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 results of biodiversity–ecosystem functioning experiments are realistic
    Jochum, Malte ; Fischer, Markus ; Isbell, Forest ; Roscher, Christiane ; Plas, Fons van der; Boch, Steffen ; Boenisch, Gerhard ; Buchmann, Nina ; Catford, Jane A. ; Cavender-Bares, Jeannine ; Ebeling, Anne ; Eisenhauer, Nico ; Gleixner, Gerd ; Hölzel, Norbert ; Kattge, Jens ; Klaus, Valentin H. ; Kleinebecker, Till ; Lange, Markus ; Provost, Gaëtane Le; Meyer, Sebastian T. ; Molina-Venegas, Rafael ; Mommer, Liesje ; Oelmann, Yvonne ; Penone, Caterina ; Prati, Daniel ; Reich, Peter B. ; Rindisbacher, Abiel ; Schäfer, Deborah ; Scheu, Stefan ; Schmid, Bernhard ; Tilman, David ; Tscharntke, Teja ; Vogel, Anja ; Wagg, Cameron ; Weigelt, Alexandra ; Weisser, Wolfgang W. ; Wilcke, Wolfgang ; Manning, Peter - \ 2020
    Nature Ecology & Evolution (2020). - ISSN 2397-334X

    A large body of research shows that biodiversity loss can reduce ecosystem functioning. However, much of the evidence for this relationship is drawn from biodiversity–ecosystem functioning experiments in which biodiversity loss is simulated by randomly assembling communities of varying species diversity, and ecosystem functions are measured. This random assembly has led some ecologists to question the relevance of biodiversity experiments to real-world ecosystems, where community assembly or disassembly may be non-random and influenced by external drivers, such as climate, soil conditions or land use. Here, we compare data from real-world grassland plant communities with data from two of the largest and longest-running grassland biodiversity experiments (the Jena Experiment in Germany and BioDIV in the United States) in terms of their taxonomic, functional and phylogenetic diversity and functional-trait composition. We found that plant communities of biodiversity experiments cover almost all of the multivariate variation of the real-world communities, while also containing community types that are not currently observed in the real world. Moreover, they have greater variance in their compositional features than their real-world counterparts. We then re-analysed a subset of experimental data that included only ecologically realistic communities (that is, those comparable to real-world communities). For 10 out of 12 biodiversity–ecosystem functioning relationships, biodiversity effects did not differ significantly between the full dataset of biodiversity experiments and the ecologically realistic subset of experimental communities. Although we do not provide direct evidence for strong or consistent biodiversity–ecosystem functioning relationships in real-world communities, our results demonstrate that the results of biodiversity experiments are largely insensitive to the exclusion of unrealistic communities and that the conclusions drawn from biodiversity experiments are generally robust.

    Decomposition of leaf litter mixtures across biomes : The role of litter identity, diversity and soil fauna
    Zhou, Shixing ; Butenschoen, Olaf ; Barantal, Sandra ; Handa, Ira Tanya ; Makkonen, Marika ; Vos, Veronique ; Aerts, Rien ; Berg, Matty P. ; McKie, Brendan ; Ruijven, Jasper Van; Hättenschwiler, Stephan ; Scheu, Stefan - \ 2020
    Journal of Ecology (2020). - ISSN 0022-0477
    litter diversity - litter identity - litter traits - mass loss - microarthropods - plant–soil (below-ground) interactions - soil fauna

    At broad spatial scales, the factors regulating litter decomposition remain ambiguous, with the understanding of these factors largely based on studies investigating site-specific single litter species, whereas studies using multi litter species mixtures across sites are rare. We exposed in microcosms containing single species and all possible mixtures of four leaf litter species differing widely in initial chemical and physical characteristics from a temperate forest to the climatic conditions of four different forests across the Northern Hemisphere for 1 year. Calcium, magnesium and condensed tannins predicted litter mass loss of single litter species and mixtures across forest types and biomes, regardless of species richness and microarthropod presence. However, relative mixture effects differed among forest types and varied with the access to the litter by microarthropods. Access to the microcosms by microarthropods modified the decomposition of individual litter species within mixtures, which differed among forest types independent of litter species richness and composition of litter mixtures. However, soil microarthropods generally only little affected litter decomposition. Synthesis. We conclude that litter identity is the dominant driver of decomposition across different forest types and the non-additive litter mixture effects vary among biomes despite identical leaf litter chemistry. These results suggest that across large spatial scales the environmental context of decomposing litter mixtures, including microarthropod communities, determine the decomposition of litter mixtures besides strong litter trait-based effects.

    A global database of soil nematode abundance and functional group composition
    Hoogen, Johan van den; Geisen, Stefan ; Wall, Diana H. ; Wardle, David A. ; Traunspurger, Walter ; Goede, Ron G.M. de; Adams, Byron J. ; Ahmad, Wasim ; Ferris, Howard ; Bardgett, Richard D. ; Bonkowski, Michael ; Campos-Herrera, Raquel ; Cares, Juvenil E. ; Caruso, Tancredi ; Brito Caixeta, Larissa de; Chen, Xiaoyun ; Costa, Sofia R. ; Creamer, Rachel ; Cunha e Castro, José Mauro da; Dam, Marie ; Djigal, Djibril ; Escuer, Miguel ; Griffiths, Bryan S. ; Gutiérrez, Carmen ; Hohberg, Karin ; Kalinkina, Daria ; Kardol, Paul ; Kergunteuil, Alan ; Korthals, Gerard ; Krashevska, Valentyna ; Kudrin, Alexey A. ; Li, Qi ; Liang, Wenju ; Magilton, Matthew ; Marais, Mariette ; Martín, José Antonio Rodríguez ; Matveeva, Elizaveta ; Mayad, El Hassan ; Mzough, E. ; Mulder, Christian ; Mullin, Peter ; Neilson, Roy ; Nguyen, Duong T.A. ; Nielsen, Uffe N. ; Okada, Hiroaki ; Rius, Juan Emilio Palomares ; Pan, Kaiwen ; Peneva, Vlada ; Pellissier, Loïc ; Silva, Julio Carlos Pereira da; Pitteloud, Camille ; Powers, Thomas O. ; Powers, Kirsten ; Quist, Casper W. ; Rasmann, Sergio ; Moreno, Sara Sánchez ; Scheu, Stefan ; Setälä, Heikki ; Sushchuk, Anna ; Tiunov, Alexei V. ; Trap, Jean ; Vestergård, Mette ; Villenave, Cecile ; Waeyenberge, Lieven ; Wilschut, Rutger A. ; Wright, Daniel G. ; Keith, Aidan M. ; Yang, Jiuein ; Schmidt, Olaf ; Bouharroud, R. ; Ferji, Z. ; Putten, Wim H. van der; Routh, Devin ; Crowther, Thomas W. - \ 2020
    Scientific Data 7 (2020)1. - ISSN 2052-4463

    As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.

    Biodiversity increases multitrophic energy use efficiency, flow and storage in grasslands
    Buzhdygan, Oksana Y. ; Meyer, Sebastian T. ; Weisser, Wolfgang W. ; Eisenhauer, Nico ; Ebeling, Anne ; Borrett, Stuart R. ; Buchmann, Nina ; Cortois, Roeland ; Deyn, Gerlinde B. De; Kroon, Hans de; Gleixner, Gerd ; Hertzog, Lionel R. ; Hines, Jes ; Lange, Markus ; Mommer, Liesje ; Ravenek, Janneke ; Scherber, Christoph ; Scherer-Lorenzen, Michael ; Scheu, Stefan ; Schmid, Bernhard ; Steinauer, Katja ; Strecker, Tanja ; Tietjen, Britta ; Vogel, Anja ; Weigelt, Alexandra ; Petermann, Jana S. - \ 2020
    Nature Ecology & Evolution 4 (2020)4. - ISSN 2397-334X - p. 393 - 405.

    The continuing loss of global biodiversity has raised questions about the risk that species extinctions pose for the functioning of natural ecosystems and the services that they provide for human wellbeing. There is consensus that, on single trophic levels, biodiversity sustains functions; however, to understand the full range of biodiversity effects, a holistic and multitrophic perspective is needed. Here, we apply methods from ecosystem ecology that quantify the structure and dynamics of the trophic network using ecosystem energetics to data from a large grassland biodiversity experiment. We show that higher plant diversity leads to more energy stored, greater energy flow and higher community-energy-use efficiency across the entire trophic network. These effects of biodiversity on energy dynamics were not restricted to only plants but were also expressed by other trophic groups and, to a similar degree, in aboveground and belowground parts of the ecosystem, even though plants are by far the dominating group in the system. The positive effects of biodiversity on one trophic level were not counteracted by the negative effects on adjacent levels. Trophic levels jointly increased the performance of the community, indicating ecosystem-wide multitrophic complementarity, which is potentially an important prerequisite for the provisioning of ecosystem services.

    Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
    Frantz, Laurent A.F. ; Haile, James ; Lin, Audrey T. ; Scheu, Amelie ; Geörg, Christina ; Benecke, Norbert ; Alexander, Michelle ; Linderholm, Anna ; Mullin, Victoria E. ; Daly, Kevin G. ; Battista, Vincent M. ; Price, Max ; Gron, Kurt J. ; Alexandri, Panoraia ; Arbogast, Rose Marie ; Arbuckle, Benjamin ; Bǎlǎşescu, Adrian ; Barnett, Ross ; Bartosiewicz, László ; Baryshnikov, Gennady ; Bonsall, Clive ; Borić, Dušan ; Boroneanţ, Adina ; Bulatović, Jelena ; Çakirlar, Canan ; Carretero, José Miguel ; Chapman, John ; Church, Mike ; Crooijmans, Richard ; Cupere, Bea De; Detry, Cleia ; Dimitrijevic, Vesna ; Dumitraşcu, Valentin ; Plessis, Louis Du; Edwards, Ceiridwen J. ; Erek, Cevdet Merih ; Erim-Özdoǧan, Asli ; Ervynck, Anton ; Fulgione, Domenico ; Gligor, Mihai ; Götherström, Anders ; Gourichon, Lionel ; Groenen, Martien A.M. ; Helmer, Daniel ; Hongo, Hitomi ; Horwitz, Liora K. ; Irving-Pease, Evan K. ; Lebrasseur, Ophélie ; Lesur, Joséphine ; Malone, Caroline ; Manaseryan, Ninna ; Marciniak, Arkadiusz ; Martlew, Holley ; Mashkour, Marjan ; Matthews, Roger ; Matuzeviciute, Giedre Motuzaite ; Maziar, Sepideh ; Meijaard, Erik ; McGovern, Tom ; Megens, Hendrik Jan ; Miller, Rebecca ; Mohaseb, Azadeh Fatemeh ; Orschiedt, Jörg ; Orton, David ; Papathanasiou, Anastasia ; Pearson, Mike Parker ; Pinhasi, Ron ; Radmanović, Darko ; Ricaut, François Xavier ; Richards, Mike ; Sabin, Richard ; Sarti, Lucia ; Schier, Wolfram ; Sheikhi, Shiva ; Stephan, Elisabeth ; Stewart, John R. ; Stoddart, Simon ; Tagliacozzo, Antonio ; Tasić, Nenad ; Trantalidou, Katerina ; Tresset, Anne ; Valdiosera, Cristina ; Hurk, Youri Van Den; Poucke, Sophie Van; Vigne, Jean Denis ; Yanevich, Alexander ; Zeeb-Lanz, Andrea ; Triantafyllidis, Alexandros ; Gilbert, M.T.P. ; Schibler, Jörg ; Rowley-Conwy, Peter ; Zeder, Melinda ; Peters, Joris ; Cucchi, Thomas ; Bradley, Daniel G. ; Dobney, Keith ; Burger, Joachim ; Evin, Allowen ; Girdland-Flink, Linus ; Larson, Greger - \ 2019
    Proceedings of the National Academy of Sciences of the United States of America 116 (2019)35. - ISSN 0027-8424 - p. 17231 - 17238.
    Domestication - Evolution - Gene flow - Neolithic

    Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

    Root chemistry and soil fauna, but not soil abiotic conditions explain the effects of plant diversity on root decomposition
    Chen, Hongmei ; Oram, Natalie J. ; Barry, Kathryn E. ; Mommer, Liesje ; Ruijven, Jasper van; Kroon, Hans de; Ebeling, Anne ; Eisenhauer, Nico ; Fischer, Christine ; Gleixner, Gerd ; Gessler, Arthur ; González Macé, Odette ; Hacker, Nina ; Hildebrandt, Anke ; Lange, Markus ; Scherer-lorenzen, Michael ; Scheu, Stefan ; Oelmann, Yvonne ; Wagg, Cameron ; Wilcke, Wolfgang ; Wirth, Christian ; Weigelt, Alexandra - \ 2017
    Oecologia 185 (2017)3. - ISSN 0029-8549 - p. 499 - 511.
    Functional groups - Jena Experiment - Root litter - SEM - Species richness
    Plant diversity influences many ecosystem functions including root decomposition. However, due to the presence of multiple pathways via which plant diversity may affect root decomposition, our mechanistic understanding of their relationships is limited. In a grassland biodiversity experiment, we simultaneously assessed the effects of three pathways—root litter quality, soil biota, and soil abiotic conditions—on the relationships between plant diversity (in terms of species richness and the presence/absence of grasses and legumes) and root decomposition using structural equation modeling. Our final structural equation model explained 70% of the variation in root mass loss. However, different measures of plant diversity included in our model operated via different pathways to alter root mass loss. Plant species richness had a negative effect on root mass loss. This was partially due to increased Oribatida abundance, but was weakened by enhanced root potassium (K) concentration in more diverse mixtures. Equally, grass presence negatively affected root mass loss. This effect of grasses was mostly mediated via increased root lignin concentration and supported via increased Oribatida abundance and decreased root K concentration. In contrast, legume presence showed a net positive effect on root mass loss via decreased root lignin concentration and increased root magnesium concentration, both of which led to enhanced root mass loss. Overall, the different measures of plant diversity had contrasting effects on root decomposition. Furthermore, we found that root chemistry and soil biota but not root morphology or soil abiotic conditions mediated these effects of plant diversity on root decomposition.
    Biodiversity effects on ecosystem functioning in a 15-year grassland experiment : Patterns, mechanisms, and open questions
    Weisser, Wolfgang ; Roscher, Christiane ; Meyer, Sebastian T. ; Ebeling, Anne ; Luo, Guangjuan ; Allan, Eric ; Beßler, Holger ; Barnard, Romain L. ; Buchmann, Nina ; Buscot, François ; Engels, Christof ; Fischer, Christine ; Fischer, Markus ; Gessler, Arthur ; Gleixner, Gerd ; Halle, Stefan ; Hildebrandt, Anke ; Hillebrand, Helmut ; Kroon, Hans de; Lange, Markus ; Leimer, Sophia ; Roux, Xavier Le; Milcu, Alexandru ; Mommer, Liesje ; Niklaus, Pascal A. ; Oelmann, Yvonne ; Proulx, Raphael ; Roy, Jacques ; Scherber, Christoph ; Scherer-lorenzen, Michael ; Scheu, Stefan ; Tscharntke, Teja ; Wachendorf, Michael ; Wagg, Cameron ; Weigelt, Alexandra ; Wilcke, Wolfgang ; Wirth, Christian ; Schulze, Ernst Detlef ; Schmid, Bernhard ; Eisenhauer, Nico - \ 2017
    Basic and Applied Ecology 23 (2017). - ISSN 1439-1791 - p. 1 - 73.
    Biomass - Carbon storage - Complementarity - Multi-trophic interactions - Nutrient cycling - Selection effect
    In the past two decades, a large number of studies have investigated the relationship between biodiversity and ecosystem functioning, most of which focussed on a limited set of ecosystem variables. The Jena Experiment was set up in 2002 to investigate the effects of plant diversity on element cycling and trophic interactions, using a multi-disciplinary approach. Here, we review the results of 15 years of research in the Jena Experiment, focussing on the effects of manipulating plant species richness and plant functional richness. With more than 85,000 measures taken from the plant diversity plots, the Jena Experiment has allowed answering fundamental questions important for functional biodiversity research.First, the question was how general the effect of plant species richness is, regarding the many different processes that take place in an ecosystem. About 45% of different types of ecosystem processes measured in the 'main experiment', where plant species richness ranged from 1 to 60 species, were significantly affected by plant species richness, providing strong support for the view that biodiversity is a significant driver of ecosystem functioning. Many measures were not saturating at the 60-species level, but increased linearly with the logarithm of species richness. There was, however, great variability in the strength of response among different processes. One striking pattern was that many processes, in particular belowground processes, took several years to respond to the manipulation of plant species richness, showing that biodiversity experiments have to be long-term, to distinguish trends from transitory patterns. In addition, the results from the Jena Experiment provide further evidence that diversity begets stability, for example stability against invasion of plant species, but unexpectedly some results also suggested the opposite, e.g. when plant communities experience severe perturbations or elevated resource availability. This highlights the need to revisit diversity-stability theory.Second, we explored whether individual plant species or individual plant functional groups, or biodiversity itself is more important for ecosystem functioning, in particular biomass production. We found strong effects of individual species and plant functional groups on biomass production, yet these effects mostly occurred in addition to, but not instead of, effects of plant species richness.Third, the Jena Experiment assessed the effect of diversity on multitrophic interactions. The diversity of most organisms responded positively to increases in plant species richness, and the effect was stronger for above- than for belowground organisms, and stronger for herbivores than for carnivores or detritivores. Thus, diversity begets diversity. In addition, the effect on organismic diversity was stronger than the effect on species abundances.Fourth, the Jena Experiment aimed to assess the effect of diversity on N, P and C cycling and the water balance of the plots, separating between element input into the ecosystem, element turnover, element stocks, and output from the ecosystem. While inputs were generally less affected by plant species richness, measures of element stocks, turnover and output were often positively affected by plant diversity, e.g. carbon storage strongly increased with increasing plant species richness. Variables of the N cycle responded less strongly to plant species richness than variables of the C cycle.Fifth, plant traits are often used to unravel mechanisms underlying the biodiversity-ecosystem functioning relationship. In the Jena Experiment, most investigated plant traits, both above- and belowground, were plastic and trait expression depended on plant diversity in a complex way, suggesting limitation to using database traits for linking plant traits to particular functions.Sixth, plant diversity effects on ecosystem processes are often caused by plant diversity effects on species interactions. Analyses in the Jena Experiment including structural equation modelling suggest complex interactions that changed with diversity, e.g. soil carbon storage and greenhouse gas emission were affected by changes in the composition and activity of the belowground microbial community. Manipulation experiments, in which particular organisms, e.g. belowground invertebrates, were excluded from plots in split-plot experiments, supported the important role of the biotic component for element and water fluxes.Seventh, the Jena Experiment aimed to put the results into the context of agricultural practices in managed grasslands. The effect of increasing plant species richness from 1 to 16 species on plant biomass was, in absolute terms, as strong as the effect of a more intensive grassland management, using fertiliser and increasing mowing frequency. Potential bioenergy production from high-diversity plots was similar to that of conventionally used energy crops. These results suggest that diverse 'High Nature Value Grasslands' are multifunctional and can deliver a range of ecosystem services including production-related services.A final task was to assess the importance of potential artefacts in biodiversity-ecosystem functioning relationships, caused by the weeding of the plant community to maintain plant species composition. While the effort (in hours) needed to weed a plot was often negatively related to plant species richness, species richness still affected the majority of ecosystem variables. Weeding also did not negatively affect monoculture performance; rather, monocultures deteriorated over time for a number of biological reasons, as shown in plant-soil feedback experiments.To summarize, the Jena Experiment has allowed for a comprehensive analysis of the functional role of biodiversity in an ecosystem. A main challenge for future biodiversity research is to increase our mechanistic understanding of why the magnitude of biodiversity effects differs among processes and contexts. It is likely that there will be no simple answer. For example, among the multitude of mechanisms suggested to underlie the positive plant species richness effect on biomass, some have received limited support in the Jena Experiment, such as vertical root niche partitioning. However, others could not be rejected in targeted analyses. Thus, from the current results in the Jena Experiment, it seems likely that the positive biodiversity effect results from several mechanisms acting simultaneously in more diverse communities, such as reduced pathogen attack, the presence of more plant growth promoting organisms, less seed limitation, and increased trait differences leading to complementarity in resource uptake. Distinguishing between different mechanisms requires careful testing of competing hypotheses. Biodiversity research has matured such that predictive approaches testing particular mechanisms are now possible.
    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.
    Data from: Root biomass and exudates link plant diversity with soil bacterial and fungal biomass
    Eisenhauer, Nico ; Strecker, Tanja ; Lanoue, Arnaud ; Scheu, Stefan ; Steinauer, Katja ; Thakur, Madhav P. ; Mommer, L. - \ 2017
    Wageningen University & Research
    plant diversity - root exudates - Soil microorganisms
    Plant diversity has been shown to determine the composition and functioning of soil biota. Although root-derived organic inputs are discussed as the main drivers of soil communities, experimental evidence is scarce. While there is some evidence that higher root biomass at high plant diversity increases substrate availability for soil biota, several studies have speculated that the quantity and diversity of root inputs into the soil, i.e. though root exudates, drive plant diversity effects on soil biota. Here we used a microcosm experiment to study the role of plant species richness on the biomass of soil bacteria and fungi as well as fungal-to-bacterial ratio via root biomass and root exudates. Plant diversity significantly increased shoot biomass, root biomass, the amount of root exudates, bacterial biomass, and fungal biomass. Fungal biomass increased most with increasing plant diversity resulting in a significant shift in the fungal-to-bacterial biomass ratio at high plant diversity. Fungal biomass increased significantly with plant diversity-induced increases in root biomass and the amount of root exudates. These results suggest that plant diversity enhances soil microbial biomass, particularly soil fungi, by increasing root-derived organic inputs.
    Possible mechanisms underlying abundance and diversity responses of nematode communities to plant diversity
    Cortois, R. ; Veen, G.F. ; Duyts, Henk ; Abbas, Maike ; Strecker, Tanja ; Kostenko, Olga ; Eisenhauer, Nico ; Scheu, Stefan ; Gleixner, Gerd ; Deyn, Gerlinde B. De; Putten, Wim H. van der - \ 2017
    Ecosphere 8 (2017)5. - ISSN 2150-8925
    C:N ratio - Functional diversity - Mechanistic linkages - Nematode diversity - Plant diversity - Plant-soil interaction - Resource quality - Resource quantity - Structural equation modeling

    Plant diversity is known to influence the abundance and diversity of belowground biota; however, patterns are not well predictable and there is still much unknown about the driving mechanisms. We analyzed changes in soil nematode community composition as affected by long-term manipulations of plant species and functional group diversity in a field experiment with plant species diversity controlled by sowing a range of 1-60 species mixtures and controlling non-sown species by hand weeding. Nematode communities contain a variety of species feeding on bacteria, fungi, plants, invertebrates, while some are omnivorous. We analyzed responses of nematode abundance and diversity to plant species and functional diversity, and used structural equation modeling (SEM) to explore the possible mechanisms underlying the observed patterns. The abundance of individuals of all nematode feeding types, except for predatory nematodes, increased with both plant species and plant functional group diversity. The abundance of microbial-feeding nematodes was related positively to aboveground plant community biomass, whereas abundance of plant-feeding nematodes was related positively to shoot C:N ratio. The abundance of predatory nematodes, in turn, was positively related to numbers of plant-feeding nematodes, but not to the abundance of microbial feeders. Interestingly, the numbers of plant-feeding nematodes per unit root mass were lowest in the high-diversity plant communities, pointing at reduced exposure to belowground herbivores when plants grow in species-diverse communities. Taxon richness of plant-feeding and microbialfeeding nematodes increased with plant species and plant functional group diversity. Increasing plant functional group diversity also enhanced taxon richness of predatory nematodes. The SEM suggests that bottom-up control effects of plant species and plant functional group diversity on abundance of nematodes in the various feeding types predominantly involve mechanistic linkages related to plant quality instead of plant quantity; especially, C:N ratios of the shoot tissues, and/or effects of plants on the soil habitat, rather than shoot quantity explained nematode abundance. Although aboveground plant properties may only partly serve as a proxy for belowground resource quality and quantity, our results encourage further studies on nematode responses to variations in plant species and plant functional diversity in relation to both quantity and quality of the belowground resources.

    Root biomass and exudates link plant diversity with soil bacterial and fungal biomass
    Eisenhauer, Nico ; Lanoue, Arnaud ; Strecker, Tanja ; Scheu, Stefan ; Steinauer, Katja ; Thakur, Madhav P. ; Mommer, Liesje - \ 2017
    Scientific Reports 7 (2017). - ISSN 2045-2322
    Plant diversity has been shown to determine the composition and functioning of soil biota. Although root-derived organic inputs are discussed as the main drivers of soil communities, experimental evidence is scarce. While there is some evidence that higher root biomass at high plant diversity increases substrate availability for soil biota, several studies have speculated that the quantity and diversity of root inputs into the soil, i.e.Though root exudates, drive plant diversity effects on soil biota. Here we used a microcosm experiment to study the role of plant species richness on the biomass of soil bacteria and fungi as well as fungal-To-bacterial ratio via root biomass and root exudates. Plant diversity significantly increased shoot biomass, root biomass, the amount of root exudates, bacterial biomass, and fungal biomass. Fungal biomass increased most with increasing plant diversity resulting in a significant shift in the fungal-To-bacterial biomass ratio at high plant diversity. Fungal biomass increased significantly with plant diversity-induced increases in root biomass and the amount of root exudates. These results suggest that plant diversity enhances soil microbial biomass, particularly soil fungi, by increasing root-derived organic inputs.
    Global soil biodiversity atlas
    Orgiazzi, A. ; Bardgett, R.D. ; Barrios, E. ; Behan-Pelletier, V. ; Briones, M.J.I. ; Chotte, J.L. ; Deyn, G.B. de; Eggleton, P. ; Fierer, N. ; Fraser, T. ; Hedlund, K. ; Jeffery, S. ; Johnson, N.C. ; Jones, A. ; Kandeler, E. ; Kaneko, N. ; Lavelle, P. ; Lemanceau, P. ; Miko, L. ; Montanarella, L. ; Moreira, F.M.S. ; Ramirez, K.S. ; Scheu, S. ; Singh, B.K. ; Six, J. ; Putten, W.H. van der; Wall, D.H. - \ 2016
    Luxembourg : European Union (EUR ) - ISBN 9789279481697 - 176
    Chapter Four : Towards an Integration of Biodiversity–Ecosystem Functioning and Food Web Theory to Evaluate Relationships between Multiple Ecosystem Services
    Hines, J. ; Putten, W.H. van der; Deyn, G.B. de; Wagg, C. ; Voigt, W. ; Mulder, C. ; Weisser, W.W. ; Engel, J. ; Melian, C. ; Scheu, S. ; Birkhofer, K. ; Ebeling, A. ; Scherber, C. ; Eisenhauer, N. - \ 2015
    Advances in Ecological Research 53 (2015). - ISSN 0065-2504 - p. 161 - 199.
    Ecosystem responses to changes in species diversity are often studied individually. However, changes in species diversity can simultaneously influence multiple interdependent ecosystem functions. Therefore, an important challenge is to determine when and how changes in species diversity that influence one function will also drive changes in other functions. By providing the underlying structure of species interactions, ecological networks can quantify connections between biodiversity and multiple ecosystem functions. Here, we review parallels in the conceptual development of biodiversity–ecosystem functioning (BEF) and food web theory (FWT) research. Subsequently, we evaluate three common principles that unite these two research areas by explaining the patterns, concentrations, and direction of the flux of nutrients and energy through the species in diverse interaction webs. We give examples of combined BEF–FWT approaches that can be used to identify vulnerable species and habitats and to evaluate links that drive trade-offs between multiple ecosystems functions. These combined approaches reflect promising trends towards better management of biodiversity in landscapes that provide essential ecosystem services supporting human well-being.
    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.
    Plant diversity shapes microbe-rhizosphere effects on P mobilisation from organic matter in soil
    Hacker, N. ; Ebeling, A. ; Gessler, A. ; Gleixner, G. ; Gonzalez Mace, O. ; Kroon, H. de; Lange, M. ; Mommer, L. ; Eisenhauer, N. ; Ravenek, J. ; Scheu, S. ; Weigelt, A. ; Wagg, C. ; Wilcke, W. ; Oelmann, S. - \ 2015
    Ecology Letters 18 (2015)12. - ISSN 1461-023X - p. 1356 - 1365.
    Plant species richness (PSR) increases nutrient uptake which depletes bioavailable nutrient pools in soil. No such relationship between plant uptake and availability in soil was found for phosphorus (P). We explored PSR effects on P mobilisation [phosphatase activity (PA)] in soil. PA increased with PSR. The positive PSR effect was not solely due to an increase in Corg concentrations because PSR remained significant if related to PA:Corg. An increase in PA per unit Corg increases the probability of the temporal and spatial match between substrate, enzyme and microorganism potentially serving as an adaption to competition. Carbon use efficiency of microorganisms (Cmic:Corg) increased with increasing PSR while enzyme exudation efficiency (PA:Cmic) remained constant. These findings suggest the need for efficient C rather than P cycling underlying the relationship between PSR and PA. Our results indicate that the coupling between C and P cycling in soil becomes tighter with increasing PSR.
    Plant species diversity affects infiltration capacity in an experimental grassland through changes in soil properties
    Fischer, C. ; Tischer, J. ; Roscher, C. ; Eisenhauer, N. ; Ravenek, J. ; Gleixner, G. ; Attinger, S. ; Jensen, B. ; Kroon, H. de; Mommer, L. ; Scheu, S. ; Hildebrandt, A. - \ 2015
    Plant and Soil 397 (2015)1. - ISSN 0032-079X - p. 1 - 16.
    Background and aims Soil hydraulic properties drive water distribution and availability in soil. There exists limited knowledge of how plant species diversity might influence soil hydraulic properties. Methods We quantified the change in infiltration capacity affected by soil structural variables (soil bulk density, porosity and organic carbon content) along a gradient of soil texture, plant species richness (1, 2, 4, 8, 16 and 60)and functional group composition (grasses, legumes, small herbs, tall herbs). We conducted two infiltration measurement campaigns (May and October 2012) using a hood infiltrometer. Results Plant species richness significantly increased infiltration capacity in the studied grasslands. Both soil porosity (or inversely bulk density) and organic carbon played an important role in mediating the plant species richness effect. Soil texture did not correlate with infiltration capacity. In spring 2012, earthworm biomass increased infiltration capacity, but this effect could not be attributed to changes in soil structural variables. Conclusions We experimentally identified important ecological drivers of infiltration capacity, suggesting complex interactions between plant species richness, earthworms, and soil structural variables, while showing little impact of soil texture. Changes in plant species richness may thus have significant effects on soil hydraulic properties with potential consequences for surface run-off and soil erosion.
    Consequences of biodiversity loss for litter decomposition across biomes
    Handa, I.T. ; Aerts, R. ; Berendse, F. ; Berg, M.P. ; Butenschoen, O. ; Bruder, A. ; Chauvet, E. ; Gessner, M.O. ; Jabiol, J. ; Makkonen, M. ; McKie, B.G. ; Malmqvist, B. ; Peeters, E.T.H.M. ; Scheu, S. ; Schmid, B. ; Ruijven, J. van; Vos, V.C.A. ; Hattenschwiler, S. - \ 2014
    Nature 509 (2014). - ISSN 0028-0836 - p. 218 - 221.
    species functional diversity - leaf-litter - ecosystems - patterns - services - climate - traits
    The decomposition of dead organic matter is a major determinant of carbon and nutrient cycling in ecosystems, and of carbon fluxes between the biosphere and the atmosphere1, 2, 3. Decomposition is driven by a vast diversity of organisms that are structured in complex food webs2, 4. Identifying the mechanisms underlying the effects of biodiversity on decomposition is critical4, 5, 6 given the rapid loss of species worldwide and the effects of this loss on human well-being7, 8, 9. Yet despite comprehensive syntheses of studies on how biodiversity affects litter decomposition4, 5, 6, 10, key questions remain, including when, where and how biodiversity has a role and whether general patterns and mechanisms occur across ecosystems and different functional types of organism4, 9, 10, 11, 12. Here, in field experiments across five terrestrial and aquatic locations, ranging from the subarctic to the tropics, we show that reducing the functional diversity of decomposer organisms and plant litter types slowed the cycling of litter carbon and nitrogen. Moreover, we found evidence of nitrogen transfer from the litter of nitrogen-fixing plants to that of rapidly decomposing plants, but not between other plant functional types, highlighting that specific interactions in litter mixtures control carbon and nitrogen cycling during decomposition. The emergence of this general mechanism and the coherence of patterns across contrasting terrestrial and aquatic ecosystems suggest that biodiversity loss has consistent consequences for litter decomposition and the cycling of major elements on broad spatial scales.
    Divergent composition but similar function of soil food webs of individual plants: plant species and community effects
    Bezemer, T.M. ; Fountain, T. ; Barea, J.M. ; Christensen, S. ; Dekker, S.C. ; Duyts, H. ; Hal, R. van; Harvey, J.A. ; Hedlund, K. ; Maraun, M. ; Mikola, J. ; Mladenov, A.G. ; Robin, C. ; Ruiter, P.C. de; Scheu, H. ; Setälä, S. ; šmilauer, P. ; Putten, W.H. van der - \ 2010
    Ecology 91 (2010)10. - ISSN 0012-9658 - p. 3027 - 3036.
    microbial communities - diversity - stability - biodiversity - grassland - feedback - ecology - real - ecosystems - succession
    Soils are extremely rich in biodiversity, and soil organisms play pivotal roles in supporting terrestrial life, but the role that individual plants and plant communities play in influencing the diversity and functioning of soil food webs remains highly debated. Plants, as primary producers and providers of resources to the soil food web, are of vital importance for the composition, structure, and functioning of soil communities. However, whether natural soil food webs that are completely open to immigration and emigration differ underneath individual plants remains unknown. In a biodiversity restoration experiment we first compared the soil nematode communities of 228 individual plants belonging to eight herbaceous species. We included grass, leguminous, and non-leguminous species. Each individual plant grew intermingled with other species, but all plant species had a different nematode community. Moreover, nematode communities were more similar when plant individuals were growing in the same as compared to different plant communities, and these effects were most apparent for the groups of bacterivorous, carnivorous, and omnivorous nematodes. Subsequently, we analyzed the composition, structure, and functioning of the complete soil food webs of 58 individual plants, belonging to two of the plant species, Lotus corniculatus (Fabaceae) and Plantago lanceolata (Plantaginaceae). We isolated and identified more than 150 taxa/groups of soil organisms. The soil community composition and structure of the entire food webs were influenced both by the species identity of the plant individual and the surrounding plant community. Unexpectedly, plant identity had the strongest effects on decomposing soil organisms, widely believed to be generalist feeders. In contrast, quantitative food web modeling showed that the composition of the plant community influenced nitrogen mineralization under individual plants, but that plant species identity did not affect nitrogen or carbon mineralization or food web stability. Hence, the composition and structure of entire soil food webs vary at the scale of individual plants and are strongly influenced by the species identity of the plant. However, the ecosystem functions these food webs provide are determined by the identity of the entire plant community. Read More: http://www.esajournals.org/doi/abs/10.1890/09-2198.1
    Long-term organic farming fosters below and aboveground biota: Implications for soil quality, biological control and productivity
    Birkhofer, K. ; Bezemer, T.M. ; Bloem, J. ; Bonkowski, M. ; Christensen, S. ; Dubois, D. ; Ekelund, F. ; Fliessbach, A. ; Gunst, L. ; Hedlund, K. ; Mäder, P. ; Mikola, J. ; Robin, C. ; Setälä, H. ; Tatin-Froux, F. ; Putten, W.H. van der; Scheu, S. - \ 2008
    Soil Biology and Biochemistry 40 (2008)9. - ISSN 0038-0717 - p. 2297 - 2308.
    microbial community structure - food-web - agricultural systems - generalist predators - mycorrhizal fungi - alternative prey - biomass - nitrogen - agroecosystems - management
    Organic farming may contribute substantially to future agricultural production worldwide by improving soil quality and pest control, thereby reducing environmental impacts of conventional farming. We investigated in a comprehensive way soil chemical, as well as below and aboveground biological parameters of two organic and two conventional wheat farming systems that primarily differed in fertilization and weed management strategies. Contrast analyses identified management related differences between ¿herbicide-free¿ bioorganic (BIOORG) and biodynamic (BIODYN) systems and conventional systems with (CONFYM) or without manure (CONMIN) and herbicide application within a long-term agricultural experiment (DOK trial, Switzerland). Soil carbon content was significantly higher in systems receiving farmyard manure and concomitantly microbial biomass (fungi and bacteria) was increased. Microbial activity parameters, such as microbial basal respiration and nitrogen mineralization, showed an opposite pattern, suggesting that soil carbon in the conventional system (CONFYM) was more easily accessible to microorganisms than in organic systems. Bacterivorous nematodes and earthworms were most abundant in systems that received farmyard manure, which is in line with the responses of their potential food sources (microbes and organic matter). Mineral fertilizer application detrimentally affected enchytraeids and Diptera larvae, whereas aphids benefited. Spider abundance was favoured by organic management, most likely a response to increased prey availability from the belowground subsystem or increased weed coverage. In contrast to most soil-based, bottom-up controlled interactions, the twofold higher abundance of this generalist predator group in organic systems likely contributed to the significantly lower abundance of aboveground herbivore pests (aphids) in these systems. Long-term organic farming and the application of farmyard manure promoted soil quality, microbial biomass and fostered natural enemies and ecosystem engineers, suggesting enhanced nutrient cycling and pest control. Mineral fertilizers and herbicide application, in contrast, affected the potential for top-down control of aboveground pests negatively and reduced the organic carbon levels. Our study indicates that the use of synthetic fertilizers and herbicide application changes interactions within and between below and aboveground components, ultimately promoting negative environmental impacts of agriculture by reducing internal biological cycles and pest control. On the contrary, organic farming fosters microbial and faunal decomposers and this propagates into the aboveground system via generalist predators thereby increasing conservation biological control. However, grain and straw yields were 23% higher in systems receiving mineral fertilizers and herbicides reflecting the trade-off between productivity and environmental responsibility.
    Contribution of planar (0-1 Ortho) and nonplanar (2-4 Ortho) fractions of aroclor 1260 to the induction of altered hepatic foci in female sprague-dawley rats
    Plas, S.A. van der; Sundberg, H. ; Berg, H. van den; Scheu, G. ; Wester, P. ; Jensen, S. ; Bergman, A. ; Boer, J. de; Koeman, J.H. ; Brouwer, A. - \ 2000
    Toxicology and Applied Pharmacology 169 (2000). - ISSN 0041-008X - p. 255 - 268.
    The hepatic tumor promoting activity of the planar 0–1 ortho (~9.7 /w) and the nonplanar 2–4 ortho (~90.3 /w) fraction of the commercial PCB mixture Aroclor 1260 was studied using a medium-term two-stage initiation/promotion bioassay in female Sprague–Dawley rats. Fractionation was carried out on an activated charcoal column. The composition of the effluent from the column was tested by GC–ECD. The absence of planar compounds in the 2–4 ortho fraction was confirmed by GC–MS analysis. The dioxin-like toxic potency of the fractions was determined with the DR-CALUX assay. The animal experiment was started with the initiation procedure (diethylnitrosamine injection, 30 mg/kg body wt ip, 24 h after 2/3 hepatectomy), followed 6 weeks later by the promotion treatment, which consisted of a weekly subcutaneous injection during 20 weeks. Exposure groups (n = 10) received the following treatments (dose/kg body wt/week): Aroclor 1260 (10 mg), 0–1 ortho fraction (0.97 mg), 2–4 ortho fraction (1, 3, or 9 mg), a reconstituted 0–4 ortho fraction (9.97 mg), 2,2′,4,4′,5,5′-hexachlorobiphenyl (PCB 153; 1 or 9 mg), 2,3,7,8-TCDD (1 g; positive control) or corn oil (1 ml; vehicle control). One group did not receive a promotion treatment. All exposure groups exhibited a significantly increased volume fraction of the liver occupied by hepatic foci positive for the placental form of glutathione-S-transferase-p compared to the corn oil control, except for the groups treated with 0–1 ortho fraction and 1 mg PCB 153/kg body wt/week. Approximately 80␘f the total tumor promoting capacity of the reconstituted 0–4 ortho fraction could be explained by the 2–4 ortho PCB fraction while the 0–1 ortho fraction had only a negligible contribution. These results suggest that the majority of the tumor promotion potential of PCB mixtures resides in the non-dioxin-like fraction, which is not taken into account in the toxic equivalency factor (TEF) approach for risk assessment of PCBs. This may result in an underestimation of the tumor promotion potential of environmental PCB mixtures.
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