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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Response of sediment bacterial community to triclosan in subtropical freshwater benthic microcosms
Peng, Feng Jiao ; Diepens, Noël J. ; Pan, Chang Gui ; Ying, Guang Guo ; Salvito, Daniel ; Selck, Henriette ; Brink, Paul J. Van den - \ 2019
Environmental Pollution 248 (2019). - ISSN 0269-7491 - p. 676 - 683.
Benthic macroinvertebrates - Microcosm - Sediment bacterial community - Toxicity - Triclosan

The response of sediment bacterial communities in subtropical freshwater benthic microcosms to sediment-associated triclosan (TCS; 28 d exposure) was analysed using Illumina high-throughput sequencing. This study highlights the interactive effects of TCS and the presence of benthic macroinvertebrates (Limnodrilus hoffmeisteri and Viviparidae bellamya) on sediment bacterial communities. Our results show that TCS alone significantly altered the taxonomic composition and decreased alpha diversity of sediment bacterial communities at concentrations ≥80 μg TCS/g dry weight (dw) sediment (sed). Regarding dominant phyla, TCS significantly reduced the relative abundance of Bacteroidetes and Firmicutes at these concentrations, whereas the relative abundance of Chloroflexi and Cyanobacteria increased. In the presence of benthic macroinvertebrates, the sediment bacterial community was affected by 8 μg TCS/g dw sed as well. However, the presence of benthic macroinvertebrates did not cause measurable changes to bacterial community in unspiked (i.e., control) sediment. These results indicate that TCS alone would not alter the sediment bacterial community at environmentally relevant concentrations (up till 8 μg/g dw sed), but may have an effect in combination with the presence of benthic macroinvertebrates. Therefore, we recommend to include benthic macroinvertebrates when assessing the response of sediment bacterial communities during exposure to environmental stress such as organic contaminants.

Correlating farmers' perception and sheep preference with the nutritional quality of grain legume fodders stored under different conditions
Akakpo, Daniel ; Oosting, S.J. ; Adjei-nsiah, Samuel ; Duncan, A. ; Boer, I.J.M. de - \ 2019
In: Trade-Offs in Science. - WIAS - p. 20 - 20.
The objective of the present study was to correlate farmers’ perception (FP), sheep preference (SP) and laboratory analysis (LA) of nutritional quality of stored grain legume fodders (GLFs). The GLFs of cowpea, groundnut and soybean were stored at 3-locations (rooftop, room and treefork) in -packaging types (polythene sacks or tied with ropes) for 120 days. FP was assessed by scoring the perceived quality of GLFs on a scale of 1 to 10 (1=bad and 0=good) based on physical appraisal by a group of farmers. SP was assessed by cafeteria feeding trial based on dry matter intake (DMI) of GLFs by a flock of 12 sheep during a 14 hr period. For LA, Organic Matter Digestibility (OMD) and Crude Protein (CP) content were assessed by Near Infra-Red Spectroscopy (NIRS). Cowpea scored higher FP (6.3) and SP (66 g DMI/14hr/sheep) than
groundnut (FP 5.5 and SP 59 g DMI/14hr/sheep) and soybean had lowest FP (2.3) and SP (39 g DMI/14hr/sheep). However, LA indicated that groundnut had higher CP content (140 g kg DM) than cowpea (115 g kg DM) and soybean (98 g kg DM). OMD, on the other hand, was higher in cowpea (686 g kg DM) than groundnut (659 g kg DM) and soybean (574 g kg DM). CP was positively orrelated with FP (r=0.35) and with SP (r=0.48). Similarly, OMD was positively correlated with FP (r=0.50) and with SP (r=0.70). Room storage had higher FP and SP than rooftop and treefork. Sack storage scored higher than tied on FP, SP and LA. The present study demonstrated that it is possible to used FP and SP to predict the nutritional quality of GLFs.
Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu-Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abecasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics (2019). - ISSN 0340-6717 - 20 p.
Genome-wide association studies have reported 56 independently associated colorectal cancer (CRC) risk variants, most of which are non-coding and believed to exert their effects by modulating gene expression. The computational method PrediXcan uses cis-regulatory variant predictors to impute expression and perform gene-level association tests in GWAS without directly measured transcriptomes. In this study, we used reference datasets from colon (n = 169) and whole blood (n = 922) transcriptomes to test CRC association with genetically determined expression levels in a genome-wide analysis of 12,186 cases and 14,718 controls. Three novel associations were discovered from colon transverse models at FDR ≤ 0.2 and further evaluated in an independent replication including 32,825 cases and 39,933 controls. After adjusting for multiple comparisons, we found statistically significant associations using colon transcriptome models with TRIM4 (discovery P = 2.2 × 10− 4, replication P = 0.01), and PYGL (discovery P = 2.3 × 10− 4, replication P = 6.7 × 10− 4). Interestingly, both genes encode proteins that influence redox homeostasis and are related to cellular metabolic reprogramming in tumors, implicating a novel CRC pathway linked to cell growth and proliferation. Defining CRC risk regions as one megabase up- and downstream of one of the 56 independent risk variants, we defined 44 non-overlapping CRC-risk regions. Among these risk regions, we identified genes associated with CRC (P < 0.05) in 34/44 CRC-risk regions. Importantly, CRC association was found for two genes in the previously reported 2q25 locus, CXCR1 and CXCR2, which are potential cancer therapeutic targets. These findings provide strong candidate genes to prioritize for subsequent laboratory follow-up of GWAS loci. This study is the first to implement PrediXcan in a large colorectal cancer study and findings highlight the utility of integrating transcriptome data in GWAS for discovery of, and biological insight into, risk loci.
Biodiversity recovery of Neotropical secondary forests
Rozendaal, Danaë M.A. ; Bongers, Frans ; Aide, T.M. ; Alvarez-Dávila, Esteban ; Ascarrunz, Nataly ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Brancalion, Pedro H.S. ; Cabral, George A.L. ; Calvo-Rodriguez, Sofia ; Chave, Jerome ; César, Ricardo G. ; Chazdon, Robin L. ; Condit, Richard ; Dallinga, Jorn S. ; Almeida-Cortez, Jarcilene S. De; Jong, Ben de; Oliveira, Alexandre De; Denslow, Julie S. ; Dent, Daisy H. ; Dewalt, Saara J. ; Dupuy, Juan Manuel ; Durán, Sandra M. ; Dutrieux, Loïc P. ; Espírito-Santo, Mario M. ; Fandino, María C. ; Fernandes, G.W. ; Finegan, Bryan ; García, Hernando ; Gonzalez, Noel ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Hubbell, Stephen ; Jakovac, Catarina C. ; Hernández, Alma Johanna ; Junqueira, André B. ; Kennard, Deborah ; Larpin, Denis ; Letcher, Susan G. ; Licona, Juan-Carlos ; Lebrija-trejos, Edwin ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita C.G. ; Mora, Francisco ; Müller, Sandra C. ; Muñoz, Rodrigo ; Oliveira Neto, Silvio Nolasco De; Norden, Natalia ; Nunes, Yule R.F. ; Ochoa-Gaona, Susana ; Ortiz-Malavassi, Edgar ; Ostertag, Rebecca ; Peña-Caros, Marielos ; Pérez-García, Eduardo A. ; Piotto, Daniel ; Powers, Jennifer S. ; Aguilar-Cano, José ; Rodriguez-Buritica, Susana ; Rodríguez-Velázquez, Jorge ; Romero-Romero, Marco Antonio ; Ruíz, Jorge ; Sanchez-Azofeifa, Arturo ; Almeida, Arlete Silva De; Silver, Whendee L. ; Schwartz, Naomi B. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Sá Sampaio, Everardo Valadares De; Breugel, Michiel van; Wal, Hans van der; Martins, Sebastião Venâncio ; Veloso, Maria D.M. ; Vester, Hans F.M. ; Vicentini, Alberto ; Vieira, Ima C.G. ; Villa, Pedro ; Williamson, G.B. ; Zanini, Kátia J. ; Zimmerman, Jess ; Poorter, Lourens - \ 2019
Science Advances 5 (2019)3. - ISSN 2375-2548 - 10 p.
Old-growth tropical forests harbor an immense diversity of tree species but are rapidly being cleared, while secondary forests that regrow on abandoned agricultural lands increase in extent. We assess how tree species richness and composition recover during secondary succession across gradients in environmental conditions and anthropogenic disturbance in an unprecedented multisite analysis for the Neotropics. Secondary forests recover remarkably fast in species richness but slowly in species composition. Secondary forests take a median time of five decades to recover the species richness of old-growth forest (80% recovery after 20 years) based on rarefaction analysis. Full recovery of species composition takes centuries (only 34% recovery after 20 years). A dual strategy that maintains both old-growth forests and species-rich secondary forests is therefore crucial for biodiversity conservation in human-modified tropical landscapes.
Applying the adverse outcome pathway (AOP) for food sensitization to support in vitro testing strategies
Lozano-Ojalvo, Daniel ; Benedé, Sara ; Antunes, Celia M. ; Bavaro, Simona L. ; Bouchaud, Grégory ; Costa, Ana ; Denery-Papini, Sandra ; Díaz-Perales, Araceli ; Garrido-Arandia, María ; Gavrovic-Jankulovic, Marija ; Hayen, Simone ; Martínez-Blanco, Mónica ; Molina, Elena ; Monaci, Linda ; Pieters, Raymond H.H. ; Villemin, Clelia ; Wichers, Harry J. ; Wróblewska, Barbara ; Willemsen, Linette E.M. ; Roggen, Erwin L. ; Bilsen, Jolanda H.M. van - \ 2019
Trends in Food Science and Technology 85 (2019). - ISSN 0924-2244 - p. 307 - 319.
Adverse outcome pathway - Dendritic cells - Epithelial cells - IgE-mediated food allergy - In vitro models - T and B cells

Background: Before introducing proteins from new or alternative dietary sources into the market, a compressive risk assessment including food allergic sensitization should be carried out in order to ensure their safety. We have recently proposed the adverse outcome pathway (AOP) concept to structure the current mechanistic understanding of the molecular and cellular pathways evidenced to drive IgE-mediated food allergies. This AOP framework offers the biological context to collect and structure existing in vitro methods and to identify missing assays to evaluate sensitizing potential of food proteins. Scope and approach: In this review, we provide a state-of-the-art overview of available in vitro approaches for assessing the sensitizing potential of food proteins, including their strengths and limitations. These approaches are structured by their potential to evaluate the molecular initiating and key events driving food sensitization. Key findings and conclusions: The application of the AOP framework offers the opportunity to anchor existing testing methods to specific building blocks of the AOP for food sensitization. In general, in vitro methods evaluating mechanisms involved in the innate immune response are easier to address than assays addressing the adaptive immune response due to the low precursor frequency of allergen-specific T and B cells. Novel ex vivo culture strategies may have the potential to become useful tools for investigating the sensitizing potential of food proteins. When applied in the context of an integrated testing strategy, the described approaches may reduce, if not replace, current animal testing approaches.

Maternal body mass index, gestational weight gain, and the risk of overweight and obesity across childhood : An individual participant data meta-analysis
Voerman, Ellis ; Santos, Susana ; Patro Golab, Bernadeta ; Amiano, Pilar ; Ballester, Ferran ; Barros, Henrique ; Bergström, Anna ; Charles, Marie Aline ; Chatzi, Leda ; Chevrier, Cécile ; Chrousos, George P. ; Corpeleijn, Eva ; Costet, Nathalie ; Crozier, Sarah ; Devereux, Graham ; Eggesbø, Merete ; Ekström, Sandra ; Fantini, Maria Pia ; Farchi, Sara ; Forastiere, Francesco ; Georgiu, Vagelis ; Godfrey, Keith M. ; Gori, Davide ; Grote, Veit ; Hanke, Wojciech ; Hertz-Picciotto, Irva ; Heude, Barbara ; Hryhorczuk, Daniel ; Huang, Rae Chi ; Inskip, Hazel ; Iszatt, Nina ; Karvonen, Anne M. ; Kenny, Louise C. ; Koletzko, Berthold ; Küpers, Leanne K. ; Lagström, Hanna ; Lehmann, Irina ; Magnus, Per ; Majewska, Renata ; Mäkelä, Johanna ; Manios, Yannis ; McAuliffe, Fionnuala M. ; McDonald, Sheila W. ; Mehegan, John ; Mommers, Monique ; Morgen, Camilla S. ; Mori, Trevor A. ; Moschonis, George ; Murray, Deirdre ; Chaoimh, Carol Ní ; Nohr, Ellen A. ; Nybo Andersen, Anne Marie ; Oken, Emily ; Oostvogels, Adriëtte J.J.M. ; Pac, Agnieszka ; Papadopoulou, Eleni ; Pekkanen, Juha ; Pizzi, Costanza ; Polanska, Kinga ; Porta, Daniela ; Richiardi, Lorenzo ; Rifas-Shiman, Sheryl L. ; Ronfani, Luca ; Santos, Ana C. ; Standl, Marie ; Stoltenberg, Camilla ; Thiering, Elisabeth ; Thijs, Carel ; Torrent, Maties ; Tough, Suzanne C. ; Trnovec, Tomas ; Turner, Steve ; Rossem, Lenie van; Berg, Andrea von; Vrijheid, Martine ; Vrijkotte, Tanja G.M. ; West, Jane ; Wijga, Alet ; Wright, John ; Zvinchuk, Oleksandr ; Sørensen, Thorkild I.A. ; Lawlor, Debbie A. ; Gaillard, Romy ; Jaddoe, Vincent W.V. - \ 2019
PLOS Medicine 16 (2019)2. - ISSN 1549-1676 - p. e1002744 - e1002744.

BACKGROUND: Maternal obesity and excessive gestational weight gain may have persistent effects on offspring fat development. However, it remains unclear whether these effects differ by severity of obesity, and whether these effects are restricted to the extremes of maternal body mass index (BMI) and gestational weight gain. We aimed to assess the separate and combined associations of maternal BMI and gestational weight gain with the risk of overweight/obesity throughout childhood, and their population impact. METHODS AND FINDINGS: We conducted an individual participant data meta-analysis of data from 162,129 mothers and their children from 37 pregnancy and birth cohort studies from Europe, North America, and Australia. We assessed the individual and combined associations of maternal pre-pregnancy BMI and gestational weight gain, both in clinical categories and across their full ranges, with the risks of overweight/obesity in early (2.0-5.0 years), mid (5.0-10.0 years) and late childhood (10.0-18.0 years), using multilevel binary logistic regression models with a random intercept at cohort level adjusted for maternal sociodemographic and lifestyle-related characteristics. We observed that higher maternal pre-pregnancy BMI and gestational weight gain both in clinical categories and across their full ranges were associated with higher risks of childhood overweight/obesity, with the strongest effects in late childhood (odds ratios [ORs] for overweight/obesity in early, mid, and late childhood, respectively: OR 1.66 [95% CI: 1.56, 1.78], OR 1.91 [95% CI: 1.85, 1.98], and OR 2.28 [95% CI: 2.08, 2.50] for maternal overweight; OR 2.43 [95% CI: 2.24, 2.64], OR 3.12 [95% CI: 2.98, 3.27], and OR 4.47 [95% CI: 3.99, 5.23] for maternal obesity; and OR 1.39 [95% CI: 1.30, 1.49], OR 1.55 [95% CI: 1.49, 1.60], and OR 1.72 [95% CI: 1.56, 1.91] for excessive gestational weight gain). The proportions of childhood overweight/obesity prevalence attributable to maternal overweight, maternal obesity, and excessive gestational weight gain ranged from 10.2% to 21.6%. Relative to the effect of maternal BMI, excessive gestational weight gain only slightly increased the risk of childhood overweight/obesity within each clinical BMI category (p-values for interactions of maternal BMI with gestational weight gain: p = 0.038, p < 0.001, and p = 0.637 in early, mid, and late childhood, respectively). Limitations of this study include the self-report of maternal BMI and gestational weight gain for some of the cohorts, and the potential of residual confounding. Also, as this study only included participants from Europe, North America, and Australia, results need to be interpreted with caution with respect to other populations. CONCLUSIONS: In this study, higher maternal pre-pregnancy BMI and gestational weight gain were associated with an increased risk of childhood overweight/obesity, with the strongest effects at later ages. The additional effect of gestational weight gain in women who are overweight or obese before pregnancy is small. Given the large population impact, future intervention trials aiming to reduce the prevalence of childhood overweight and obesity should focus on maternal weight status before pregnancy, in addition to weight gain during pregnancy.

Twenty-five years of total antioxidant capacity measurement of foods and biological fluids : merits and limitations
Pellegrini, Nicoletta ; Vitaglione, Paola ; Granato, Daniel ; Fogliano, Vincenzo - \ 2019
Journal of the Science of Food and Agriculture (2019). - ISSN 0022-5142
epidemiological studies - food antioxidants - food, diet - in vitro total antioxidant capacity - phenolic compounds - plasma total antioxidant capacity

This review summarises 25 years of investigations on antioxidants research in foods and biological fluids and critically analyses the merits and limitations of using the total antioxidant capacity (TAC) measurement in the metabolomic era. An enormous bulk of knowledge was produced regarding the antioxidant capacity of foods and large TAC databases were developed. A direct link between a food TAC value and any health benefit is erroneous and has led to several cases of consumer deception. However, the striking epidemiological evidence associating a high dietary TAC with some disease prevention and the availability of well-constructed TAC databases deserve attention and must be taken into account to establish the usefulness of measuring TAC in both foods and biological samples. The in vivo TAC measurement, usually performed in plasma, is influenced by many external factors, such as dietary habits, as well as environmental and behavioural factors, which are integrated towards homeostatic control by fine physiological mechanisms with high inter-individual variability. Therefore, plasma TAC cannot be considered as a unique biomarker of individual antioxidant status. However, the combined evaluation of plasma TAC with known markers of disease, individual metabolism, inflammation and genetics, as well as with markers of gut microbiota composition and activity, may lead to the identification of populations that are more responsive to food/diet TAC. In this framework, the appropriate use of TAC measurement both in food and in vivo can still provide support for the interpretation of complex phenomena and be a tool for sample screening when making a quick decision toward in-depth research investigations.

The yield normal stress
Cagny, Henri De; Fazilati, Mina ; Habibi, Mehdi ; Denn, Morton M. ; Bonn, Daniel - \ 2019
Journal of Rheology 63 (2019)2. - ISSN 0148-6055 - p. 285 - 290.

Normal stresses in complex fluids lead to new flow phenomena because they can be comparable to, or even larger than, the shear stress. In addition, they are of paramount importance for formulating and testing constitutive equations for predicting nonviscometric flow behavior. Very little attention has thus far been paid to the normal stresses of yield stress fluids, which are difficult to measure. We report the first systematic study of the first and second normal stress differences in both continuous and slow oscillatory shear of three model nonthixotropic yield stress fluids, with N 1 > 0 and N 2 < 0. We show that both normal stress differences are quadratic functions of the shear stress both above and below the shear yield stress, leading to the existence of a yield normal stress. However, the contribution of the normal stresses to the von Mises yield criterion for these materials is small.

What agricultural practices are most likely to deliver “sustainable intensification” in the UK?
Dicks, Lynn V. ; Rose, David C. ; Ang, Frederic ; Aston, Stephen ; Birch, A.N.E. ; Boatman, Nigel ; Bowles, Elizabeth L. ; Chadwick, David ; Dinsdale, Alex ; Durham, Sam ; Elliott, John ; Firbank, Les ; Humphreys, Stephen ; Jarvis, Phil ; Jones, Dewi ; Kindred, Daniel ; Knight, Stuart M. ; Lee, Michael R.F. ; Leifert, Carlo ; Lobley, Matt ; Matthews, Kim ; Midmer, Alice ; Moore, Mark ; Morris, Carol ; Mortimer, Simon ; Murray, T.C. ; Norman, Keith ; Ramsden, Stephen ; Roberts, Dave ; Smith, Laurence G. ; Soffe, Richard ; Stoate, Chris ; Taylor, Bryony ; Tinker, David ; Topliff, Mark ; Wallace, John ; Williams, Prysor ; Wilson, Paul ; Winter, Michael ; Sutherland, William J. - \ 2019
Food and Energy Security 8 (2019)1.

Sustainable intensification is a process by which agricultural productivity is enhanced whilst also creating environmental and social benefits. We aimed to identify practices likely to deliver sustainable intensification, currently available for UK farms but not yet widely adopted. We compiled a list of 18 farm management practices with the greatest potential to deliver sustainable intensification in the UK, following a well-developed stepwise methodology for identifying priority solutions, using a group decision-making technique with key agricultural experts. The list of priority management practices can provide the focal point of efforts to achieve sustainable intensification of agriculture, as the UK develops post-Brexit agricultural policy, and pursues the second Sustainable Development Goal, which aims to end hunger and promote sustainable agriculture. The practices largely reflect a technological, production-focused view of sustainable intensification, including for example, precision farming and animal health diagnostics, with less emphasis on the social and environmental aspects of sustainability. However, they do reflect an integrated approach to farming, covering many different aspects, from business organization and planning, to soil and crop management, to landscape and nature conservation. For a subset of 10 of the priority practices, we gathered data on the level of existing uptake in English and Welsh farms through a stratified survey in seven focal regions. We find substantial existing uptake of most of the priority practices, indicating that UK farming is an innovative sector. The data identify two specific practices for which uptake is relatively low, but which some UK farmers find appealing and would consider adopting. These practices are: prediction of pest and disease outbreaks, especially for livestock farms; staff training on environmental issues, especially on arable farms.

External reviewer for PhD thesis of Daniel Paiva
Doughty, Karolina - \ 2019
Soil Chemistry Aspects of Predicting Future Phosphorus Requirements in Sub-Saharan Africa
Magnone, Daniel ; Niasar, Vahid J. ; Bouwman, A.F. ; Beusen, A.H.W. ; Zee, S.E.A.T.M. van der; Sattari, S.Z. - \ 2019
Journal of Advances in Modeling Earth Systems 11 (2019)1. - ISSN 1942-2466 - p. 327 - 337.
Phosphorus (P) is a finite resource and critical to plant growth and therefore food security. Regional‐ and continental‐scale studies propose how much P would be required to feed the world by 2050. These indicate that Sub‐Saharan Africa soils have the highest soil P deficit globally. However, the spatial heterogeneity of the P deficit caused by heterogeneous soil chemistry in the continental scale has never been addressed. We provide a combination of a broadly adopted P‐sorption model that is integrated into a highly influential, large‐scale soil phosphorus cycling model. As a result, we show significant differences between the model outputs in both the soil‐P concentrations and total P required to produce future crops for the same predicted scenarios. These results indicate the importance of soil chemistry for soil‐nutrient modeling and highlight that previous influential studies may have overestimated P required. This is particularly the case in Somalia where conventional modeling predicts twice as much P required to 2050 as our new proposed model.
Sedimentary alkalinity generation and long-term alkalinity development in the Baltic Sea
Gustafsson, Erik ; Hagens, Mathilde ; Sun, Xiaole ; Reed, Daniel C. ; Humborg, Christoph ; Slomp, Caroline P. ; Gustafsson, Bo G. - \ 2019
Biogeosciences 16 (2019)2. - ISSN 1726-4170 - p. 437 - 456.

Enhanced release of alkalinity from the seafloor, principally driven by anaerobic degradation of organic matter under low-oxygen conditions and associated secondary redox reactions, can increase the carbon dioxide (CO2) buffering capacity of seawater and therefore oceanic CO2 uptake. The Baltic Sea has undergone severe changes in oxygenation state and total alkalinity (TA) over the past decades. The link between these concurrent changes has not yet been investigated in detail. A recent system-wide TA budget constructed for the past 50 years using BALTSEM, a coupled physical-biogeochemical model for the whole Baltic Sea area revealed an unknown TA source. Here we use BALTSEM in combination with observational data and one-dimensional reactivetransport modeling of sedimentary processes in the Farö Deep, a deep Baltic Sea basin, to test whether sulfate (SO2- 4 ) reduction coupled to iron (Fe) sulfide burial can explain the missing TA source in the Baltic Proper. We calculated that this burial can account for up to 26%of the missing source in this basin, with the remaining TA possibly originating from unknown river inputs or submarine groundwater discharge. We also show that temporal variability in the input of Fe to the sediments since the 1970s drives changes in sulfur (S) burial in the Farö Deep, suggesting that Fe availability is the ultimate limiting factor for TA generation under anoxic conditions. The implementation of projected climate change and two nutrient load scenarios for the 21st century in BALTSEM shows that reducing nutrient loads will improve deep water oxygen conditions, but at the expense of lower surface water TA concentrations, CO2 buffering capacities and faster acidification. When these changes additionally lead to a decrease in Fe inputs to the sediment of the deep basins, anaerobic TA generation will be reduced even further, thus exacerbating acidification. This work highlights that Fe dynamics plays a key role in the release of TA from sediments where Fe sulfide formation is limited by Fe availability, as exemplified by the Baltic Sea. Moreover, it demonstrates that burial of Fe sulfides should be included in TA budgets of low-oxygen basins.

Does phloem osmolality affect diurnal diameter changes of twigs but not of stems in Scots pine?
Lazzarin, Martina ; Zweifel, Roman ; Anten, Niels ; Sterck, Frank J. ; Epron, Daniel - \ 2019
Tree Physiology 39 (2019)2. - ISSN 0829-318X - p. 275 - 283.
Diel stem diameter changes measured at the stem base of temperate tree species can be mostly explained by a hydraulic system of flow and storage compartments passively driven by transpiration. Active, osmotic processes are considered to play a minor role only. Here we explore whether such osmotic processes have a stronger impact on diel changes in twig diameter than in stem diameter because twigs are closer to the leaves, the main source of newly acquired carbon. We investigated stem and twig diameter changes of wood and bark of pine trees in parallel to fluctuations of the osmolality in needles and in the bark at the stem base. We found consistent twig bark size increments concurrent with twig wood size decreases during daylight hours whereas needle osmolality was not consistently increasing even on sunny days. The size changes of bark and wood either reversed or ran in parallel from late afternoon onwards until the next morning. No such patterns were measurable at the stem base. Stem wood was hardly changing in size, whereas stem bark followed the regular pattern of a decrease during the daylight hours and an increase during the night. Osmolality at the stem base showed no particular course over 24 h. We conclude that assimilates from the needles were rapidly transported to the twigs where they increased the osmolality of the bark tissue by sugar loading, explaining the bark size increase (over-) compensating the xylem size decrease. The stem base largely followed the expectation of a passive, hydraulic system without a measurable role of osmoregulation. Diameter changes thus follow different diurnal dynamics in twigs and at the stem base.
Risk to the supply of ecosystem services across aquatic ecosystems
Culhane, Fiona ; Teixeira, Heliana ; Nogueira, Antonio J.A. ; Borgwardt, Florian ; Trauner, Daniel ; Lillebø, Ana ; Piet, Gerjan ; Kuemmerlen, Mathias ; McDonald, Hugh ; O'Higgins, Tim ; Barbosa, Ana Luisa ; Wal, Jan Tjalling Van Der; Iglesias-Campos, Alejandro ; Arevalo-Torres, Juan ; Barbière, Julian ; Robinson, Leonie A. - \ 2019
Science of the Total Environment 660 (2019). - ISSN 0048-9697 - p. 611 - 621.
Sustainability - Biodiversity
The capacity of ecosystems to supply ecosystem services is decreasing. Sustaining this supply requires an under- standing of the links between the impacts of pressures introduced by human activities and how this can lead to
changes in the supply of services. Here, we apply a novel approach, assessing‘
risk to ecosystem service supply’ (RESS), across a range of aquatic ecosystems in seven case studies. We link aggregate impact risk from human activities on ecosystem components, with a relative score of their potential to supply services. The greatest RESS is found where an ecosystem component with a high potential to supply services is subject to high impact risk. In this context, we explore variability in RESS across 99 types of aquatic ecosystem component from 11 realms, ranging from oceanic to wetlands. We explore some causes of variability in the RESS observed, including assessment area, Gross Domestic Product (GDP) and population density. We found that Lakes, Rivers, Inlets and
Coastal realms had some of the highest RESS, though this was highly dependent on location. We found a positive relationship between impact risk and service supply potential, indicating the ecosystem components we rely on mostfor services, are also those most at risk. However, variability in this relationship indicates that protecting the supply of ecosystem services alone will not protect all parts of the ecosystem at high risk. Broad socio-economic factors explained some of the variability found in RESS. For example, RESS was positively associated with GDP and artificial and agricultural land use in most realms, highlighting the need to achieve balance between increasing GDP and sustaining ecosystem health and human wellbeing more broadly. This approach can be used for sustainablemanagement of ecosystemservice use, to highlight the ecosystemcomponents mostcriticalto supplying services, and those most at risk

Characterizing diversity of food systems in view of sustainability transitions. A review
Gaitán-Cremaschi, Daniel ; Klerkx, Laurens ; Duncan, Jessica ; Trienekens, Jacques H. ; Huenchuleo, Carlos ; Dogliotti, Santiago ; Contesse, María E. ; Rossing, Walter A.H. - \ 2019
Agronomy for Sustainable Development 39 (2019)1. - ISSN 1774-0746 - 22 p.
Agricultural innovation systems - Agricultural production systems - Agroecology - Food regime - Food system - Grassroots movements - Sustainability transitions - System diagnosis - Transformations - Value chains

Dominant food systems are configured from the productivist paradigm, which focuses on producing large amounts of inexpensive and standardized foods. Although these food systems continue being supported worldwide, they are no longer considered fit-for-purpose as they have been proven unsustainable in environmental and social terms. A large body of scientific literature argues that a transition from the dominant food systems to alternative ones built around the wider principles of sustainable production and rural development is needed. Promoting such a sustainability transition would benefit from a diagnosis of food system types to identify those systems that may harbor promising characteristics for a transition to sustainable food systems. While research on food system transitions abounds, an operational approach to characterize the diversity of food systems taking a system perspective is still lacking. In this paper we review the literature on how transitions to sustainable food systems may play out and present a framework based on the Multi-Level Perspective on Socio-Technical Transitions, which builds upon conceptual developments from social and natural science disciplines. The objectives of the framework are to (i) characterize the diversity of existing food systems at a certain geographical scale based on a set of structural characteristics and (ii) classify the food systems in terms of their support by mainstream practices, i.e., dominant food systems connected to regimes; deviate radically from them, niche food systems such as those based on grassroots innovation; or share elements of dominant and niche food systems, i.e., hybrid food systems. An example is given of application of our framework to vegetable food systems with a focus on production, distribution, and consumption of low-or-no pesticide vegetables in Chile. Drawing on this illustrative example we reflect on usefulness, shortcomings, and further development and use of the diagnostic framework.

Linking biodiversity to ecosystem services supply: Patterns across aquatic ecosystems
Teixeira, Heliana ; Lillebø, Ana I. ; Culhane, Fiona ; Robinson, Leonie ; Trauner, Daniel ; Borgwardt, Florian ; Kummerlen, Mathias ; Barbosa, Ana ; McDonald, Hugh ; Funk, Andrea ; O'Higgins, Tim ; Wal, Jan Tjalling Van Der; Piet, Gerjan ; Hein, Thomas ; Arévalo-Torres, Juan ; Iglesias-Campos, Alejandro ; Barbière, Julian ; Nogueira, António J.A. - \ 2019
Science of the Total Environment 657 (2019). - ISSN 0048-9697 - p. 517 - 534.
Global initiatives have been increasingly focusing on mainstreaming the values of biodiversity and ecosystem services into decision-making at all levels. Due to the accelerated rate at which biodiversity is declining and its consequences for the functioning of ecosystems and subsequently, the services they provide, there is need to develop comprehensive assessments of the services and the benefits nature delivers to society. Based on expertevaluation, we identified relevant flow linkages in the supply-side of the socio-ecological system, i.e. from biodiversity to ecosystem services supply for eight case studies across European aquatic ecosystems covering freshwater, transitional, coastal and marine waters realms. Biological mediated services were considered, as well as those reliant on purely physical aspects of the ecosystem, i.e. abiotic outputs, since both have implications for spatial planning, management and decision-making. Due to the multidimensional nature of ecosystems and their biodiversity, our approach used ecosystem components such as habitats and biota as proxies for biodiversity and as the focal point for linkage identification. Statistical analysis revealed the importance of considering mobile biota in the spatial assessment of habitats. Contrary to literature evidences so far, our results showed significantly different and complementary ecosystem services supply patterns across the continuum of aquatic realms. The implemented score of ecosystem services supply has a high potential for integrated aquatic ecosystem service supply assessments in the context of ecosystem-based management.
Fate and effects of sediment-associated polycyclic musk HHCB in subtropical freshwater microcosms
Peng, Feng Jiao ; Kiggen, Fionne ; Pan, Chang Gui ; Bracewell, Sally A. ; Ying, Guang Guo ; Salvito, Daniel ; Selck, Henriette ; Brink, Paul J. Van den - \ 2019
Ecotoxicology and Environmental Safety 169 (2019). - ISSN 0147-6513 - p. 902 - 910.
Bacterial community - Benthic macroinvertebrates - Bioaccumulation - Dissipation - HHCB - Toxicity

Galaxolide (HHCB) is used as a fragrance ingredient in household and personal care products, and has been ubiquitously detected in the environment. Here we investigated the fate of HHCB in subtropical freshwater microcosms, and evaluated effects of sediment-associated HHCB on a biological community consisting of algae, Daphnia, benthic macroinvertebrates and bacteria. The concentrations of sediment-associated HHCB did not change significantly during a 28 days exposure period, but HHCB accumulated in worms with biota-sediment accumulation-factor (BSAF) values in the range of 0.29–0.66 for Branchiura sowerbyi and 0.94–2.11 for Limnodrilus hoffmeisteri. There was no significant effects of HHCB (30 μg/g dry weight (dw) sediment) on chlorophyll-a content, sediment bacterial community composition, and survival and growth of benthic macroinvertebrates. However, the presence of benthic macroinvertebrates altered the sediment bacterial community structure relative to microcosms without introduced organisms. The findings of this study suggest that a single high-dose of HHCB, over 28 days, at environmentally relevant concentrations would not impose direct toxicological risks to aquatic organisms such as benthic macroinvertebrates.

Transcriptional effects of cadmium on iron homeostasis differ in calamine accessions of Noccaea caerulescens
Halimaa, Pauliina ; Blande, Daniel ; Baltzi, Erol ; Aarts, Mark G.M. ; Granlund, Lars ; Keinänen, Markku ; Kärenlampi, Sirpa O. ; Kozhevnikova, Anna D. ; Peräniemi, Sirpa ; Schat, Henk ; Seregin, Ilya V. ; Tuomainen, Marjo ; Tervahauta, Arja I. - \ 2019
The Plant Journal 97 (2019)2. - ISSN 0960-7412 - p. 306 - 320.
cadmium - Illumina - iron deficiency - IRT1 - Noccaea caerulescens - RNA-seq - spectral imaging - Thlaspi caerulescens - transcriptome

Calamine accessions of the zinc/cadmium/nickel hyperaccumulator, Noccaea caerulescens, exhibit striking variation in foliar cadmium accumulation in nature. The Ganges accession (GA) from Southern France displays foliar cadmium hyperaccumulation (>1000 μg g−1 DW), whereas the accession La Calamine (LC) from Belgium, with similar local soil metal composition, does not (<100 μg g−1 DW). All calamine accessions are cadmium hypertolerant. To find out the differences between LC and GA in their basic adaptation mechanisms, we bypassed the cadmium excluding phenotype of LC by exposing the plants to 50 μm cadmium in hydroponics, achieving equal cadmium accumulation in the shoots. The iron content increased in the roots of both accessions. GA exhibited significant decreases in manganese and zinc contents in the roots and shoots, approaching those in LC. Altogether 702 genes responded differently to cadmium exposure between the accessions, 157 and 545 in the roots and shoots, respectively. Cadmium-exposed LC showed a stress response and had decreased levels of a wide range of photosynthesis-related transcripts. GA showed less changes, mainly exhibiting an iron deficiency-like response. This included increased expression of genes encoding five iron deficiency-regulated bHLH transcription factors, ferric reduction oxidase FRO2, iron transporters IRT1 and OPT3, and nicotianamine synthase NAS1, and decreased expression of genes encoding ferritins and NEET (a NEET family iron-sulfur protein), which is possibly involved in iron transfer, distribution and/or management. The function of the IRT1 gene in the accessions was compared. We conclude that the major difference between the two accessions is in the way they cope with iron under cadmium exposure.

25 years of the WOFOST cropping systems model
Wit, Allard de; Boogaard, Hendrik ; Fumagalli, Davide ; Janssen, Sander ; Knapen, Rob ; Kraalingen, Daniel van; Supit, Iwan ; Wijngaart, Raymond van der; Diepen, Kees van - \ 2019
Agricultural Systems 168 (2019). - ISSN 0308-521X - p. 154 - 167.
open source - Regional scale - Simulation Model - yield forecasting

The WOFOST cropping systems model has been applied operationally over the last 25 years as part of the MARS crop yield forecasting system. In this paper we provide an updated description of the model and reflect on the lessons learned over the last 25 years. The latter includes issues like system performance, model sensitivity, spatial model setup, parameterization and calibration approaches as well as software implementation and version management. Particularly for spatial model calibrations we provide experience and guidelines on how to execute calibrations and how to evaluate WOFOST model simulation results, particularly under conditions of limited field data availability. As an open source model WOFOST has been a success with at least 10 different implementations of the same concept. An overview is provided for those implementations which are managed by MARS or Wageningen groups. However, the proliferation of WOFOST implementations has also led to questions on the reproducibility of results from different implementations as is demonstrated with an example from MARS. In order to certify that the different WOFOST implementations and versions available can reproduce basic sets of inputs and outputs we make available a large set of test cases as appendix to this publication. Finally, new methodological extensions have been added to WOFOST in simulating the impact of nutrients limitations, extreme events and climate variability. Also, a difference is made in the operational and scientific versions of WOFOST with different licensing models and possible revenue generation. Capitalizing both on academic development as well as model testing in real-world situations will help to enable new applications of the WOFOST model in precision agriculture and smart farming.

Exploring variability in environmental impact risk from human activities across aquatic ecosystems
Borgwardt, Florian ; Robinson, Leonie ; Trauner, Daniel ; Teixeira, Heliana ; Nogueira, Antonio J.A. ; Lillebø, Ana I. ; Piet, Gerjan ; Kuemmerlen, Mathias ; O'Higgins, Tim ; McDonald, Hugh ; Arevalo-Torres, Juan ; Barbosa, Ana Luisa ; Iglesias-Campos, Alejandro ; Hein, Thomas ; Culhane, Fiona - \ 2019
Science of the Total Environment 652 (2019). - ISSN 0048-9697 - p. 1396 - 1408.
Aquatic ecosystem - Freshwater - Marine - Coastal - Biodiversity - Drivers
Aquatic ecosystems are under severe pressure. Human activities introduce an array of pressures that impact ecosystems and their components. In this study we focus on the aquatic domains of fresh, coastal and marine waters, including rivers, lakes and riparian habitats to transitional, coastal as well as shelf and oceanic habitats. In an environmental risk assessment approach, we identified impact chains that link 45 human activities through 31 pressures to 82 ecosystem components. In this linkage framework >22,000 activity-pressure-ecosystem component interactions were found across seven European case studies. We identified the environmental impact risk posed by each impact chain by first categorically weighting the interactions according to five criteria: spatial extent, dispersal potential, frequency of interaction, persistence of pressure and severity of the interaction, where extent, dispersal, frequency and persistence account for the exposure to risk (spatial and temporal), and the severity accounts for the consequence of the risk. After assigning a numerical score to each risk criterion, we came up with an overall environmental impact risk score for each impact chain. This risk score was analysed in terms of (1) the activities and pressures that introduce the greatest risk to European aquatic domains, and (2) the aquatic ecosystem components and realms that are at greatest risk from human activities. Activities related to energy production were relevant across the aquatic domains. Fishing was highly relevant in marine and environmental engineering in fresh waters. Chemical and physical pressures introduced the greatest risk to the aquatic realms. Ecosystem components that can be seen as ecotones between different ecosystems had high impact risk. We show how this information can be used in informing management on trade-offs in freshwater, coastal and marine resource use and aid decision-making
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