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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    Global plant trait relationships extend to the climatic extremes of the tundra biome
    Thomas, H.J.D. ; Bjorkman, A.D. ; Myers-Smith, I.H. ; Elmendorf, S.C. ; Kattge, J. ; Diaz, S. ; Vellend, M. ; Blok, D. ; Cornelissen, J.H.C. ; Forbes, B.C. ; Henry, G.H.R. ; Hollister, R.D. ; Normand, S. ; Prevéy, J.S. ; Rixen, C. ; Schaepman-Strub, G. ; Wilmking, M. ; Wipf, S. ; Cornwell, W.K. ; Beck, P.S.A. ; Georges, D. ; Goetz, S.J. ; Guay, K.C. ; Rüger, N. ; Soudzilovskaia, N.A. ; Spasojevic, M.J. ; Alatalo, J.M. ; Alexander, H.D. ; Anadon-Rosell, A. ; Angers-Blondin, S. ; Beest, M. te; Berner, L.T. ; Björk, R.G. ; Buchwal, A. ; Buras, A. ; Carbognani, M. ; Christie, K.S. ; Collier, L.S. ; Cooper, E.J. ; Elberling, B. ; Eskelinen, A. ; Frei, E.R. ; Grau, O. ; Grogan, P. ; Hallinger, M. ; Heijmans, M.M.P.D. ; Hermanutz, L. ; Hudson, J.M.G. ; Johnstone, J.F. ; Hülber, K. ; Iturrate-Garcia, M. ; Iversen, C.M. ; Jaroszynska, F. ; Kaarlejarvi, E. ; Kulonen, A. ; Lamarque, L.J. ; Lantz, T.C. ; Lévesque, E. ; Little, C.J. ; Michelsen, A. ; Milbau, A. ; Nabe-Nielsen, J. ; Nielsen, S.S. ; Ninot, J.M. ; Oberbauer, S.F. ; Olofsson, J. ; Onipchenko, V.G. ; Petraglia, A. ; Rumpf, S.B. ; Shetti, R. ; Speed, J.D.M. ; Suding, K.N. ; Tape, K.D. ; Tomaselli, M. ; Trant, A.J. ; Treier, U.A. ; Tremblay, M. ; Venn, S.E. ; Vowles, T. ; Weijers, S. ; Wookey, P.A. ; Zamin, T.J. ; Bahn, M. ; Blonder, B. ; Bodegom, P.M. van; Bond-Lamberty, B. ; Campetella, G. ; Cerabolini, B.E.L. ; Chapin, F.S. ; Craine, J.M. ; Dainese, M. ; Green, W.A. ; Jansen, S. ; Kleyer, M. ; Manning, P. ; Niinemets, ; Onoda, Y. ; Ozinga, W.A. ; Peñuelas, J. ; Poschlod, P. ; Reich, P.B. ; Sandel, B. ; Schamp, B.S. ; Sheremetiev, S.N. ; Vries, F.T. de - \ 2020
    Nature Communications 11 (2020)1. - ISSN 2041-1723

    The majority of variation in six traits critical to the growth, survival and reproduction of plant species is thought to be organised along just two dimensions, corresponding to strategies of plant size and resource acquisition. However, it is unknown whether global plant trait relationships extend to climatic extremes, and if these interspecific relationships are confounded by trait variation within species. We test whether trait relationships extend to the cold extremes of life on Earth using the largest database of tundra plant traits yet compiled. We show that tundra plants demonstrate remarkably similar resource economic traits, but not size traits, compared to global distributions, and exhibit the same two dimensions of trait variation. Three quarters of trait variation occurs among species, mirroring global estimates of interspecific trait variation. Plant trait relationships are thus generalizable to the edge of global trait-space, informing prediction of plant community change in a warming world.

    Traditional plant functional groups explain variation in economic but not size-related traits across the tundra biome
    Thomas, H.J.D. ; Myers-Smith, I.H. ; Bjorkman, A.D. ; Elmendorf, S.C. ; Blok, D. ; Cornelissen, J.H.C. ; Forbes, B.C. ; Hollister, R.D. ; Normand, S. ; Prevéy, J.S. ; Rixen, C. ; Schaepman-Strub, G. ; Wilmking, M. ; Wipf, S. ; Cornwell, W. ; Kattge, J. ; Goetz, S.J. ; Guay, K.C. ; Alatalo, J.M. ; Anadon-Rosell, A. ; Angers-Blondin, S. ; Berner, L.T. ; Björk, R.G. ; Buchwal, A. ; Buras, A. ; Carbognani, M. ; Christie, K. ; Siegwart Collier, L. ; Cooper, E.J. ; Eskelinen, A. ; Frei, E.R. ; Grau, O. ; Grogan, P. ; Hallinger, M. ; Heijman, M.M.P.D. ; Hermanutz, L. ; Hudson, J.M.G. ; Hülber, K. ; Iturrate-Garcia, M. ; Iversen, C.M. ; Jaroszynska, F. ; Johnstone, J.F. ; Kaarlejärvi, E. ; Kulonen, A. ; Lamarque, L.J. ; Lévesque, E. ; Beest, M. Te; Vries, F.T. de; Ozinga, W.A. ; Bodegom, P.M. van - \ 2019
    Global Ecology and Biogeography 28 (2019)2. - ISSN 1466-822X - p. 78 - 95.
    cluster analysis - community composition - ecosystem function - plant functional groups - plant functional types - plant traits - tundra biome - vegetation change

    Aim: Plant functional groups are widely used in community ecology and earth system modelling to describe trait variation within and across plant communities. However, this approach rests on the assumption that functional groups explain a large proportion of trait variation among species. We test whether four commonly used plant functional groups represent variation in six ecologically important plant traits. Location: Tundra biome. Time period: Data collected between 1964 and 2016. Major taxa studied: 295 tundra vascular plant species. Methods: We compiled a database of six plant traits (plant height, leaf area, specific leaf area, leaf dry matter content, leaf nitrogen, seed mass) for tundra species. We examined the variation in species-level trait expression explained by four traditional functional groups (evergreen shrubs, deciduous shrubs, graminoids, forbs), and whether variation explained was dependent upon the traits included in analysis. We further compared the explanatory power and species composition of functional groups to alternative classifications generated using post hoc clustering of species-level traits. Results: Traditional functional groups explained significant differences in trait expression, particularly amongst traits associated with resource economics, which were consistent across sites and at the biome scale. However, functional groups explained 19% of overall trait variation and poorly represented differences in traits associated with plant size. Post hoc classification of species did not correspond well with traditional functional groups, and explained twice as much variation in species-level trait expression. Main conclusions: Traditional functional groups only coarsely represent variation in well-measured traits within tundra plant communities, and better explain resource economic traits than size-related traits. We recommend caution when using functional group approaches to predict tundra ecosystem change, or ecosystem functions relating to plant size, such as albedo or carbon storage. We argue that alternative classifications or direct use of specific plant traits could provide new insight into ecological prediction and modelling.

    Tundra Trait Team : A database of plant traits spanning the tundra biome
    Bjorkman, Anne D. ; Myers-Smith, Isla H. ; Elmendorf, Sarah C. ; Normand, Signe ; Thomas, Haydn J.D. ; Alatalo, Juha M. ; Alexander, Heather ; Anadon-Rosell, Alba ; Angers-Blondin, Sandra ; Bai, Yang ; Baruah, Gaurav ; Beest, Mariska te; Berner, Logan ; Björk, Robert G. ; Blok, Daan ; Bruelheide, Helge ; Buchwal, Agata ; Buras, Allan ; Carbognani, Michele ; Christie, Katherine ; Collier, Laura S. ; Cooper, Elisabeth J. ; Cornelissen, J.H.C. ; Dickinson, Katharine J.M. ; Dullinger, Stefan ; Elberling, Bo ; Eskelinen, Anu ; Forbes, Bruce C. ; Frei, Esther R. ; Iturrate-Garcia, Maitane ; Good, Megan K. ; Grau, Oriol ; Green, Peter ; Greve, Michelle ; Grogan, Paul ; Haider, Sylvia ; Hájek, Tomáš ; Hallinger, Martin ; Happonen, Konsta ; Harper, Karen A. ; Heijmans, Monique M.P.D. ; Henry, Gregory H.R. ; Hermanutz, Luise ; Hewitt, Rebecca E. ; Hollister, Robert D. ; Hudson, James ; Hülber, Karl ; Iversen, Colleen M. ; Jaroszynska, Francesca ; Jiménez-Alfaro, Borja - \ 2018
    Global Ecology and Biogeography 27 (2018)12. - ISSN 1466-822X - p. 1402 - 1411.
    alpine - Arctic - plant functional traits - tundra

    Motivation: The Tundra Trait Team (TTT) database includes field-based measurements of key traits related to plant form and function at multiple sites across the tundra biome. This dataset can be used to address theoretical questions about plant strategy and trade-offs, trait–environment relationships and environmental filtering, and trait variation across spatial scales, to validate satellite data, and to inform Earth system model parameters. Main types of variable contained: The database contains 91,970 measurements of 18 plant traits. The most frequently measured traits (> 1,000 observations each) include plant height, leaf area, specific leaf area, leaf fresh and dry mass, leaf dry matter content, leaf nitrogen, carbon and phosphorus content, leaf C:N and N:P, seed mass, and stem specific density. Spatial location and grain: Measurements were collected in tundra habitats in both the Northern and Southern Hemispheres, including Arctic sites in Alaska, Canada, Greenland, Fennoscandia and Siberia, alpine sites in the European Alps, Colorado Rockies, Caucasus, Ural Mountains, Pyrenees, Australian Alps, and Central Otago Mountains (New Zealand), and sub-Antarctic Marion Island. More than 99% of observations are georeferenced. Time period and grain: All data were collected between 1964 and 2018. A small number of sites have repeated trait measurements at two or more time periods. Major taxa and level of measurement: Trait measurements were made on 978 terrestrial vascular plant species growing in tundra habitats. Most observations are on individuals (86%), while the remainder represent plot or site means or maximums per species. Software format: csv file and GitHub repository with data cleaning scripts in R; contribution to TRY plant trait database (www.try-db.org) to be included in the next version release.

    Biodiversity of the Sebangau tropical peat swamp forest, Indonesian Borneo
    Husson, S.J. ; Limin, S.H. ; Adul, ; Boyd, N.S. ; Brousseau, J.J. ; Collier, S. ; Cheyne, S.M. ; Arcy, L.J. D'; Dow, R.A. ; Schreven, Stijn - \ 2018
    Mires and Peat 22 (2018). - ISSN 1819-754X - p. 1 - 50.
    The importance of Southeast Asia’s tropical peat swamp forests for biodiversity is becoming increasingly recognised. Information on species presence within peatland areas is scant, however, limiting our ability to develop species conservation strategies and monitor responses to human activities. We compile species presence records for the Sebangau forest in Indonesian Borneo since 1993 and present the most complete Bornean PSF biodiversity inventory yet published. Including morpho-species that are likely to represent true species, this list comprises 215 tree, 92 non-tree flora, 73 ant, 66 butterfly, 297 spider, 41 dragon/damselfly, 55 fish, 11 amphibian, 46 reptile, 172 bird and 65 mammal taxa. Of these, 46 species are globally threatened and 59 are currently protected in Indonesia; 22 vertebrate species are Borneo endemics. Because our sampling is both biased and incomplete, the true number of species found at this site is likely to be much higher. Little is known about many of these taxa in Sebangau and peat swamp forests elsewhere. Many of these species are considered forest dependent, and the entire community is expected to be important for maintaining the resilience of the peat swamp forest ecosystem and the environmental services that it provides. This highlights the need for urgent conservation of Sebangau and its diverse biological community.
    Groundwater flow and heat transport for systems undergoing freeze-thaw : Intercomparison of numerical simulators for 2D test cases
    Grenier, Christophe ; Anbergen, Hauke ; Bense, Victor ; Chanzy, Quentin ; Coon, Ethan ; Collier, Nathaniel ; Costard, François ; Ferry, Michel ; Frampton, Andrew ; Frederick, Jennifer ; Gonçalvès, Julio ; Holmén, Johann ; Jost, Anne ; Kokh, Samuel ; Kurylyk, Barret ; McKenzie, Jeffrey ; Molson, John ; Mouche, Emmanuel ; Orgogozo, Laurent ; Pannetier, Romain ; Rivière, Agnès ; Roux, Nicolas ; Rühaak, Wolfram ; Scheidegger, Johanna ; Selroos, Jan Olof ; Therrien, René ; Vidstrand, Patrik ; Voss, Clifford - \ 2018
    Advances in Water Resources 114 (2018). - ISSN 0309-1708 - p. 196 - 218.
    Code benchmarking - Numerical simulation - Permafrost - Sharp interface problems - Thermo-hydrological coupling
    In high-elevation, boreal and arctic regions, hydrological processes and associated water bodies can be strongly influenced by the distribution of permafrost. Recent field and modeling studies indicate that a fully-coupled multidimensional thermo-hydraulic approach is required to accurately model the evolution of these permafrost-impacted landscapes and groundwater systems. However, the relatively new and complex numerical codes being developed for coupled non-linear freeze-thaw systems require verification. This issue is addressed by means of an intercomparison of thirteen numerical codes for two-dimensional test cases with several performance metrics (PMs). These codes comprise a wide range of numerical approaches, spatial and temporal discretization strategies, and computational efficiencies. Results suggest that the codes provide robust results for the test cases considered and that minor discrepancies are explained by computational precision. However, larger discrepancies are observed for some PMs resulting from differences in the governing equations, discretization issues, or in the freezing curve used by some codes.
    Seagrass ecosystem trajectory depends on the relative timescales of resistance, recovery and disturbance
    O'Brien, Katherine R. ; Waycott, Michelle ; Maxwell, Paul ; Kendrick, Gary A. ; Udy, James W. ; Ferguson, Angus J.P. ; Kilminster, Kieryn ; Scanes, Peter ; McKenzie, Len J. ; McMahon, Kathryn ; Adams, Matthew P. ; Samper-Villarreal, Jimena ; Collier, Catherine ; Lyons, Mitchell ; Mumby, Peter J. ; Radke, Lynda ; Christianen, Marjolijn J.A. ; Dennison, William C. - \ 2018
    Marine Pollution Bulletin 134 (2018). - ISSN 0025-326X - p. 166 - 176.
    Colonizing - Opportunistic - Persistent - Recovery - Resilience - Resistance - Seagrass - Trajectory
    Seagrass ecosystems are inherently dynamic, responding to environmental change across a range of scales. Habitat requirements of seagrass are well defined, but less is known about their ability to resist disturbance. Specific means of recovery after loss are particularly difficult to quantify. Here we assess the resistance and recovery capacity of 12 seagrass genera. We document four classic trajectories of degradation and recovery for seagrass ecosystems, illustrated with examples from around the world. Recovery can be rapid once conditions improve, but seagrass absence at landscape scales may persist for many decades, perpetuated by feedbacks and/or lack of seed or plant propagules to initiate recovery. It can be difficult to distinguish between slow recovery, recalcitrant degradation, and the need for a window of opportunity to trigger recovery. We propose a framework synthesizing how the spatial and temporal scales of both disturbance and seagrass response affect ecosystem trajectory and hence resilience.
    Contribution of Dairy to Nutrient Intake in the Western Diet
    Hettinga, Kasper ; Valenberg, Hein van - \ 2017
    In: Nutrients in Dairy and Their Implications for Health and Disease / Watson, Ronald Ross, Collier, Robert J., Preedy, Victor R., Academic Press - ISBN 9780128097625 - p. 251 - 258.
    Dairy - Dietary patterns - Minerals - Nutrient density - Omega-3 fatty acids - Protein quality - Vitamins

    Milk and dairy products play an important role in providing nutrients in both Western and developing countries. Most research in this area focuses on the intake of individual nutrients from food products, like dairy products. However, nutrients are not consumed, and do not function, in isolation. Looking at nutrient intake from the perspective of whole food products, or even whole dietary patterns, may be a more suitable way to quantify the contribution of dairy to the intake of nutrients. A mathematical approach, the nutrient-rich food score, is explained and discussed in this chapter. Such models could in the future even be extended beyond nutrition (e.g., including sustainability or cost parameters) to even better guide healthy eating habits for consumers.

    A first approach to deal with cumulative effects on birds and bats of offshore wind farms and other human activities in the southern North Sea
    Leopold, M.F. ; Boonman, M. ; Collier, M.P. ; Davaasuren, N. ; Jongbloed, R.H. ; Lagerveld, S. ; Wal, J.T. van der; Scholl, M.M. - \ 2014
    Den Burg : IMARES (Report / IMARES Wageningen UR C166/14) - 188
    regionale planning - windmolenpark - zeevogels - chiroptera - vogels - nadelige gevolgen - noordzee - regional planning - wind farms - sea birds - chiroptera - birds - adverse effects - north sea
    Around 100 offshore wind farms are scheduled to be operational by 2023 in the southern North Sea (51-56°N) alone. There may be two sides to this development in environmental terms: on the one hand this will help reduce CO2 emissions, on the other hand protected North Sea biota may be negatively impacted. This report considers the cumulative impact of all projected wind farms in the southern North Sea (by 2023) on birds and bats.
    Kaartjes rijgen groene parels tot een collier
    Koedoot, M. ; Stobbelaar, D.J. - \ 2013
    Trouw (2013). - p. 17 - 17.
    Molecular ecological analysis of the gastrointestinal microbiota: A review
    Zoetendal, E.G. ; Collier, C.T. ; Koike, S.T. ; Mackie, R.I. ; Gaskins, H.R. - \ 2004
    The Journal of Nutrition 134 (2004)2. - ISSN 0022-3166 - p. 465 - 472.
    16s ribosomal-rna - gradient gel-electrophoresis - targeted oligonucleotide probes - in-situ hybridization - human fecal samples - real-time pcr - sulfate-reducing bacteria - polymerase chain-reaction - rdna sequence-analysis - human feces
    The gastrointestinal (GI) microbiota of mammals is characterized by its high population density, wide diversity and complexity of interactions. While all major groups of microbes are represented, bacteria predominate. Importantly, bacterial cells outnumber animal (host) cells by a factor of ten and have a profound influence on nutritional, physiological and immunological processes in the host animal. Our knowledge of the molecular and cellular bases of host-microbe interactions is limited, though critically needed to determine if and how the GI microbiota contributes to various enteric disorders in humans and animals. Traditionally, GI bacteria have been studied via cultivation-based techniques, which are labor intensive and require previous knowledge of individual nutritional and growth requirements. Recently, findings from culture-based methods have been supplemented with molecular ecology techniques that are based on the 16S rRNA gene. These techniques enable characterization and quantification of the microbiota, while also providing a classification scheme to predict phylogenetic relationships. The choice of a particular molecular-based approach depends on the questions being addressed. Clone libraries can be sequenced to identify the composition of the microbiota, often to the species level. Microbial community structure can be analyzed via fingerprinting techniques, while dot blot hybridization or fluorescent in situ hybridization can measure abundance of particular taxa. Emerging approaches, such as those based on functional genes and their expression and the combined use of stable isotopes and biomarkers, are being developed and optimized to study metabolic activities of groups or individual organisms in situ. Here, a critical summary is provided of current molecular ecological approaches for studying the GI microbiota.
    Effects of Tylosin on Bacterial Mucolysis, Clostridium perfringens Colonization, and Intestinal Barrier Function in a Chick Model of necrotic Enteritis
    Collier, C.T. ; Klis, J.D. van der; Deplancke, B. ; Anderson, D.B. ; Gaskins, G.R. - \ 2003
    Antimicrobial Agents and Chemotherapy 47 (2003)10. - ISSN 0066-4804 - p. 3311 - 3317.
    gradient gel-electrophoresis - broiler-chickens - resistance - fragments - community - sediments - growth - diets - flora - drugs
    Necrotic enteritis (NE) is a worldwide poultry disease caused by the alpha toxin-producing bacterium Clostridium perfringens. Disease risk factors include concurrent coccidial infection and the dietary use of cereal grains high in nonstarch polysaccharides (NSP), such as wheat, barley, rye, and oats. Outbreaks of NE can be prevented or treated by the use of in-feed antibiotics. However, the current debate regarding the prophylactic use of antibiotics in animal diets necessitates a better understanding of factors that influence intestinal colonization by C. perfringens as well as the pathophysiological consequences of its growth. We report a study with a chick model of NE, which used molecular (16S rRNA gene [16S rDNA]) and culture-based microbiological techniques to investigate the impact of the macrolide antibiotic tylosin phosphate (100 ppm) and a dietary NSP (pectin) on the community structure of the small intestinal microbiota relative to colonization by C. perfringens. The effects of tylosin and pectin on mucolytic activity of the microbiota and C. perfringens colonization and their relationship to pathological indices of NE were of particular interest. The data demonstrate that tylosin reduced the percentage of mucolytic bacteria in general and the concentration of C. perfringens in particular, and these responses correlated in a temporal fashion with a reduction in the occurrence of NE lesions and an improvement in barrier function. The presence of pectin did not significantly affect the variables measured. Thus, it appears that tylosin can control NE through its modulation of C. perfringens colonization and the mucolytic activity of the intestinal microbiota.
    Voluntary agreements as a form of deregulation? The Dutch experience.
    Liefferink, D. ; Mol, A.P.J. - \ 1998
    In: Deregulation in the European Union: environmental perspectives / Collier, U., London : Routledge - p. 181 - 197.
    Multiple radar estimation of rainfall: Perspectives for hydrological purposes.
    Uijlenhoet, R. ; Stricker, J.N.M. ; Russchenberg, H.W.J. ; Wessels, H.R.A. - \ 1994
    In: COST 75 weather radar systems, C.G. Collier (ed.). EC, Luxembourg - p. 701 - 712.
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