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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The need for bottom-up assessments of climate risks and adaptation in climate-sensitive regions
Conway, Declan ; Nicholls, Robert J. ; Brown, Sally ; Tebboth, Mark G.L. ; Adger, William Neil ; Ahmad, Bashir ; Biemans, Hester ; Crick, Florence ; Lutz, Arthur F. ; Campos, Ricardo Safra De; Said, Mohammed ; Singh, Chandni ; Zaroug, Modathir Abdalla Hassan ; Ludi, Eva ; New, Mark ; Wester, Philippus - \ 2019
Nature Climate Change 9 (2019)7. - ISSN 1758-678X - p. 503 - 511.

Studies of climate change at specific intervals of future warming have primarily been addressed through top-down approaches using climate projections and modelled impacts. In contrast, bottom-up approaches focus on the recent past and present vulnerability. Here, we examine climate signals at different increments of warming and consider the need to reconcile top-down and bottom-up approaches. We synthesise insights from recent studies in three climate-sensitive systems where change is a defining feature of the human-environment system. Whilst top-down and bottom-up approaches generate complementary insights into who and what is at risk, integrating their results is a much-needed step towards developing relevant information to address the needs of immediate adaptation decisions.

European mushroom assemblages are darker in cold climates
Krah, Franz Sebastian ; Büntgen, Ulf ; Schaefer, Hanno ; Müller, Jörg ; Andrew, Carrie ; Boddy, Lynne ; Diez, Jeffrey ; Egli, Simon ; Freckleton, Robert ; Gange, Alan C. ; Halvorsen, Rune ; Heegaard, Einar ; Heideroth, Antje ; Heibl, Christoph ; Heilmann-Clausen, Jacob ; Høiland, Klaus ; Kar, Ritwika ; Kauserud, Håvard ; Kirk, Paul M. ; Kuyper, Thomas W. ; Krisai-Greilhuber, Irmgard ; Norden, Jenni ; Papastefanou, Phillip ; Senn-Irlet, Beatrice ; Bässler, Claus - \ 2019
Nature Communications 10 (2019). - ISSN 2041-1723

Thermal melanism theory states that dark-colored ectotherm organisms are at an advantage at low temperature due to increased warming. This theory is generally supported for ectotherm animals, however, the function of colors in the fungal kingdom is largely unknown. Here, we test whether the color lightness of mushroom assemblages is related to climate using a dataset of 3.2 million observations of 3,054 species across Europe. Consistent with the thermal melanism theory, mushroom assemblages are significantly darker in areas with cold climates. We further show differences in color phenotype between fungal lifestyles and a lifestyle differentiated response to seasonality. These results indicate a more complex ecological role of mushroom colors and suggest functions beyond thermal adaption. Because fungi play a crucial role in terrestrial carbon and nutrient cycles, understanding the links between the thermal environment, functional coloration and species’ geographical distributions will be critical in predicting ecosystem responses to global warming.

Loss rates of honey bee colonies during winter 2017/18 in 36 countries participating in the COLOSS survey, including effects of forage sources
Gray, Alison ; Brodschneider, Robert ; Adjlane, Noureddine ; Ballis, Alexis ; Brusbardis, Valters ; Charrière, Jean Daniel ; Chlebo, Robert ; F. Coffey, Mary ; Cornelissen, Bram ; Amaro da Costa, Cristina ; Csáki, Tamás ; Dahle, Bjørn ; Danihlík, Jiří ; Dražić, Marica Maja ; Evans, Garth ; Fedoriak, Mariia ; Forsythe, Ivan ; Graaf, Dirk de; Gregorc, Aleš ; Johannesen, Jes ; Kauko, Lassi ; Kristiansen, Preben ; Martikkala, Maritta ; Martín-Hernández, Raquel ; Medina-Flores, Carlos Aurelio ; Mutinelli, Franco ; Patalano, Solenn ; Petrov, Plamen ; Raudmets, Aivar ; Ryzhikov, Vladimir A. ; Simon-Delso, Noa ; Stevanovic, Jevrosima ; Topolska, Grazyna ; Uzunov, Aleksandar ; Vejsnaes, Flemming ; Williams, Anthony ; Zammit-Mangion, Marion ; Soroker, Victoria - \ 2019
Journal of Apicultural Research 58 (2019)4. - ISSN 0021-8839 - p. 479 - 485.
Apis mellifera - beekeeping - citizen science - colony winter losses - forage sources - monitoring - mortality - survey

This short article presents loss rates of honey bee colonies over winter 2017/18 from 36 countries, including 33 in Europe, from data collected using the standardized COLOSS questionnaire. The 25,363 beekeepers supplying data passing consistency checks in total wintered 544,879 colonies, and reported 26,379 (4.8%, 95% CI 4.7–5.0%) colonies with unsolvable queen problems, 54,525 (10.0%, 95% CI 9.8–10.2%) dead colonies after winter and another 8,220 colonies (1.5%, 95% CI 1.4–1.6%) lost through natural disaster. This gave an overall loss rate of 16.4% (95% CI 16.1–16.6%) of honey bee colonies during winter 2017/18, but this varied greatly from 2.0 to 32.8% between countries. The included map shows relative risks of winter loss at regional level. The analysis using the total data-set confirmed findings from earlier surveys that smaller beekeeping operations with at most 50 colonies suffer significantly higher losses than larger operations (p <.001). Beekeepers migrating their colonies had significantly lower losses than those not migrating (p <.001), a different finding from previous research. Evaluation of six different forage sources as potential risk factors for colony loss indicated that intensive foraging on any of five of these plant sources (Orchards, Oilseed Rape, Maize, Heather and Autumn Forage Crops) was associated with significantly higher winter losses. This finding requires further study and explanation. A table is included giving detailed results of loss rates and the impact of the tested forage sources for each country and overall.

Patterns of nitrogen-fixing tree abundance in forests across Asia and America
Menge, Duncan N.L. ; Chisholm, Ryan A. ; Davies, Stuart J. ; Abu Salim, Kamariah ; Allen, David ; Alvarez, Mauricio ; Bourg, Norm ; Brockelman, Warren Y. ; Bunyavejchewin, Sarayudh ; Butt, Nathalie ; Cao, Min ; Chanthorn, Wirong ; Chao, Wei Chun ; Clay, Keith ; Condit, Richard ; Cordell, Susan ; Silva, João Batista da; Dattaraja, H.S. ; Andrade, Ana Cristina Segalin de; Oliveira, Alexandre A. de; Ouden, Jan den; Drescher, Michael ; Fletcher, Christine ; Giardina, Christian P. ; Savitri Gunatilleke, C.V. ; Gunatilleke, I.A.U.N. ; Hau, Billy C.H. ; He, Fangliang ; Howe, Robert ; Hsieh, Chang Fu ; Hubbell, Stephen P. ; Inman-Narahari, Faith M. ; Jansen, Patrick A. ; Johnson, Daniel J. ; Kong, Lee Sing ; Král, Kamil ; Ku, Chen Chia ; Lai, Jiangshan ; Larson, Andrew J. ; Li, Xiankun ; Li, Yide ; Lin, Luxiang ; Lin, Yi Ching ; Liu, Shirong ; Lum, Shawn K.Y. ; Lutz, James A. ; Ma, Keping ; Malhi, Yadvinder ; McMahon, Sean ; McShea, William ; Mi, Xiangcheng ; Morecroft, Michael ; Myers, Jonathan A. ; Nathalang, Anuttara ; Novotny, Vojtech ; Ong, Perry ; Orwig, David A. ; Ostertag, Rebecca ; Parker, Geoffrey ; Phillips, Richard P. ; Abd. Rahman, Kassim ; Sack, Lawren ; Sang, Weiguo ; Shen, Guochun ; Shringi, Ankur ; Shue, Jessica ; Su, Sheng Hsin ; Sukumar, Raman ; Fang Sun, I. ; Suresh, H.S. ; Tan, Sylvester ; Thomas, Sean C. ; Toko, Pagi S. ; Valencia, Renato ; Vallejo, Martha I. ; Vicentini, Alberto ; Vrška, Tomáš ; Wang, Bin ; Wang, Xihua ; Weiblen, George D. ; Wolf, Amy ; Xu, Han ; Yap, Sandra ; Zhu, Li ; Fung, Tak - \ 2019
Journal of Ecology (2019). - ISSN 0022-0477
forest - legume - nitrogen fixation - nutrient limitation - Smithsonian ForestGEO - symbiosis

Symbiotic nitrogen (N)-fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N-fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N-fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America or Asia. In addition, we examined whether the observed pattern of abundance of N-fixing trees was correlated with mean annual temperature and precipitation. Outside the tropics, N-fixing trees were consistently rare in the forest plots we examined. Within the tropics, N-fixing trees were abundant in American but not Asian forest plots (~7% versus ~1% of basal area and stems). This disparity was not explained by mean annual temperature or precipitation. Our finding of low N-fixing tree abundance in the Asian tropics casts some doubt on recent high estimates of N fixation rates in this region, which do not account for disparities in N-fixing tree abundance between the Asian and American tropics. Synthesis. Inputs of nitrogen to forests depend on symbiotic nitrogen fixation, which is constrained by the abundance of N-fixing trees. By analysing a large dataset of ~4 million trees, we found that N-fixing trees were consistently rare in the Asian tropics as well as across higher latitudes in Asia, America and Europe. The rarity of N-fixing trees in the Asian tropics compared with the American tropics might stem from lower intrinsic N limitation in Asian tropical forests, although direct support for any mechanism is lacking. The paucity of N-fixing trees throughout Asian forests suggests that N inputs to the Asian tropics might be lower than previously thought.

Connecting business with the agricultural landscape: business strategies for sustainable rural development
Swaffield, Simon R. ; Corry, Robert C. ; Opdam, Paul ; McWilliam, Wendy ; Primdahl, Jørgen - \ 2019
Business Strategy and the Environment (2019). - ISSN 0964-4733
cogovernance - food supply systems - placemaking - provenance - socioecological networks

Agribusiness enterprises link rural landscapes to global and regional markets. The nature of these business–landscape relationships is vital to the sustainability transition. Decisions by farmers and agriculture policymakers aggregate to changes in the ecology of landscapes, but the influence of food supply system businesses on rural landscape sustainability also requires scrutiny. This article uses four international cases to present a conceptual framework for investigating how different business strategies can support agricultural landscape sustainability. Insights from North America, New Zealand, The Netherlands, and Denmark inform the framework dimensions of horizontal/territorial and vertical/systemic business–landscape relationships. Three types of business model that promote rural sustainability are highlighted: provenance, cogovernance, and placemaking. These models engage strategies such as environmental management systems, certification, ecosystem and landscape services, and spatial planning. Research directions that will improve understanding about how business can engage with rural stakeholders for more sustainable rural landscapes are identified, including the need for cross disciplinary perspectives incorporating social, ecological, and business knowledge.

Strategies for robust and accurate experimental approaches to quantify nanomaterial bioaccumulation across a broad range of organisms
Petersen, Elijah J. ; Mortimer, Monika ; Burgess, Robert M. ; Handy, Richard ; Hanna, Shannon ; Ho, Kay T. ; Johnson, Monique ; Loureiro, Susana ; Selck, Henriette ; Scott-Fordsmand, Janeck J. ; Spurgeon, David ; Unrine, Jason ; Brink, Nico W. Van Den; Wang, Ying ; White, Jason ; Holden, Patricia - \ 2019
Environmental Science: Nano covers the benefits... 6 (2019)6. - ISSN 2051-8153 - p. 1619 - 1656.

One of the key components for environmental risk assessment of engineered nanomaterials (ENMs) is data on bioaccumulation potential. Accurately measuring bioaccumulation can be critical for regulatory decision-making regarding material hazard and risk, and for understanding the mechanism of toxicity. This perspective provides expert guidance for performing ENM bioaccumulation measurements across a broad range of test organisms and species. To accomplish this aim, we critically evaluated ENM bioaccumulation within three categories of organisms: single-celled species, multicellular species excluding plants, and multicellular plants. For aqueous exposures of suspended single-celled and small multicellular species, it is critical to perform a robust procedure to separate suspended ENMs and small organisms to avoid overestimating bioaccumulation. For many multicellular organisms, it is essential to differentiate between the ENMs adsorbed to external surfaces or in the digestive tract and the amount absorbed across epithelial tissues. For multicellular plants, key considerations include how exposure route and the role of the rhizosphere may affect the quantitative measurement of uptake, and that the efficiency of washing procedures to remove loosely attached ENMs to the roots is not well understood. Within each organism category, case studies are provided to illustrate key methodological considerations for conducting robust bioaccumulation experiments for different species within each major group. The full scope of ENM bioaccumulation measurements and interpretations are discussed including conducting the organism exposure, separating organisms from the ENMs in the test media after exposure, analytical methods to quantify ENMs in the tissues or cells, and modeling the ENM bioaccumulation results. One key finding to improve bioaccumulation measurements was the critical need for further analytical method development to identify and quantify ENMs in complex matrices. Overall, the discussion, suggestions, and case studies described herein will help improve the robustness of ENM bioaccumulation studies.

Biting patterns of malaria vectors of the lower Shire valley, southern Malawi
Mburu, Monicah M. ; Mzilahowa, Themba ; Amoah, Benjamin ; Chifundo, Duster ; Phiri, Kamija S. ; Berg, Henk van den; Takken, Willem ; McCann, Robert S. - \ 2019
Acta Tropica 197 (2019). - ISSN 0001-706X
Anophelines - Biting - Culicines - HLC - Indoors - Malawi - Outdoors

Assessing the biting behaviour of malaria vectors plays an integral role in understanding the dynamics of malaria transmission in a region. Biting times and preference for biting indoors or outdoors varies among mosquito species and across regions. These behaviours may also change over time in response to vector control measures such as long-lasting insecticidal nets (LLINs). Data on these parameters can provide the sites and times at which different interventions would be effective for vector control. This study assessed the biting patterns of malaria vectors in Chikwawa district, southern Malawi. The study was conducted during the dry and wet seasons in 2016 and 2017, respectively. In each season, mosquitoes were collected indoors and outdoors for 24 nights in six houses per night using the human landing catch. Volunteers were organized into six teams of two individuals, whereby three teams collected mosquitoes indoors and the other three collected mosquitoes outdoors each night, and the teams were rotated among twelve houses. All data were analyzed using Poisson log-linear models. The most abundant species were Anopheles gambiae sensu lato (primarily An. arabiensis) and An. funestus s.l. (exclusively An. funestus s.s.). During the dry season, the biting activity of An. gambiaes.l. was constant outdoors across the categorized hours (18:00 h to 08:45 h), but highest in the late evening hours (21:00 h to 23:45 h) during the wet season. The biting activity of An. funestus s.l. was highest in the late evening hours (21:00 h to 23:45 h) during the dry season and in the late night hours (03:00 h to 05:45 h) during the wet season. Whereas the number of An. funestuss.l. biting was constant (P = 0.662) in both seasons, that of An. gambiaes.l. was higher during the wet season than in the dry season (P = 0.001). Anopheles gambiae s.l. was more likely to bite outdoors than indoors in both seasons. During the wet season, An. funestus s.l. was more likely to bite indoors than outdoors but during the dry season, the bites were similar both indoors and outdoors. The biting activity that occurred in the early and late evening hours, both indoors and outdoors coincides with the times at which individuals may still be awake and physically active, and therefore unprotected by LLINs. Additionally, a substantial number of anopheline bites occurred outdoors. These findings imply that LLINs would only provide partial protection from malaria vectors, which would affect malaria transmission in this area. Therefore, protection against bites by malaria mosquitoes in the early and late evening hours is essential and can be achieved by designing interventions that reduce vector-host contacts during this period.

High-density mapping of triple rust resistance in barley using DArT-seq markers
Dracatos, Peter M. ; Haghdoust, Rouja ; Singh, Ravi P. ; Huerta Espino, Julio ; Barnes, Charles W. ; Forrest, Kerrie ; Hayden, Matthew ; Niks, Rients E. ; Park, Robert F. ; Singh, Davinder - \ 2019
Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
Barley - DArT-Seq markers - High-density linkage map - QTL - Rust resistance

The recent availability of an assembled and annotated genome reference sequence for the diploid crop barley (Hordeum vulgare L.) provides new opportunities to study the genetic basis of agronomically important traits such as resistance to stripe [Puccinia striiformis f. sp. hordei (Psh)], leaf [P. hordei (Ph)], and stem [P. graminis f. sp. tritici (Pgt)] rust diseases. The European barley cultivar Pompadour is known to possess high levels of resistance to leaf rust, predominantly due to adult plant resistance (APR) gene Rph20. We developed a barley recombinant inbred line (RIL) population from a cross between Pompadour and the leaf rust and stripe rust susceptible selection Biosaline-19 (B-19), and genotyped this population using DArT-Seq genotyping by sequencing (GBS) markers. In the current study, we produced a high-density linkage map comprising 8,610 (SNP and in silico) markers spanning 5957.6 cM, with the aim of mapping loci for resistance to leaf rust, stem rust, and stripe rust. The RIL population was phenotyped in the field with Psh (Mexico and Ecuador) and Ph (Australia) and in the greenhouse at the seedling stage with Australian Ph and Pgt races, and at Wageningen University with a European variant of Psh race 24 (PshWUR). For Psh, we identified a consistent field QTL on chromosome 2H across all South American field sites and years. Two complementary resistance genes were mapped to chromosomes 1H and 4H at the seedling stage in response to PshWUR, likely to be the loci rpsEm1 and rpsEm2 previously reported from the cultivar Emir from which Pompadour was bred. For leaf rust, we determined that Rph20 in addition to two minor-effect QTL on 1H and 3H were effective at the seedling stage, whilst seedling resistance to stem rust was due to QTL on chromosomes 3H and 7H conferred by Pompadour and B-19, respectively.

Extending the linear-noise approximation to biochemical systems influenced by intrinsic noise and slow lognormally distributed extrinsic noise
Keizer, Emma M. ; Bastian, Björn ; Smith, Robert W. ; Grima, Ramon ; Fleck, Christian - \ 2019
Physical Review. E, Statistical nonlinear, and soft matter physics 99 (2019)5. - ISSN 2470-0045

It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from the interaction of unknown molecular components with the network and from the cell's changing environment. While there are many methods to study the effect of intrinsic noise on the system dynamics, few exist to study the influence of both types of noise. Here we show how one can extend the conventional linear-noise approximation to allow for the rapid evaluation of the molecule numbers statistics of a biochemical network influenced by intrinsic noise and by slow lognormally distributed extrinsic noise. The theory is applied to simple models of gene regulatory networks and its validity confirmed by comparison with exact stochastic simulations. In particular, we consider three important biological examples. First, we investigate how extrinsic noise modifies the dependence of the variance of the molecule number fluctuations on the rate constants. Second, we show how the mutual information between input and output of a network motif is affected by extrinsic noise. And third, we study the robustness of the ubiquitously found feed-forward loop motifs when subjected to extrinsic noise.

Review of the evidence regarding the use of antenatal multiple micronutrient supplementation in low- and middle-income countries
Bourassa, Megan W. ; Osendarp, Saskia J.M. ; Adu-Afarwuah, Seth ; Ahmed, Saima ; Ajello, Clayton ; Bergeron, Gilles ; Black, Robert ; Christian, Parul ; Cousens, Simon ; Pee, Saskia de; Dewey, Kathryn G. ; Arifeen, Shams El ; Engle-Stone, Reina ; Fleet, Alison ; Gernand, Alison D. ; Hoddinott, John ; Klemm, Rolf ; Kraemer, Klaus ; Kupka, Roland ; McLean, Erin ; Moore, Sophie E. ; Neufeld, Lynnette M. ; Persson, Lars Åke ; Rasmussen, Kathleen M. ; Shankar, Anuraj H. ; Smith, Emily ; Sudfeld, Christopher R. ; Udomkesmalee, Emorn ; Vosti, Stephen A. - \ 2019
Annals of the New York Academy Of Sciences 1444 (2019)1. - ISSN 0077-8923 - p. 6 - 21.
LMICs - micronutrient - pregnancy - supplements

Inadequate micronutrient intakes are relatively common in low- and middle-income countries (LMICs), especially among pregnant women, who have increased micronutrient requirements. This can lead to an increase in adverse pregnancy and birth outcomes. This review presents the conclusions of a task force that set out to assess the prevalence of inadequate micronutrient intakes and adverse birth outcomes in LMICs; the data from trials comparing multiple micronutrient supplements (MMS) that contain iron and folic acid (IFA) with IFA supplements alone; the risks of reaching the upper intake levels with MMS; and the cost-effectiveness of MMS compared with IFA. Recent meta-analyses demonstrate that MMS can reduce the risks of preterm birth, low birth weight, and small for gestational age in comparison with IFA alone. An individual-participant data meta-analysis also revealed even greater benefits for anemic and underweight women and female infants. Importantly, there was no increased risk of harm for the pregnant women or their infants with MMS. These data suggest that countries with inadequate micronutrient intakes should consider supplementing pregnant women with MMS as a cost-effective method to reduce the risk of adverse birth outcomes.

Substantial extracellular metabolic differences found between phylogenetically closely related probiotic and pathogenic strains of Escherichia coli
Hooft, Justin J.J. Van Der; Goldstone, Robert J. ; Harris, Susan ; Burgess, Karl E.V. ; Smith, David G.E. - \ 2019
Frontiers in Microbiology 10 (2019)FEB. - ISSN 1664-302X
Escherichia coli - Extracellular metabolome - Mass spectrometry - Metabolomics - Nissle 1917 - Pathogenic - Probiotic

Since its first isolation a century ago, the gut inhabitant Escherichia coli strain Nissle 1917 has been shown to have probiotic activities; however, it is yet not fully elucidated which differential factors play key roles in its beneficial interactions with the host. To date, no metabolomics studies have been reported investigating the potential role of small molecules in functional strain differentiation of Nissle from its genetically close neighbors. Here, we present results of liquid chromatography coupled to high-resolution mass spectrometry characterization of extracellular metabolomes of E. coli strains as a proxy of their bioactivity potential. We found that phylogroup B2 strains exported a more diverse arsenal of metabolites than strains of other phylogroups. Zooming into the phylogroup B2 metabolome identified consistent substantial differences between metabolic output of E. coli Nissle and other strains, particularly in metabolites associated to the Argimine biosynthesis pathway. Nissle was found to release higher levels of Ornithine and Citrulline whilst depleting greater amounts of Arginine from the medium. Moreover, a novel Nissle-specific metabolite not reported before in bacteria, 5-(Carbamoylamino)-2-hydroxypentanoic acid (Citrulline/Arginic Acid related) was observed. Finally, Nissle, CFT073 and NCTC12241/ATCC25922 shared the excretion of N5-Acetylornithine, whereas other strains released N2-Acetylornithine or no N-Acetylornithine at all. Thus, we found substantial metabolic differences in phylogenetically very similar E. coli strains, an observation which suggests that it is justified to further investigate roles of small molecules as potential modulators of the gut environment by probiotic, commensal, and pathogenic strains, including E. coli Nissle 1917.

Tussenevaluatie van de nota Duurzame Oogst, Gezonde Groei: Deelproject Economie: Rapport Naleving
Stokkers, Robert ; Verstand, Daan - \ 2019
Wageningen : Stichting Wageningen Research, Wageningen Plant Research, Business unit Open Teelten (Stichting Wageningen Research, Wageningen Plant Research, Business unit Open Teelten rapport 789) - 31
Deze evaluatiestudie gaat na in hoeverre de naleving van wet- en regelgeving van het gewasbeschermingsbeleid is verbeterd of tenminste op het niveau van 2014 is gebleven. Dat is gedaan op basis van NVWA nalevingsrapporten. Uit deze analyse blijkt dat in één sector een significante verbetering van de naleving is opgetreden, terwijl er in een andere sector een significante verslechtering heeft plaatsgevonden. Omdat er in een aantal sectoren maar één NVWA nalevingsrapport in de evaluatieperiode (2012-2018) is verschenen, kan er geen vergelijking gemaakt worden en wordt er in dit rapport dus niet aangegeven of de naleving verbeterd of verslechterd is.
Contrasting effects of host species and phylogenetic diversity on the occurrence of HPAI H5N1 in European wild birds
Huang, Zheng Y.X. ; Xu, Chi ; Langevelde, Frank van; Ma, Yuying ; Langendoen, Tom ; Mundkur, Taej ; Si, Yali ; Tian, Huaiyu ; Kraus, Robert H.S. ; Gilbert, Marius ; Han, Guan Zhu ; Ji, Xiang ; Prins, Herbert H.T. ; Boer, Willem F. de - \ 2019
Journal of Animal Ecology 88 (2019)7. - ISSN 0021-8790 - p. 1044 - 1053.
avian influenza - community composition - dilution effect - diversity–disease relationship - phylogenetic distance - waterfowl

Studies on the highly pathogenic avian influenza (HPAI) H5N1 suggest that wild bird migration may facilitate its long-distance spread, yet the role of wild bird community composition in its transmission risk remains poorly understood. Furthermore, most studies on the diversity–disease relationship focused on host species diversity without considering hosts’ phylogenetic relationships, which may lead to rejecting a species diversity effect when the community has host species that are only distantly related. Here, we explored the influence of waterbird community composition for determining HPAI H5N1 occurrence in wild birds in a continental-scale study across Europe. In particular, we tested the diversity–disease relationship using both host species diversity and host phylogenetic diversity. Our results provide the first demonstration that host community composition—compared with previously identified environmental risk factors—can also effectively explain the spatial pattern of H5N1 occurrence in wild birds. We further show that communities with more higher risk host species and more closely related species have a higher risk of H5N1 outbreaks. Thus, both host species diversity and community phylogenetic structure, in addition to environmental factors, jointly influence H5N1 occurrence. Our work not only extends the current theory on the diversity–disease relationship, but also has important implications for future monitoring of H5N1 and other HPAI subtypes.

Soil Salinity Limits Plant Shade Avoidance
Hayes, Scott ; Pantazopoulou, Chrysoula K. ; Gelderen, Kasper van; Reinen, Emilie ; Tween, Adrian Louis ; Sharma, Ashutosh ; Vries, Michel de; Prat, Salomé ; Schuurink, Robert C. ; Testerink, Christa ; Pierik, Ronald - \ 2019
Current Biology 29 (2019)10. - ISSN 0960-9822 - p. 1669 - 1676.e4.
abscisic acid - brassinosteroids - phytochrome - phytohormones - PIF - plant photobiology - salt response - salt stress

Global food production is set to keep increasing despite a predicted decrease in total arable land [1]. To achieve higher production, denser planting will be required on increasingly degraded soils. When grown in dense stands, crops elongate and raise their leaves in an effort to reach sunlight, a process termed shade avoidance [2]. Shade is perceived by a reduction in the ratio of red (R) to far-red (FR) light and results in the stabilization of a class of transcription factors known as PHYTOCHROME INTERACTING FACTORS (PIFs) [3, 4]. PIFs activate the expression of auxin biosynthesis genes [4, 5] and enhance auxin sensitivity [6], which promotes cell-wall loosening and drives elongation growth. Despite our molecular understanding of shade-induced growth, little is known about how this developmental program is integrated with other environmental factors. Here, we demonstrate that low levels of NaCl in soil strongly impair the ability of plants to respond to shade. This block is dependent upon abscisic acid (ABA) signaling and the canonical ABA signaling pathway. Low R:FR light enhances brassinosteroid (BR) signaling through BRASSINOSTEROID SIGNALING KINASE 5 (BSK5) and leads to the activation of BRI1 EMS SUPPRESSOR 1 (BES1). ABA inhibits BSK5 upregulation and interferes with GSK3-like kinase inactivation by the BR pathway, thus leading to a suppression of BES1:PIF function. By demonstrating a link between light, ABA-, and BR-signaling pathways, this study provides an important step forward in our understanding of how multiple environmental cues are integrated into plant development. Intensively farmed crops often experience multiple stresses simultaneously. Here, Hayes et al. show that low-level soil salinity suppresses shade avoidance in plants. Through investigation of the mechanisms underlying this trait, they uncover a regulatory pathway that converges at the level of brassinosteroid signaling.

Optogenetic control shows that kinetic proofreading regulates the activity of the T cell receptor
Yousefi, O.S. ; Günther, Matthias ; Hörner, Maximilian ; Chalupsky, Julia ; Wess, Maximilian ; Brandl, Simon M. ; Smith, Robert W. ; Fleck, Christian ; Kunkel, Tim ; Zurbriggen, Matias D. ; Höfer, Thomas ; Weber, Wilfried ; Schamel, Wolfgang W.A. - \ 2019
eLife 8 (2019). - ISSN 2050-084X
A. thaliana - dynamics - human - immunology - inflammation - ligand-receptor - optogenetics - signaling - T cells

The immune system distinguishes between self and foreign antigens. The kinetic proofreading (KPR) model proposes that T cells discriminate self from foreign ligands by the different ligand binding half-lives to the T cell receptor (TCR). It is challenging to test KPR as the available experimental systems fall short of only altering the binding half-lives and keeping other parameters of the interaction unchanged. We engineered an optogenetic system using the plant photoreceptor phytochrome B (PhyB) as a ligand to selectively control the dynamics of ligand binding to the TCR by light. This opto-ligand-TCR system was combined with the unique property of PhyB to continuously cycle between the binding and non-binding states under red light, with the light intensity determining the cycling rate and thus the binding duration. Mathematical modeling of our experimental datasets showed that indeed the ligand-TCR interaction half-life is the decisive factor for activating downstream TCR signaling, substantiating KPR.

The Effect of Allogenic Versus Autologous Fecal Microbiota Transfer on Symptoms, Visceral Perception and Fecal and Mucosal Microbiota in Irritable Bowel Syndrome: A Randomized Controlled Study
Holster, Savanne ; Lindqvist, Carl Mårten ; Repsilber, Dirk ; Salonen, Anne ; Vos, Willem M. de; König, Julia ; Brummer, Robert J. - \ 2019
Clinical and Translational Gastroenterology 10 (2019)4. - ISSN 2155-384X - p. e00034 - e00034.

OBJECTIVES: Fecal microbiota transfer (FMT) is suggested as a potential treatment for patients with irritable bowel syndrome (IBS). We aimed to study the effect of allogenic and autologous FMT on IBS symptoms, visceral sensitivity, and compositional changes in fecal and mucosa-adherent microbiota. METHODS: Seventeen patients with IBS were randomized either to receive fecal material from a healthy donor (allogenic) or to receive their own fecal material (autologous). The fecal material was administered into the cecum by whole colonoscopy after bowel cleansing. RESULTS: No significant differences were found between the allogenic and the autologous FMT regarding symptom scores. However, symptom scores of patients receiving allogenic fecal material significantly decreased after FMT compared with baseline (P = 0.02), which was not the case in the autologous group (P = 0.16). Visceral sensitivity was not affected except for a small beneficial effect on urge scores in the autologous group (P < 0.05). While both fecal and mucosa-adherent microbiota of some patients shifted to their respective donor's fecal microbiota, some patients showed no relevant microbial changes after allogenic FMT. Large compositional shifts in fecal and mucosa-adherent microbiota also occurred in the autologous group. CONCLUSIONS: This study showed that a single FMT by colonoscopy may have beneficial effects in IBS; however, the allogenic fecal material was not superior to the autologous fecal material. This suggests that bowel cleansing prior to the colonoscopy and/or processing of the fecal material as part of the FMT routine contribute to symptoms and gut microbiota composition changes in IBS.

In the way: Perpetuating land dispossession of the indigenous Hai//om and the collective action lawsuit for etosha national park and mangetti west, Namibia
Koot, Stasja ; Hitchcock, Robert - \ 2019
Nomadic Peoples 23 (2019)1. - ISSN 0822-7942 - p. 55 - 77.
Etosha - Hai//om San - Indigenous peoples - Land - Namibia

As former mobile foraging peoples, the indigenous Hai//om San of Namibia lost most of their land - including Etosha National Park and Mangetti West - to other groups and the state in the nineteenth and twentieth centuries. After independence (1990), the government redistributed some of this land to various expropriated groups. In the following overview, we delve into this complex history to argue that the recent decision by the Hai//om (2015) to file a collective action lawsuit against the government of Namibia over Etosha and Mangetti West must be seen in a context of ongoing, often subtle, processes of land dispossession simultaneously taking place as a result of marginalisation and structural disempowerment.

Success of lake restoration depends on spatial aspects of nutrient loading and hydrology
Janssen, Annette B.G. ; Wijk, Dianneke van; Gerven, Luuk P.A. van; Bakker, Elisabeth S. ; Brederveld, Robert J. ; DeAngelis, Donald L. ; Janse, Jan H. ; Mooij, Wolf M. - \ 2019
Science of the Total Environment 679 (2019). - ISSN 0048-9697 - p. 248 - 259.
Alternative stable states - Diffuse source - Management - PCLake - Point source - Spatial heterogeneity

Many aquatic ecosystems have deteriorated due to human activities and their restoration is often troublesome. It is proposed here that the restoration success of deteriorated lakes critically depends on hitherto largely neglected spatial heterogeneity in nutrient loading and hydrology. A modelling approach is used to study this hypothesis by considering four lake types with contrasting nutrient loading (point versus diffuse)and hydrology (seepage versus drainage). By comparing the longterm effect of common restoration measures (nutrient load reduction, lake flushing or biomanipulation)in these four lake types, we found that restoration through reduction of nutrient loading is effective in all cases. In contrast, biomanipulation only works in seepage lakes with diffuse nutrient inputs, while lake flushing will even be counterproductive in lakes with nutrient point sources. The main conclusion of the presented analysis is that a priori assessment of spatial heterogeneity caused by nutrient loading and hydrology is essential for successful restoration of lake ecosystems.

Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
Poorter, L. ; Rozendaal, Danaë ; Bongers, F. ; Almeida-Cortez, Jarcilene S. ; Almeyda Zambrano, Angélica María ; Álvarez, Francisco S. ; Andrade, José Luís ; Villa, Luis Felipe Arreola ; Balvanera, Patricia ; Becknell, Justin M. ; Bentos, Tony V. ; Bhaskar, Radika ; Boukili, Vanessa ; Brancalion, Pedro H.S. ; Broadbent, Eben N. ; César, Ricardo Gomes ; Chave, Jerome ; Chazdon, Robin L. ; Colletta, Gabriel Dalla ; Craven, Dylan ; Jong, Ben H.J. de; Denslow, Julie S. ; Dent, Daisy H. ; DeWalt, Saara J. ; García, Elisa Díaz ; Dupuy, Juan M. ; Durán, Sandra M. ; Espírito Santo, Mário Marcos ; Fandiño, María C. ; Fernandes, Geraldo Wilson ; Finegan, Bryan ; Moser, Vanessa Granda ; Hall, Jefferson S. ; Hernández-Stefanoni, José Luis ; Jakovac, A.C. ; Junqueira, André B. ; Kennard, Deborah ; Lebrija-Trejos, Edwin ; Letcher, Susan G. ; Lohbeck, M.W.M. ; Lopez, Omar R. ; Marín-Spiotta, Erika ; Martínez-Ramos, Miguel ; Martins, Sebastião Venâncio ; Massoca, Paulo E.S. ; Meave, Jorge A. ; Mesquita, Rita ; Mora, Francisco ; Souza Moreno, Vanessa De; Müller, Sandra C. ; Muñoz, Rodrigo ; Muscarella, Robert ; Oliveira Neto, Silvio Nolasco De; Nunes, Yule Roberta Ferreira ; Ochoa-Gaona, Susana ; Paz, Horacio ; Pena Claros, M. ; Piotto, Daniel ; Ruíz, Jorge ; Sanaphre-Villanueva, Lucía ; Sanchez-Azofeifa, Arturo ; Schwartz, Naomi B. ; Steininger, Marc K. ; Thomas, William Wayt ; Toledo, Marisol ; Uriarte, Maria ; Breugel, Michiel van; Wal, Hans van der - \ 2019
secondary succession - community assembly - community-weighted mean - wood density - Neotropics - tropical forest - Latin America
We analyse how community wood density (WD) recovers during secondary tropical forest succession. In wet forests succession proceeds from low to high WD, in dry forests from high to low WD, resulting in convergence of community WD of dry and wet forests over time, as vegetation cover builds up.
The fatal flaws of compassionate conservation
Oommen, Meera Anna ; Cooney, Rosie ; Ramesh, Madhuri ; Archer, Michael ; Brockington, Daniel ; Buscher, Bram ; Fletcher, Robert ; Natusch, Daniel J.D. ; Vanak, Abi T. ; Webb, Grahame ; Shanker, Kartik - \ 2019
Conservation Biology (2019). - ISSN 0888-8892
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