changes with reductions during June - October (up to -25%) and substantial increases during November – December (up to 36%). A follow-up modelling assessment for the Mekong Delta shows substantial increases in flood hazards under climate change and sea level rise, shown by higher flood frequencies and flood depths across the whole delta. Increasing flood hazards therefore represents a key issue to be addressed in terms of future adaptation. The adaptation appraisal study further shows that effective adaptation requires looking beyond sole infrastructural investments. Instead, technological innovations for flood risk management combined with improved governance and institutional capacities offer ample opportunities to adapt to future hydrological changes.

This study projects substantial future hydrological changes under future climate change and accelerating socioeconomic developments and shows potentially serious consequences for water related safety and sustainable water resources uses and allocations. Furthermore, this study demonstrates amble opportunities to manage future changes through strategic development planning and through adaptive interventions. Insights from this study address the needs for quantified future hydrological changes and emphasize adequate adaptation to the associated risks in an important international river experiencing climate change and rapid socioeconomic developments.

Dynamic photosynthesis under a fluctuating environment: a modelling-based analysis
Morales Sierra, Alejandro - \ 2017
University. Promotor(en): Paul Struik; Jaap Molenaar, co-promotor(en): Xinyou Yin; Jeremy Harbinson. - Wageningen : Wageningen University - ISBN 9789463430456 - 282
photosynthesis - modeling - analysis - environmental factors - light - canopy - leaves - crop physiology - metabolism - fotosynthese - modelleren - analyse - milieufactoren - licht - kroondak - bladeren - gewasfysiologie - metabolisme

In their natural environment, leaves are exposed to rapid fluctuations of irradiance. Research on CO2 assimilation under fluctuating irradiance often relies on measurements of gas exchange during transients where irradiance is rapidly increased or decreased, after the leaf has adapted to a particular set of environmental conditions. In the field, such increases and decreases occur mostly because of sunflecks (rapid increases in irradiance on a low irradiance background) created by gaps in the canopy and plant movement by wind, and cloudflecks (rapid decreases in irradiance on a high irradiance background) generated by clouds that transiently block the sun.

In this dissertation, the metabolic regulation of photosynthesis and how this may limit dynamic CO2 assimilation is studied in silico with the development and application of simulation models. In order to support the development of the models, a review of the literature was performed as well as an experiment designed to generate data on dynamic CO2 assimilation for different photosynthetic mutants of Arabidopsis thaliana. In addition to providing these models to the research community, this dissertation also identifies multiple targets that may be used for improving dynamic CO2 assimilation in plants. It further demonstrates that the dynamic responses of CO2 assimilation to changes in irradiance has a significant effect on canopy CO2 assimilation, even for dense canopies exposed to open skies, resembling the conditions of commercial crops.

In Chapter 1, the context of this dissertation is presented. The societal relevance of this research is argued, making reference to the role that photosynthesis could play in addressing global problems such as food and energy security. The necessary background on the physiology of photosynthesis is provided, with special emphasis on the terminology and concepts required to understand the rest of the dissertation, with the aim of making the contents more accessible to a wider audience. Then, prior literature on the specific topics of this dissertation (i.e., photosynthesis in a dynamic environment and its mathematical modelling) is presented, with a chronological approach that analyses the evolution of ideas and methodologies up to the present.

In Chapter 2, the current literature on dynamic CO2 assimilation is reviewed, with an emphasis on the effects of environmental conditions ([CO2], temperature, and air humidity) on the rates of photosynthetic induction and loss of induction. This review reveals major knowledge gaps, especially on the loss of induction. The little data available indicates that rates of photosynthetic induction increase with [CO2], which could be explained by a weak effect on Rubisco activation and a strong effect on stomatal opening. Increases in temperature also increase the rates of photosynthetic induction, up to an optimum, beyond which a strong negative effect can be observed, which could be attributed to deactivation of Rubisco activase.

In Chapter 3, an experiment is presented that makes use of several photosynthetic mutants of A. thaliana. Downregulating non-photochemical quenching and sucrose synthesis did not have any significant effect on dynamic CO2 assimilation, whereas CO2 diffusion and Rubisco activation exerted stronger limitations. Further analysis reveals that whether stomatal opening limits CO2 assimilation after an increase in irradiance depends on the stomatal conductance prior to the change in irradiance. A threshold value of 0.12 mol m−2 s−1 (defined for fluxes of water vapour) could be defined, above which stomata did not affect the rates of photosynthetic induction. The comparison of measurements across irradiance levels also indicated that the apparent rate constant of Rubisco activation is irradiance-dependent, at least for irradiance levels below 150 μmol m−2 s−1.

In Chapter 4, a phenomenological model of leaf-level CO2 assimilation is presented. The model is described in detail and all the parameters are first estimated with published data, and later refined by fitting the model to the data from Chapter 3. Additional data from the experiment in Chapter 3 is used to validate predictions of CO2 assimilation under lightflecks for the different photosynthetic mutants. The model predicts accurately dynamic CO2 assimilation for the different photosynthetic mutants by only modifying those parameters that are affected by the mutation. This demonstrates that the model has a high predictive power and that the equations, although phenomenological in nature, have a solid physiological basis.

The model is further used to analyse, in silico, the limitations imposed by different photosynthetic processes on dynamic CO2 assimilation at the leaf and canopy level, allowing a more in depth analysis than in Chapter 3. The analysis demonstrates that results obtained at the leaf level should not be extrapolated directly to the canopy level, as the spatial and temporal distribution of irradiance within a canopy is more complex than what is achieved in experimental protocols. Both at the leaf and canopy level, CO2 diffusion is strongly limiting, followed by photoinhibition, chloroplast movements and Rubisco activation.

In Chapter 5, a mechanistic model of the dynamic, metabolic regulation of the electron transport chain is presented. The model is described in detail and all the parameters are estimated from published literature, using measurements on A. thaliana when available. Predictions of the model are tested with steady-state and dynamic measurements of gas exchange, chlorophyll fluorescence and absorbance spectroscopy on A. thaliana, with success.

The analysis in silico indicates that a significant amount of alternative electron transport is required to couple ATP and NADPH production and demand, and most of it is associated with nitrogen assimilation and export of redox power through the malate shuttle. The analysis also reveals that the relationship between ATP synthesis and the proton motive force is highly regulated by the concentrations of substrates (ADP, ATP and inorganic phosphate), and this regulation facilitates an increase in non-photochemical quenching under conditions of low metabolic activity in the stroma.

In Chapter 6, the findings of Chapters 2–5 are summarised and employed to answer in detail the four research questions formulated in Chapter 1. Of great interest is the identification of six potential targets that may be used to improve dynamic CO2 assimilation. These targets are: (i) regulation of Rubisco activity through changes in the amount or regulation of Rubisco activase, (ii) acceleration of stomatal opening and closure, (iii) a lower /ATP for ATP synthesis, (iv) faster relaxation of non-photochemical quenching, (v) reduced chloroplast movements, and (vi) reduced photoinhibition by increased rates of repair of Photosystem II.

Modelling of ammonia volatilisation in fertilised and flooded rice systems
Khairudin, Nurulhuda - \ 2017
University. Promotor(en): Nurul Khairudin, co-promotor(en): Karel Keesman; Mohamad Pauzi Zakaria. - Wageningen : Wageningen University - ISBN 9789462576698 - 209
oryza - flooded rice - ammonia - volatilization - modeling - dynamic modeling - flooded land - nitrogen - natte rijst - ammoniak - vervluchtiging - modelleren - dynamisch modelleren - overstroomde gronden - stikstof

In flooded rice systems that are broadcast with urea, significant amounts of nitrogen (N) may be lost to the atmosphere in the form of ammonia (NH3). Many models with different complexities with regards to describing the process of NH3 volatilisation and the overall N dynamics in the systems are available. However, given the differences in local conditions, both too simple and too complex models may not be able to predict NH3 volatilisation correctly or may lead to large prediction uncertainties. Therefore, the main objective of this thesis is to provide a framework to determine an appropriate process-based model with corresponding uncertainty characteristics for estimating NH3 volatilisation in fertilised and flooded rice systems.

As a first step in the selection of a model for a specific application, an overview on the modelling concepts and the performance of 14 models developed to simulate N dynamics in flooded soil systems is given. Next, in order to understand differences in modelling concepts for a specific process, co-validation was conducted at single process level: urea hydrolysis, NH3 volatilisation, and floodwater pH. Then, a new process-based model for estimating NH3 volatilisation in fertilised and flooded rice systems, which is of a complexity appropriate for scarce soil N data, is presented and evaluated with field observations. For the flooded rice systems in the Philippines, conceptualisation of the two-step urea hydrolysis, partitioning between ammonium and NH3, and a time-varying rate coefficient of NH3 volatilisation in the proposed model improved the prediction of the net NH3 loss. Subsequently, a set-membership parameter estimation approach with soft-error-bounds was used to characterise the uncertainty in the parameter estimates in the proposed model. The set-membership approach is appropriate for poor quality data sets as it allows simultaneous consideration of the different sources of uncertainty affecting the model prediction, such as uncertainty in the model structure, parameters, and observations. Findings of this study can be used as criteria for stakeholders to make an informed selection of models, to modify the existing models for a specific purpose, and to interpret model-output responses critically.

Physiologically based kinetic modelling based prediction of oral systemic bioavailability of flavonoids, their metabolites, and their biological effects
Boonpawa, Rungnapa - \ 2017
University. Promotor(en): Ivonne Rietjens, co-promotor(en): Arjen Punt. - Wageningen : Wageningen University - ISBN 9789463430371 - 180
flavonoids - bioavailability - modeling - metabolites - quercetin - physiology - hesperidin - flavonoïden - biologische beschikbaarheid - modelleren - metabolieten - quercetine - fysiologie - hesperidine

Flavonoids, abundantly present in fruits and vegetables, have been reported to exert various positive health effects based on in vitro bioassays. However, effects detected in in vitro models cannot be directly correlated to human health as most in vitro studies have been performed using flavonoid aglycones at high concentration ignoring extensive metabolism of flavonoids in the human body. To better understand positive health effects of flavonoids in humans, it is of importance to gain insight in at which form and concentration flavonoids are present in the systemic circulation after consumption. This insight can be obtained using physiologically based kinetic (PBK) computer modeling. The results obtained show that PBK modeling provides a useful additional research tool for studies on the fate of flavonoids in the human body and can reveal at what oral dose levels of flavonoids in vitro positive health effects can be expected to occur in vivo, presenting opportunities that are not easily provided by other methods.

The TOXSWA model version 3.3 for pesticide behaviour in small surface waters : description of processes
Horst, M.M.S. ter; Beltman, W.H.J. ; Berg, F. van den - \ 2016
Wageningen : Statutory Research Tasks Unit for Nature & the Environment (WOt-technical report 84) - 72
pesticides - surface water - models - modeling - aquatic ecosystems - drainage - runoff - pesticiden - oppervlaktewater - modellen - modelleren - aquatische ecosystemen - oppervlakkige afvoer
In the European Union (EU) the risk of plant protection products to aquatic organisms is assessed accordingto regulation 1107/2009. For this assessment the FOCUS Surface Water Scenarios have been developed. TheTOXSWA model is included in the FOCUS Surface Water Software tools to calculate the exposureconcentration in the water systems defined in those scenarios. At the national level the TOXSWA model isused to assess the exposure concentration in the water system defined in national scenarios. In this report adescription is given of the hydrology in the Dutch and EU water body systems and the fate of pesticides andtheir metabolites in water and sediment. The pesticide can enter the system by spray drift and/or drainageand run-off. The transport in the water system is described by advection, dispersion and diffusion. Theexchange at the water-sediment interface is described based on advection/diffusion. Other processes aresorption, volatilisation at the water – air interface and transformation in both the water layer and thesediment. The formation and transformation of metabolites in both compartments are described. The reportpresents an outlook on the improvements in the next version as well as on future developments.
The assessment of advanced pre-treatment chains. TO2 Advanced pre-treatment of biomass; Task A3
Meesters, K.P.H. ; Annevelink, E. ; Keijsers, E.R.P. - \ 2016
Wageningen UR - Food & Biobased Research - ISBN 9789462577213 - 23 p.
value chain analysis - supply chain management - biomass - biobased materials - biobased economy - bioenergy - biorefinery - modeling - pretreatment - waardeketenanalyse - ketenmanagement - biomassa - materialen uit biologische grondstoffen - bio-energie - bioraffinage - modelleren - voorbehandeling
The overall objective of the TO2 project ‘Advanced pre-treatment of biomass’ was to design optimal energy-driven refinery chains for the susta inable valorization of non-woody biomass to biobased commodities. Therefore optimal combination s need to be found of upstream biorefining and the production of high-quality (sol id) energy carriers from a broad spectrum of non-woody biomass streams. Task A3. within this TO2 project focused on modelling chains and performing an economic evaluation of these chains. Three cases of biomass chains were modelled and evaluated in this report.
Met Hoofd Hart en Handen
Adelhart Toorop, R.L. de; Veluw, C. van - \ 2016
Ekoland 2016 (2016)10. - ISSN 0926-9142 - p. 24 - 25.
biologische landbouw - agrarisch onderwijs - bedrijfssystemen - modelleren - agrarische bedrijfsvoering - geitenhouderij - organic farming - agricultural education - farming systems - modeling - farm management - goat keeping
Wageningen is een van de weinige plekken in Europa waar een masterprogramma Organic Agriculture wordt aangeboden. Hoewel het binnen WUR een van de meest praktische opleidingen is, wordt het gros van de kennis binnen de collegezalen overgedragen. In het vak ‘Analyse en Ontwerp van Biologische Bedrijfssystemen’ verdiepen studenten zich in de zomer vier weken lang in de praktijk van de boeren van een biologisch bedrijf.
Modeling the coupled exchange of water and CO2 over croplands
Combe, Marie - \ 2016
University. Promotor(en): Wouter Peters; Maarten Krol, co-promotor(en): Jordi Vila-Guerau de Arellano. - Wageningen : Wageningen University - ISBN 9789462579255 - 152
carbon cycle - carbon dioxide - modeling - water - energy exchange - crop yield - grain crops - atmosphere - koolstofcyclus - kooldioxide - modelleren - energie-uitwisseling - gewasopbrengst - graangewassen - atmosfeer

Croplands are a managed type of vegetation, with a carbon storage that is highly optimized for food production. For instance, their sowing dates are chosen by the farmers, their genetic potential is bred for high grain yields, and their on-field competition with other species is reduced to the minimum. As a result of human intervention, croplands are a major land cover type (roughly one fifth of the land area over Europe) and they experience a short growing season during which they exchange carbon and water intensively with the atmosphere. Their growth significantly affects the seasonal amplitude of CO2 mole fractions over the globe, interact with extreme weather events such as droughts and heat waves, and impact surface hydrology due to their water consumption. However, and in spite of their relevance, terrestrial biosphere models used in carbon cycle and atmospheric research often assume the phenology of croplands to be similar to the one of grasslands, and they also ignore the impact of crop management. This oversimplification is the motivation for this thesis. We focus on understanding and modeling the key surface and atmospheric processes that shape the cropland water and CO2 exchange, and the resulting impact on the CO2 mole fractions of the atmosphere overhead. We study these processes from the daily to the seasonal scale, for croplands of the mid-latitudes. In the end, we come with recommendations and a new modeling framework to represent the cropland CO2 and water exchange in the Earth System, weather and climate models.

The ecology of ditches : a modeling perspective
Gerven, Luuk P.A. - \ 2016
University. Promotor(en): W.M. Mooij, co-promotor(en): Jeroen de Klein; J.H. Janse. - Wageningen : Wageningen University - ISBN 9789462579316 - 137
ditches - aquatic ecology - ecology - modeling - aquatic plants - aquatic ecosystems - water flow - sloten - aquatische ecologie - ecologie - modelleren - waterplanten - aquatische ecosystemen - waterstroming

The Netherlands is well-known for its extended networks of drainage ditches, with a total ditch length of about 300.000 km. Their main function is to enable agriculture by draining water. Nonetheless, ditches also have important ecological functions. They serve as ecological corridors and harbor a high biodiversity in which water plants play a crucial role. The last decades, the ecological quality of ditches is at stake. Enhanced nutrient inputs promoted the invasion by dense mats of free-floating plants like duckweed. Underneath these mats the water becomes dark and anoxic, which severely constrains aquatic life.

In this thesis I developed new concepts to better understand, predict and combat the dominance by free-floating plants in ditches. The following questions are addressed. Are floating plants a self-stabilizing state - an alternative stable state - which would make it more difficult to combat floating-plant dominance (chapter 2)? Does it make sense to fight floating-plant dominance by reducing nitrogen (N) inputs to the ditches or will it lead to an invasion of floating plants that can fix N2 from the atmosphere (chapter 3)? What about spatial aspects, does the vulnerability of a ditch to floating plants depend on the position of a ditch in a polder, like its distance to the polder outlet (chapter 4)? To answer these questions, I used ecological models that predict the abundance of free-floating plants based on the competition for nutrients and light with other plants such as submerged plants, and where possible validated these models with field data. Starting from the ecosystem model PCDitch, I developed and combined models with different complexity to see how theoretical concepts, developed in minimal models, translate to the ecosystem level. Chapter 5 deals with a method that facilitates this up- and downscaling in model complexity.

Are floating plants an alternative stable state? To answer this question I extended mechanistic resource competition theory with a framework (minimal model) describing the competition of floating and submerged plants for light and nutrients. The model predicts that the competitive advantage of floating plants - they have a primacy for light and shade submerged plants, giving rise to asymmetry in competition for light - makes that floating plants always dominate at high supply of light and nutrients. At intermediate nutrient supply, there can be alternative stable states: either the submerged plants or the floating plants dominate depending on who established first. However, based on the traits of common floating plants (duckweed; Lemna) and submerged plants (waterweed; Elodea) the model predicts, in line with field data, that floating plants are not an alternative stable state. Furthermore, from a theoretical point of view this study shows that the asymmetry in light competition ensures that common rules from standard competition theory do not apply anymore. Like the R* rule, which states that the species that can persist at the lowest resource levels always wins the competition.

Can duckweed-dominance be combatted by reducing N inputs to the ditches? Or does this promote other floating plants like water fern (Azolla) that can fix N2 from the atmosphere? Important is the question whether such N2-fixers can provide enough N to prevent N-limitation and keep the system P-limited, which would make steering on N inputs ineffective. To investigate this, I considered the competition between Lemna and Azolla for N, P and light. Both a minimal model, an ecosystem model (PCDitch) and field data reveal that N2-fixation is unlikely to lead to P-limitation. This can be explained by N2-fixers typically requiring higher P concentrations to persist, implying that they cannot keep the P concentration low enough for non-N2-fixers to become P-limited. In combination with field data that hint at constraints on N2-fixation that prevent N2-fixers from becoming abundant at low N availability, this suggests that it certainly pays off to combat floating plant-dominance by reducing N inputs.

Is every ditch in a polder equally vulnerable to floating plants? Each ditch in a polder receives water and nutrients from the adjacent land. This leads to a spatial gradient in water flow and associated nutrient loading, from low in the remote polder sites to high in the direction of the polder outlet where the water leaves the polder. I explored if this spatial gradient affects the vulnerability of a ditch to floating plants, by investigating with a simple nutrient model how this gradient affects the nutrient concentration of the ditches and by subsequently predicting the gradient's effect on the ditch ecology by applying the ecosystem model PCDitch spatially, through coupling PCDitch to the 1-D hydrodynamic model SOBEK. Surprisingly, we found that every ditch is equally vulnerable to floating plants, despite the spatial gradient in water flow and nutrient loading. It turned out that the ecological state of each ditch could already be predicted by regarding only the lateral supply of water and nutrients from the adjacent land, and not the supply from upstream ditches. However, these findings are violated when there is spatial heterogeneity in the water and nutrient supply from the adjacent land or in ditch characteristics like depth and sediment type. Then, the chance on floating-plant dominance differs throughout the network and a spatial modelling approach (PCDitch-SOBEK) is required to predict this chance.

Developing and combining models of different complexity plays an important role in this thesis. To do so, I used a Database Approach To Modelling (DATM), a recently developed method in which a model is stored in tables in a clear and clean way, which facilitates model development. In addition, with DATM a model can be automatically implemented in a modelling environment of choice. This relieves technical implementation issues and leaves room to focus on ecology rather than technology. I illustrated the use of DATM by implementing and analyzing the ecosystem model PCDitch and its twin model for shallow lakes PCLake in different modelling environments by using DATM. This showed that DATM allows one to use the environment one is familiar with and eases the switch to other environments for complementary analyses, including analysis in a spatial 1-D to 3-D setting.

The insights provided by this thesis can help us to improve the ecological quality of ditches. A challenging task, given the fast human-driven environmental changes at both local and global level. To predict and to anticipate the effect of these changes on the ecology, it is essential to understand how the ditch ecosystem functions. The developed and applied methods described in this thesis may be helpful in that. For example, using models of different complexity makes it possible to translate fundamental theory to the ecosystem scale, which is essential to better grasp the behavior of an ecosystem. Furthermore, the in this thesis established coupling between PCDitch and SOBEK breaks new grounds for spatial ecosystem modelling. In combination with the growing amount of remote sensing data from satellites and drones, which allow for the continuous and potentially real-time validation and calibration of spatial ecosystem models, such a spatial approach has the potential to greatly increase our ecological understanding of ditches. These advances facilitate the development of successful management strategies that make our ditch ecosystems future-proof.

Making eco logic and models work : an integrative approach to lake ecosystem modelling
Kuiper, Jan Jurjen - \ 2016
University. Promotor(en): W.M. Mooij, co-promotor(en): J.H. Janse; Jeroen de Klein. - Wageningen : Wageningen University - ISBN 9789462579446 - 192
ecology - models - ecosystems - modeling - aquatic ecology - water management - water quality - databases - ecologie - modellen - ecosystemen - modelleren - aquatische ecologie - waterbeheer - waterkwaliteit - databanken

Dynamical ecosystem models are important tools that can help ecologists understand complex systems, and turn understanding into predictions of how these systems respond to external changes. This thesis revolves around PCLake, an integrated ecosystem model of shallow lakes that is used by both scientists and water quality managers to understand and predict eutrophication effects in shallow lake ecosystems. Shallow lakes provide some of the clearest examples of alternative stable states in natural systems. PCLake can be used to calculate the critical nutrient loading, that is, the nutrient loading where an abrupt regime shift occurs from a clear aquatic plant dominated state to a turbid phytoplankton dominated state, or vice versa. Four different aspects of modelling with PCLake are addressed in this thesis: (1) making the model better accessible for the modelling community, (2) improving the model, (3) developing scientific theory, and (4) exploring new applications for water quality management.

Following a general introduction to the thesis in chapter 1, the Database Approach To Modelling (DATM) is introduced in chapter 2. DATM is invented to make dynamic models more accessible. The idea of DATM is that the mathematical equations of a model are stored in a database independently of program language and software specific information. From the database, the information can be automatically translated, augmented and compiled into working model code of various different modelling frameworks (software programs).

In chapter 3 the weak link between ecosystem models and real ecosystems is discussed in relation to model calibration and improvement. In a previous stage PCLake has been calibrated using data of more than 40 lakes to obtain a best overall fit, which has greatly increased the scope of the model by making it suitable for more generalized studies on temperate shallow lakes. However, because of this calibration, adding missing functional components to the model at a later stage does not automatically increase the validity of the model, as it may bring the model ‘out of balance’. This is exemplified by adding filter feeding zoobenthos to PCLake, which were previously ignored.

In chapter 4, the relation between food-web theory and alternative stable states theory is scrutinized. Both theoretical paradigms are highly influential in modern ecology as they help scientists understand how stability emerges in complex natural ecosystems. Unfortunately, they developed independently and it is largely unclear how the resilience of a food web relates to the stability of the complete ecosystem. For this study PCLake was used as a virtual reality from which ‘empirical’ information is sampled to parameterize a food web model, following traditional food web methods. This allowed calculating the stability of the food web along a gradient of environmental change, knowing that the complete ecosystem shows a regime shift once the critical nutrient loading is exceeded.

In chapter 5 the question is asked to what extent models of a different form can be used to describe the same natural phenomenon, and hence, how these models can be used for a better understanding of such natural phenomena. Using three classical extensions of the famous Lotka-Volterra equations, which unlike PCLake can be fully mathematically understood, we analyze the consequence of changing a system with a sophisticated functional response term (e.g. Holling type II or III) into a system with a simpler functional response term while maintaining equilibrium densities and material fluxes. These results give new insight into when empirical data can be linked to mathematical models to estimate the stability properties of real ecosystems.

Although PCLake is predominantly applied in the context of ecosystem restoration of turbid phytoplankton dominated lakes, chapter 6 focusses on the clear water state after the reestablishment of aquatic plant dominance as occured. Dense stands of aquatic plants easily cause nuisance, and hence the removal of aquatic plants is an emerging management issue. Yet, because aquatic plants play an important role in stabilizing the clear water state, the removal of plant biomass can potentially trigger a critical transition back to the turbid water state. Currently there is only limited empirical and theoretical understanding of how harvesting of aquatic plants affects ecosystem functioning, which frustrates effective and efficient ecosystem management. With PCLake the impact of harvesting is evaluated, in terms of reducing nuisance and ecosystem stability, for a wide range of external nutrient loadings, mowing intensities and timings. Additionally, the model is used to estimate how much phosphorus is removed from the system during harvesting.

In chapter 7 I discuss the added value of taking an integrative approach to modelling, and discuss the integrated nature of the studies presented in this thesis. It’s also important to note that these studies were part of a larger research project with the overall aim of increasing the usefulness and the validity of PCLake and its twin model PCDitch, and to enhance the confidence in the models among water quality managers. A synopsis of the overarching collaborative research project on PCLake and PCDitch is presented in chapter 8.

Refining a model-based assessment strategy to estimate the ammonia emission from floors in dairy cow houses
Snoek, Dennis J.W. - \ 2016
University. Promotor(en): Peter Groot Koerkamp, co-promotor(en): Nico Ogink; Hans Stigter. - Wageningen : Wageningen University - ISBN 9789462578852 - 182
dairy cows - stalls - ammonia emission - floors - modeling - mitigation - sensors - ph - temperature - urea - melkkoeien - stallen - ammoniakemissie - vloeren - modelleren - mitigatie - temperatuur - ureum

Ammonia (NH3) emission is still high, and agriculture is still the dominant contributor. In The Netherlands, the NH3 emission from dairy cow houses is one of the most important sources. A lot of research has been conducted to understand and model NH3 emission, to measure it, and to reduce it using identified and developed reduction measures. However, our understanding of how to measure and how to reduce the NH3 emission is still limited. In addition, the set emission ceilings were lowered for 2020.

The objective of this thesis was to refine a model-based assessment strategy to estimate the ammonia emission from floors in dairy cow houses. First the most important input variables and process parameters were identified with a sensitivity analysis in currently available mechanistic NH3 emission models and theory. It was concluded that five puddle related input variables caused the largest variation in NH3 emission estimation, being the puddle pH, depth (Dp), urinary urea nitrogen concentration (UUN), surface area (Ap), and temperature (Tliq). For each input variable the available data was scarce, and it was therefore recommended to measure these five most important variables in practice. However, measurement methods were hardly available. Therefore, sensors were chosen, new measurement methods were developed, and these were combined in a protocol to measure the pH, Dp, UUN, Ap and Tliq of fresh, random and manually created urine puddles in commercial dairy cow houses.

In total 16 commercial dairy cow houses were assessed in a factorial experimental setup based on four floor-management types in two Seasons, with PREclean treatment. PREclean represented intense-floor-cleaning that was compared to on-farm manure scraping. A V-shaped asphalt floor had significantly larger values for both Ap (1.04 m2) and Dp (1.5 mm) than did the slatted and grooved floors (0.76 m2, 0.93 mm). For both Ap and Dp the variation within a farm was large, but was negligible between farms. The Dp values and variation were 3 to 6 times larger than currently assumed. With PREclean treatment the Dp resulted in about 3 times lower values compared to the on-farm scraping. In short, the potential NH3 emission reduction of good floor cleaning is large. Overall mean values were 4.27 kg m-3 for UUN, an initial pH(t=0) of 8.3, both in fresh puddles, and a pH(t=ξ) of 9.0 for random puddles at a random time. For UUN both the variation within and between farms was large, whereas the variation for pH was small. Both the mean UUN and pH showed lower values than currently assumed. In a separate 4 h time series experiment at 3 commercial farms was shown that the pH, on average, quickly increased initially, declined after 1 h and then became stable. The calculated NH3 in kg puddle-1 showed a huge range and was considerably larger than currently assumed for the reference situation.

Compared to the aforementioned sensitivity analysis outcome, the UUN range at farm level is both slightly smaller and shifts to slightly lower values, while for Dp the range and values are both larger. These two variables caused the largest variation in the estimated NH3 emissions, and not the pH. In conclusion, these two variables certainly need to be measured in individual commercial dairy cow houses to estimate the NH3 emission. For Ap, pH and Tair the measured ranges at farm level were less large. The pH turns out to be fairly stable in commercial cow houses and, related to that, it causes less variation in the estimated NH3 emission. Nevertheless, the pH still ranks as the third most important variable, and therefore needs to be measured in individual cow houses. The Ap is fairly stable between farms, but varies within farms and it still has a significant effect on the NH3 emission. The floor design clearly affects the puddle area Ap. Therefore, it is not necessary to measure Ap at each individual farm, but it is sufficient to measure the Ap in only one commercial cow house per floor design. The Tair variable is of limited importance compared to the aforementioned four variables, but it is still significant.

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