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.

    Erratum to: The sponge microbiome project
    Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2018
    GigaScience 7 (2018)12. - ISSN 2047-217X
    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.

    Plant functional trait change across a warming tundra biome
    Bjorkman, Anne D. ; Myers-Smith, Isla H. ; Elmendorf, Sarah C. ; Normand, Signe ; Rüger, Nadja ; Beck, Pieter S.A. ; Blach-Overgaard, Anne ; Blok, Daan ; Cornelissen, J.H.C. ; Forbes, Bruce C. ; Georges, Damien ; Goetz, Scott J. ; Guay, Kevin C. ; Henry, Gregory H.R. ; Hillerislambers, Janneke ; Hollister, Robert D. ; Karger, Dirk N. ; Kattge, Jens ; Manning, Peter ; Prevéy, Janet S. ; Rixen, Christian ; Schaepman-Strub, Gabriela ; Thomas, Haydn J.D. ; Vellend, Mark ; Wilmking, Martin ; Wipf, Sonja ; Carbognani, Michele ; Hermanutz, Luise ; Lévesque, Esther ; Molau, Ulf ; Petraglia, Alessandro ; Soudzilovskaia, Nadejda A. ; Spasojevic, Marko J. ; Tomaselli, Marcello ; Vowles, Tage ; Alatalo, Juha M. ; Alexander, Heather D. ; Anadon-Rosell, Alba ; Angers-Blondin, Sandra ; Beest, Mariska te; Berner, Logan ; Björk, Robert G. ; Buchwal, Agata ; Buras, Allan ; Christie, Katherine ; Heijmans, Monique M.P.D. ; Ozinga, Wim A. - \ 2018
    Nature 526 (2018). - ISSN 0028-0836 - p. 57 - 62.
    The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature–trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming.
    Considerations and consequences of allowing DNA sequence data as types of fungal taxa
    Zamora, Juan Carlos ; Svensson, Måns ; Kirschner, Roland ; Olariaga, Ibai ; Ryman, Svengunnar ; Parra, Luis Alberto ; Geml, József ; Rosling, Anna ; Adamčík, Slavomír ; Ahti, Teuvo ; Aime, M.C. ; Ainsworth, A.M. ; Albert, László ; Albertó, Edgardo ; García, Alberto Altés ; Ageev, Dmitry ; Agerer, Reinhard ; Aguirre-Hudson, Begoña ; Ammirati, Joe ; Andersson, Harry ; Angelini, Claudio ; Antonín, Vladimír ; Aoki, Takayuki ; Aptroot, André ; Argaud, Didier ; Sosa, Blanca Imelda Arguello ; Aronsen, Arne ; Arup, Ulf ; Asgari, Bita ; Assyov, Boris ; Atienza, Violeta ; Bandini, Ditte ; Baptista-Ferreira, João Luís ; Baral, Hans-Otto ; Baroni, Tim ; Barreto, Robert Weingart ; Beker, Henry ; Bell, Ann ; Bellanger, Jean-Michel ; Bellù, Francesco ; Bemmann, Martin ; Bendiksby, Mika ; Bendiksen, Egil ; Bendiksen, Katriina ; Benedek, Lajos ; Bérešová-Guttová, Anna ; Berger, Franz ; Berndt, Reinhard ; Bernicchia, Annarosa ; Biketova, Alona Yu. ; Bizio, Enrico ; Bjork, Curtis ; Boekhout, Teun ; Boertmann, David ; Böhning, Tanja ; Boittin, Florent ; Boluda, Carlos G. ; Boomsluiter, Menno W. ; Borovička, Jan ; Brandrud, Tor Erik ; Braun, Uwe ; Brodo, Irwin ; Bulyonkova, Tatiana ; Burdsall, Harold H. ; Buyck, Bart ; Burgaz, Ana Rosa ; Calatayud, Vicent ; Callac, Philippe ; Campo, Emanuele ; Candusso, Massimo ; Capoen, Brigitte ; Carbó, Joaquim ; Carbone, Matteo ; Castañeda-ruiz, Rafael F. ; Castellano, Michael A. ; Chen, Jie ; Clerc, Philippe ; Consiglio, Giovanni ; Corriol, Gilles ; Courtecuisse, Régis ; Crespo, Ana ; Cripps, Cathy ; Crous, Pedro W. ; Silva, Gladstone Alves Da ; Silva, Meiriele Da ; Dam, Marjo ; Dam, Nico ; Dämmrich, Frank ; Das, Kanad ; Davies, Linda ; Crop, Eske De; Kesel, Andre De; Kuijper, T.W.M. - \ 2018
    IMA fungus 9 (2018)1. - ISSN 2210-6340 - p. 167 - 185.
    Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
    The sponge microbiome project
    Moitinho-Silva, Lucas ; Nielsen, Shaun ; Amir, Amnon ; Gonzalez, Antonio ; Ackermann, Gail L. ; Cerrano, Carlo ; Astudillo-Garcia, Carmen ; Easson, Cole ; Sipkema, Detmer ; Liu, Fang ; Steinert, Georg ; Kotoulas, Giorgos ; McCormack, Grace P. ; Feng, Guofang ; Bell, James J. ; Vicente, Jan ; Björk, Johannes R. ; Montoya, Jose M. ; Olson, Julie B. ; Reveillaud, Julie ; Steindler, Laura ; Pineda, Mari Carmen ; Marra, Maria V. ; Ilan, Micha ; Taylor, Michael W. ; Polymenakou, Paraskevi ; Erwin, Patrick M. ; Schupp, Peter J. ; Simister, Rachel L. ; Knight, Rob ; Thacker, Robert W. ; Costa, Rodrigo ; Hill, Russell T. ; Lopez-Legentil, Susanna ; Dailianis, Thanos ; Ravasi, Timothy ; Hentschel, Ute ; Li, Zhiyong ; Webster, Nicole S. ; Thomas, Torsten - \ 2017
    GigaScience 6 (2017)10. - ISSN 2047-217X
    16S rRNA gene - Archaea - Bacteria - Marine sponges - Microbial diversity - Microbiome - Symbiosis
    Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.
    Sustaining creative entrepreneurship: The role of innovation systems
    Huijbens, Edward H. ; Hjalager, Anne Mette ; Björk, Peter ; Nordin, Sara ; Flagestad, Arvid - \ 2009
    In: Tourism and Entrepreneurship Butterworth-Heinemann - ISBN 9780080942728 - p. 55 - 74.
    Use of coupled models to predict biodiversity in managed ecosystems
    Dobben, H. van; Wamelink, W. ; Schouwenberg, E. ; Mol, J. - \ 2002
    In: Proceedings of the SUFOR International Workshop : Sustainable Forestry in Temperate Regions, Lund, Sweden: April 7-9, 2002 / Bjork, L., Lund, Sweden : LUND University - p. 76 - 85.
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