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 root traits (GRooT) database
    Guerrero-Ramírez, Nathaly R. ; Mommer, Liesje ; Freschet, Grégoire T. ; Iversen, Colleen M. ; McCormack, M.L. ; Kattge, Jens ; Poorter, Hendrik ; Plas, Fons van der; Bergmann, Joana ; Kuyper, Thom W. ; York, Larry M. ; Bruelheide, Helge ; Laughlin, Daniel C. ; Meier, Ina C. ; Roumet, Catherine ; Semchenko, Marina ; Sweeney, Christopher J. ; Ruijven, Jasper van; Valverde-Barrantes, Oscar J. ; Aubin, Isabelle ; Catford, Jane A. ; Manning, Peter ; Martin, Adam ; Milla, Rubén ; Minden, Vanessa ; Pausas, Juli G. ; Smith, Stuart W. ; Soudzilovskaia, Nadejda A. ; Ammer, Christian ; Butterfield, Bradley ; Craine, Joseph ; Cornelissen, Johannes H.C. ; Vries, Franciska T. de; Isaac, Marney E. ; Kramer, Koen ; König, Christian ; Lamb, Eric G. ; Onipchenko, Vladimir G. ; Peñuelas, Josep ; Reich, Peter B. ; Rillig, Matthias C. ; Sack, Lawren ; Shipley, Bill ; Tedersoo, Leho ; Valladares, Fernando ; Bodegom, Peter van; Weigelt, Patrick ; Wright, Justin P. ; Weigelt, Alexandra - \ 2020
    Global Ecology and Biogeography (2020). - ISSN 1466-822X
    Belowground ecology - functional biogeography - macroecological studies - plant form and function - publicly-available database - root traits

    Motivation: Trait data are fundamental to the quantitative description of plant form and function. Although root traits capture key dimensions related to plant responses to changing environmental conditions and effects on ecosystem processes, they have rarely been included in large-scale comparative studies and global models. For instance, root traits remain absent from nearly all studies that define the global spectrum of plant form and function. Thus, to overcome conceptual and methodological roadblocks preventing a widespread integration of root trait data into large-scale analyses we created the Global Root Trait (GRooT) Database. GRooT provides ready-to-use data by combining the expertise of root ecologists with data mobilization and curation. Specifically, we (a) determined a set of core root traits relevant to the description of plant form and function based on an assessment by experts, (b) maximized species coverage through data standardization within and among traits, and (c) implemented data quality checks. Main types of variables contained: GRooT contains 114,222 trait records on 38 continuous root traits. Spatial location and grain: Global coverage with data from arid, continental, polar, temperate and tropical biomes. Data on root traits were derived from experimental studies and field studies. Time period and grain: Data were recorded between 1911 and 2019. Major taxa and level of measurement: GRooT includes root trait data for which taxonomic information is available. Trait records vary in their taxonomic resolution, with subspecies or varieties being the highest and genera the lowest taxonomic resolution available. It contains information for 184 subspecies or varieties, 6,214 species, 1,967 genera and 254 families. Owing to variation in data sources, trait records in the database include both individual observations and mean values. Software format: GRooT includes two csv files. A GitHub repository contains the csv files and a script in R to query the database.

    Towards an integrative understanding of soil biodiversity
    Thakur, Madhav P. ; Phillips, Helen R.P. ; Brose, Ulrich ; Vries, Franciska T. De; Lavelle, Patrick ; Loreau, Michel ; Mathieu, Jerome ; Mulder, Christian ; Putten, Wim H. Van der; Rillig, Matthias C. ; Wardle, David A. ; Bach, Elizabeth M. ; Bartz, Marie L.C. ; Bennett, Joanne M. ; Briones, Maria J.I. ; Brown, George ; Decaëns, Thibaud ; Eisenhauer, Nico ; Ferlian, Olga ; Guerra, Carlos António ; König-Ries, Birgitta ; Orgiazzi, Alberto ; Ramirez, Kelly S. ; Russell, David J. ; Rutgers, Michiel ; Wall, Diana H. ; Cameron, Erin K. - \ 2020
    Biological Reviews 95 (2020)2. - ISSN 1464-7931 - p. 350 - 364.
    alpha diversity - beta diversity - biodiversity theory - metacommunity theory - neutral theory - niche theory - spatial scale - species–energy relationship - theory of island biogeography

    Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species–energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity.

    Global distribution of earthworm diversity
    Phillips, Helen R.P. ; Guerra, Carlos A. ; Bartz, Marie L.C. ; Briones, Maria J.I. ; Brown, George ; Crowther, Thomas W. ; Ferlian, Olga ; Gongalsky, Konstantin B. ; Hoogen, Johan Van Den; Krebs, Julia ; Orgiazzi, Alberto ; Routh, Devin ; Schwarz, Benjamin ; Bach, Elizabeth M. ; Bennett, Joanne ; Brose, Ulrich ; Decaëns, Thibaud ; König-Ries, Birgitta ; Loreau, Michel ; Mathieu, Jérôme ; Mulder, Christian ; Putten, Wim H. Van Der; Ramirez, Kelly S. ; Rillig, Matthias C. ; Russell, David ; Rutgers, Michiel ; Thakur, Madhav P. ; Vries, Franciska T. De; Wall, Diana H. ; Wardle, David A. ; Arai, Miwa ; Ayuke, Fredrick O. ; Baker, Geoff H. ; Beauséjour, Robin ; Bedano, José C. ; Birkhofer, Klaus ; Blanchart, Eric ; Blossey, Bernd ; Bolger, Thomas ; Bradley, Robert L. ; Callaham, Mac A. ; Capowiez, Yvan ; Caulfield, Mark E. ; Choi, Amy ; Crotty, Felicity V. ; Dávalos, Andrea ; Diaz Cosin, Darío J. ; Dominguez, Anahí ; Duhour, Andrés Esteban ; Eekeren, Nick Van; Emmerling, Christoph ; Falco, Liliana B. ; Fernández, Rosa ; Fonte, Steven J. ; Fragoso, Carlos ; Franco, André L.C. ; Fugère, Martine ; Fusilero, Abegail T. ; Gholami, Shaieste ; Gundale, Michael J. ; Gutiérrez Lopez, Monica ; Hackenberger, Davorka K. ; Hernández, Luis M. ; Hishi, Takuo ; Holdsworth, Andrew R. ; Holmstrup, Martin ; Hopfensperger, Kristine N. ; Lwanga, Esperanza Huerta ; Huhta, Veikko ; Hurisso, Tunsisa T. ; Iannone, Basil V. ; Iordache, Madalina ; Joschko, Monika ; Kaneko, Nobuhiro ; Kanianska, Radoslava ; Keith, Aidan M. ; Kelly, Courtland A. ; Kernecker, Maria L. ; Klaminder, Jonatan ; Koné, Armand W. ; Kooch, Yahya ; Kukkonen, Sanna T. ; Lalthanzara, H. ; Lammel, Daniel R. ; Lebedev, Iurii M. ; Li, Yiqing ; Jesus Lidon, Juan B. ; Lincoln, Noa K. ; Loss, Scott R. ; Marichal, Raphael ; Matula, Radim ; Moos, Jan Hendrik ; Moreno, Gerardo ; Mor n-Ríos, Alejandro ; Muys, Bart ; Neirynck, Johan ; Norgrove, Lindsey ; Novo, Marta ; Nuutinen, Visa ; Nuzzo, Victoria ; Mujeeb Rahman, P. ; Pansu, Johan ; Paudel, Shishir ; Pérès, Guénola ; Pérez-Camacho, Lorenzo ; Piñeiro, Raúl ; Ponge, Jean François ; Rashid, Muhammad Imtiaz ; Rebollo, Salvador ; Rodeiro-Iglesias, Javier ; Rodríguez, Miguel ; Roth, Alexander M. ; Rousseau, Guillaume X. ; Rozen, Anna ; Sayad, Ehsan ; Schaik, Loes Van; Scharenbroch, Bryant C. ; Schirrmann, Michael ; Schmidt, Olaf ; Schröder, Boris ; Seeber, Julia ; Shashkov, Maxim P. ; Singh, Jaswinder ; Smith, Sandy M. ; Steinwandter, Michael ; Talavera, José A. ; Trigo, Dolores ; Tsukamoto, Jiro ; Valença, Anne W. De; Vanek, Steven J. ; Virto, Iñigo ; Wackett, Adrian A. ; Warren, Matthew W. ; Wehr, Nathaniel H. ; Whalen, Joann K. ; Wironen, Michael B. ; Wolters, Volkmar ; Zenkova, Irina V. ; Zhang, Weixin ; Cameron, Erin K. ; Eisenhauer, Nico - \ 2019
    Science 366 (2019)6464. - ISSN 0036-8075 - p. 480 - 485.

    Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.

    Priorities for research in soil ecology
    Eisenhauer, Nico ; Antunes, Pedro M. ; Bennett, Alison E. ; Birkhofer, Klaus ; Bissett, Andrew ; Bowker, Matthew A. ; Caruso, Tancredi ; Chen, Baodong ; Coleman, David C. ; Boer, Wietse de; Ruiter, Peter de; DeLuca, Thomas H. ; Frati, Francesco ; Griffiths, Bryan S. ; Hart, Miranda M. ; Hättenschwiler, Stephan ; Haimi, Jari ; Heethoff, Michael ; Kaneko, Nobuhiro ; Kelly, Laura C. ; Leinaas, Hans Petter ; Lindo, Zoë ; Macdonald, Catriona ; Rillig, Matthias C. ; Ruess, Liliane ; Scheu, Stefan ; Schmidt, Olaf ; Seastedt, Timothy R. ; Straalen, Nico M. van; Tiunov, Alexei V. ; Zimmer, Martin ; Powell, Jeff R. - \ 2017
    Pedobiologia 63 (2017). - ISSN 0031-4056 - p. 1 - 7.
    Aboveground-belowground interactions - Biodiversity–ecosystem functioning - Biogeography - Chemical ecology - Climate change - Ecosystem services - Global change - Microbial ecology - Novel environments - Plant-microbe interactions - Soil biodiversity - Soil food web - Soil management - Soil processes
    The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia – Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia. The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.
    Where less may be more: how the rare biosphere pulls ecosystems strings
    Jousset, A. ; Bienhold, C. ; Chatzinotas, A. ; Gallien, L. ; Gobet, A. ; Kurm, V. ; Küsel, K. ; Rillig, M.C. ; Rivett, D.W. ; Salles, J.F. ; Heijden, M.G.A. van der; Youssef, N.H. ; Zhang, X.W. ; Wei, Z. ; Hol, W.H.G. - \ 2017
    ISME Journal 11 (2017)4. - ISSN 1751-7362 - p. 853 - 862.
    Rare species are increasingly recognized as crucial, yet vulnerable components of Earth’s ecosystems. This is also true for microbial communities, which are typically composed of a high number of relatively rare species. Recent studies have demonstrated that rare species can have an over-proportional role in biogeochemical cycles and may be a hidden driver of microbiome function. In this review, we provide an ecological overview of the rare microbial biosphere, including causes of rarity and the impacts of rare species on ecosystem functioning. We discuss how rare species can have a preponderant role for local biodiversity and species turnover with rarity potentially bound to phylogenetically conserved features. Rare microbes may therefore be overlooked keystone species regulating the functioning of host-associated, terrestrial and aquatic environments. We conclude this review with recommendations to guide scientists interested in investigating this rapidly emerging research area.
    Toward a global platform for linking soil biodiversity data
    Ramirez, K.S. ; Döring, M. ; Eisenhauer, N. ; Gardi, C. ; Ladau, J. ; Leff, J.W. ; Lentendu, G. ; Lindo, Z. ; Rillig, M.C. ; Russell, D. ; Scheu, S. ; John, M. ; Vries, F.T. de; Wubet, T. ; Putten, W.H. van der; Wall, D.H. - \ 2015
    Frontiers in Ecology and Evolution 3 (2015). - ISSN 2296-701X - 7 p.
    Soil biodiversity is immense, with an estimated 10–100 million organisms belonging to over 5000 taxa in a handful of soil. In spite of the importance of soil biodiversity for ecosystem functions and services, information on soil species, from taxonomy to biogeographical patterns, is incomplete and there is no infrastructure to connect pre-existing or future data. Here, we propose a global platform to allow for greater access to soil biodiversity information by linking databases and repositories through a single open portal. The proposed platform would for the first time, link data on soil organisms from different global sites and biomes, and will be inclusive of all data types, from molecular sequences to morphology measurements and other supporting information. Access to soil biodiversity species records and information will be instrumental to progressing scientific research and education. Further, as demonstrated by previous biodiversity synthesis efforts, data availability is key for adapting to, and creating mitigation plans in response to global changes. With the rapid influx of soil biodiversity data, now is the time to take the first steps forward in establishing a global soil biodiversity information platform.
    Mycorrhizal responses to biochar in soil-concepts and mechanisms.
    Warnock, D.D. ; Lehmann, J. ; Kuyper, T.W. ; Rillig, M.C. - \ 2007
    Plant and Soil 300 (2007)1-2. - ISSN 0032-079X - p. 9 - 20.
    arbuscular mycorrhizae - chemical-properties - helper bacteria - ectomycorrhiza formation - carbon sequestration - charcoal production - ecosystem processes - western montana - ponderosa pine - black carbon
    Experiments suggest that biomass-derived black carbon (biochar) affects microbial populations and soil biogeochemistry. Both biochar and mycorrhizal associations, ubiquitous symbioses in terrestrial ecosystems, are potentially important in various ecosystem services provided by soils, contributing to sustainable plant production, ecosystem restoration, and soil carbon sequestration and hence mitigation of global climate change. As both biochar and mycorrhizal associations are subject to management, understanding and exploiting interactions between them could be advantageous. Here we focus on biochar effects on mycorrhizal associations. After reviewing the experimental evidence for such effects, we critically examine hypotheses pertaining to four mechanisms by which biochar could influence mycorrhizal abundance and/or functioning. These mechanisms are (in decreasing order of currently available evidence supporting them): (a) alteration of soil physico-chemical properties; (b) indirect effects on mycorrhizae through effects on other soil microbes; (c) plant¿fungus signaling interference and detoxification of allelochemicals on biochar; and (d) provision of refugia from fungal grazers. We provide a roadmap for research aimed at testing these mechanistic hypotheses.
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