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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    Disturbance regulates the density–body mass relationship of soil fauna
    Langevelde, Frank van; Comor, Vincent ; Bie, Steven de; Prins, Herbert H.T. ; Thakur, Madhav P. - \ 2020
    Ecological Applications 30 (2020)1. - ISSN 1051-0761
    Theory on the density‐body mass (DBM) relationship predicts that the density of animal species decreases by the power of −0.75 per unit increase in their body mass, or by the power of −1 when taxa across trophic levels are studied. This relationship is, however, largely debated as the slope often deviates from the theoretical predictions. Here, we tested the ability of the DBM relationship to reflect changes in the structure of communities subjected to an anthropogenic disturbance. The slope would become less steep if smaller animals were more impacted by the disturbance than the larger ones, whereas the slope would become steeper if larger animals were more affected than the smaller ones. We tested the changes in the DBM relationship by sampling soil fauna, i.e. nematodes, Collembola and larger arthropods, from a semi‐arid grassland before and after spraying diesel fuel as disturbance. We applied three different treatments: a control, a light disturbance and an intense disturbance. We found that the slopes of the DBM relationships before the disturbance were around −1 as predicted by theory. The slope became more positive (i.e. less steep) just after the disturbance, especially after the intense disturbance as smaller fauna suffered the most and early colonizers had larger body mass. Interestingly, we observed that the slopes converged back to −1 in two months post‐disturbance. Our findings show that the response of soil fauna communities to anthropogenic disturbances could explain the large variation in observed slopes of the DBM relationships. We experimentally demonstrate that an animal community, when disturbed, shows a temporal pattern of DBM relationships ranging from deviations from the predicted slope to convergence to the predicted slope with time. We recommend that deviations in the DBM relationships after disturbances can provide insights in the trajectory community recovery, and hence could be used for biomonitoring.
    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.

    Trophic Regulations of the Soil Microbiome
    Thakur, Madhav P. ; Geisen, Stefan - \ 2019
    Trends in Microbiology 27 (2019)9. - ISSN 0966-842X - p. 771 - 780.
    bacteria - climate change - food webs - fungi - predators - top-down control

    The soil microbiome regulates vital ecosystem functions ranging from primary production to soil carbon sequestration. Yet, we have only begun to understand the factors regulating the soil microbiome. While the importance of abiotic factors is increasingly recognized, the roles of trophic regulations in driving the structure and function of the soil microbiome remain less explored. Here, we review the current understanding of how and when microbial and top predators of the soil shape the community structure and function of the soil microbiome via both direct and indirect effects. We finally highlight that the structure and function of the soil microbiome depend on the interactive effects among predation, plant inputs, and abiotic variables present in the soil.

    Data from: Disturbance regulates the density–body mass relationship of soil fauna
    Langevelde, Frank van; Comor, Vincent ; Bie, Steven ; Prins, Herbert ; Thakur, Madhav P. - \ 2019
    Wageningen University & Research
    Theory on the density-body mass (DBM) relationship predicts that the density of animal species decreases by the power of −0.75 per unit increase in their body mass, or by the power of −1 when taxa across trophic levels are studied. This relationship is, however, largely debated as the slope often deviates from the theoretical predictions. Here, we tested the ability of the DBM relationship to reflect changes in the structure of communities subjected to an anthropogenic disturbance. The slope would become less steep if smaller animals were more impacted by the disturbance than the larger ones, whereas the slope would become steeper if larger animals were more affected than the smaller ones. We tested the changes in the DBM relationship by sampling soil fauna, i.e. nematodes, Collembola and larger arthropods, from a semi-arid grassland before and after spraying diesel fuel as disturbance. We applied three different treatments: a control, a light disturbance and an intense disturbance. We found that the slopes of the DBM relationships before the disturbance were around −1 as predicted by theory. The slope became more positive (i.e. less steep) just after the disturbance, especially after the intense disturbance as smaller fauna suffered the most and early colonizers had larger body mass. Interestingly, we observed that the slopes converged back to −1 in two months post-disturbance. Our findings show that the response of soil fauna communities to anthropogenic disturbances could explain the large variation in observed slopes of the DBM relationships. We experimentally demonstrate that an animal community, when disturbed, shows a temporal pattern of DBM relationships ranging from deviations from the predicted slope to convergence to the predicted slope with time. We recommend that deviations in the DBM relationships after disturbances can provide insights in the trajectory community recovery, and hence could be used for biomonitoring.
    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.

    Microbial invasions in terrestrial ecosystems
    Thakur, Madhav P. ; Putten, Wim H. van der; Cobben, Marleen M.P. ; Kleunen, Mark van; Geisen, Stefan - \ 2019
    Nature Reviews Microbiology (2019). - ISSN 1740-1526 - p. 1 - 11.

    Human travel and global trade have tremendously increased the spread of invasive microorganisms in new regions. Experimental and observational studies in terrestrial ecosystems are beginning to shed light on processes of microbial invasions, their ecological impacts and implications for ecosystem functioning. We provide examples of terrestrial invasive microorganisms, including bacteria, fungi, oomycetes and other protists, and viruses, and discuss the impacts of pathogenic and non-pathogenic invasive microorganisms at levels ranging from host species to ecosystems. This Review highlights that despite the recent progress in microbial invasion research, we are only beginning to understand how alien microorganisms interact with native microorganisms, and the implications of those interactions. Finally, we propose three research themes — microbial interactions, impacts and climate change — to make microbial invasion research a truly integrative discipline.

    Two-dimensional solute transport with exponential initial concentration distribution and varying flow velocity
    Thakur, C.K. ; Chaudhary, M. ; Zee, S.E.A.T.M. van der; Singh, M.K. - \ 2019
    Pollution 5 (2019)4. - ISSN 2383-451X - p. 721 - 737.
    The transport mechanism of contaminated groundwater has been a problematic issue for many decades, mainly due to the bad impact of the contaminants on the quality of the groundwater system. In this paper, the exact solution of two-dimensional advection-dispersion equation (ADE) is derived for a semi-infinite porous media with spatially dependent initial and uniform/flux boundary conditions. The flow velocity is considered temporally dependent in homogeneous media however, both spatially and temporally dependent is considered in heterogeneous porous media. First-order degradation term is taken into account to obtain a solution using Laplace Transformation Technique (LTT) for both the medium. The solute concentration distribution and breakthrough are depicted graphically. The effect of different transport parameters is studied through proposed analytical investigation. Advection-dispersion theory of contaminant mass transport in porous media is employed. Numerical solution is also obtained using Crank Nicholson method and compared with analytical result. Furthermore, accuracy of the result is discussed with root mean square error (RMSE) for both the medium. This study has developed a transport and prediction 2-D model that allows the early remediation and removal of possible pollutant in both the porous structures. The result may also be used as a preliminary predictive tool for groundwater resource and management.
    Soil Biodiversity uncovered
    Groot, G.A. de; Geisen, Stefan - \ 2018

    Soil biodiversity is the richest biotic resource on Earth. However, we only now start to have the tools to perform integrated studies of all components of this vast diversity. In this talk, we will give an overview of the diversity and role of key groups of soil biota, including viruses, bacteria, archaea, fungi, protists, and fauna. We will highlight method combinations that provide a better knowledge of ecological processes in soils. Therewith, we will introduce the talks within this session that applied such methods for in depth studies of the diversity, functions, interactions of soil biota, and their spatial and temporal variation. Both alpha and beta diversity will be impacted by land management (Maarten Schrama). This is at least partly due to complex interactions between vegetation and soil organisms (plant-soil feedbacks), as soil biota may govern plant performance (S. Emilia Hannula and Dina in 't Zandt). Given such complex interactions, making links between components of the soil diversity more explicit by visualizing co-occurence patterns will be needed to better understand ecosystem functions (Basten L. Snoek). Last, soil biodiversity is shown to represent a key resource to study and test ecological theories which is so far underused (Madhav P. Thakur)
    The burden of cardiovascular diseases among us states, 1990-2016
    Roth, Gregory A. ; Johnson, Catherine O. ; Abate, Kalkidan Hassen ; Abd-Allah, Foad ; Ahmed, Muktar ; Alam, Khurshid ; Alam, Tahiya ; Alvis-Guzman, Nelson ; Ansari, Hossein ; Ärnlöv, Johan ; Atey, Tesfay Mehari ; Awasthi, Ashish ; Awoke, Tadesse ; Barac, Aleksandra ; Bärnighausen, Till ; Bedi, Neeraj ; Bennett, Derrick ; Bensenor, Isabela ; Biadgilign, Sibhatu ; Castañeda-Orjuela, Carlos ; Catalá-López, Ferrán ; Davletov, Kairat ; Dharmaratne, Samath ; Ding, Eric L. ; Dubey, Manisha ; Faraon, Emerito Jose Aquino ; Farid, Talha ; Farvid, Maryam S. ; Feigin, Valery ; Fernandes, João ; Frostad, Joseph ; Gebru, Alemseged ; Geleijnse, Johanna M. ; Gona, Philimon Nyakauru ; Griswold, Max ; Hailu, Gessessew Bugssa ; Hankey, Graeme J. ; Hassen, Hamid Yimam ; Havmoeller, Rasmus ; Hay, Simon ; Heckbert, Susan R. ; Irvine, Caleb Mackay Salpeter ; James, Spencer Lewis ; Jara, Dube ; Kasaeian, Amir ; Khan, Abdur Rahman ; Khera, Sahil ; Khoja, Abdullah T. ; Khubchandani, Jagdish ; Kim, Daniel ; Kolte, Dhaval ; Lal, Dharmesh ; Larsson, Anders ; Linn, Shai ; Lotufo, Paulo A. ; Razek, Hassan Magdy Abd El; Mazidi, Mohsen ; Meier, Toni ; Mendoza, Walter ; Mensah, George A. ; Meretoja, Atte ; Mezgebe, Haftay Berhane ; Mirrakhimov, Erkin ; Mohammed, Shafiu ; Moran, Andrew Edward ; Nguyen, Grant ; Nguyen, Minh ; Ong, Kanyin Liane ; Owolabi, Mayowa ; Pletcher, Martin ; Pourmalek, Farshad ; Purcell, Caroline A. ; Qorbani, Mostafa ; Rahman, Mahfuzar ; Rai, Rajesh Kumar ; Ram, Usha ; Reitsma, Marissa Bettay ; Renzaho, Andre M.N. ; Rios-Blancas, Maria Jesus ; Safiri, Saeid ; Salomon, Joshua A. ; Sartorius, Benn ; Sepanlou, Sadaf Ghajarieh ; Shaikh, Masood Ali ; Silva, Diego ; Stranges, Saverio ; Tabarés-Seisdedos, Rafael ; Atnafu, Niguse Tadele ; Thakur, J.S. ; Topor-Madry, Roman ; Truelsen, Thomas ; Tuzcu, E.M. ; Tyrovolas, Stefanos ; Ukwaja, Kingsley Nnanna ; Vasankari, Tommi ; Vlassov, Vasiliy ; Vollset, Stein Emil ; Wakayo, Tolassa ; Weintraub, Robert ; Wolfe, Charles ; Workicho, Abdulhalik ; Xu, Gelin ; Yadgir, Simon ; Yano, Yuichiro ; Yip, Paul ; Yonemoto, Naohiro ; Younis, Mustafa ; Yu, Chuanhua ; Zaidi, Zoubida ; Sayed Zaki, Maysaa El; Zipkin, Ben ; Afshin, Ashkan ; Gakidou, Emmanuela ; Lim, Stephen S. ; Mokdad, Ali H. ; Naghavi, Mohsen ; Vos, Theo ; Murray, Christopher J.L. - \ 2018
    JAMA Cardiology 3 (2018)5. - ISSN 2380-6583 - p. 375 - 389.
    Importance: Cardiovascular disease (CVD) is the leading cause of death in the United States, but regional variation within the United States is large. Comparable and consistent state-level measures of total CVD burden and risk factors have not been produced previously. Objective: To quantify and describe levels and trends of lost health due to CVD within the United States from 1990 to 2016 as well as risk factors driving these changes. Design, setting, and participants: Using the Global Burden of Disease methodology, cardiovascular disease mortality, nonfatal health outcomes, and associated risk factors were analyzed by age group, sex, and year from 1990 to 2016 for all residents in the United States using standardized approaches for data processing and statistical modeling. Burden of disease was estimated for 10 groupings of CVD, and comparative risk analysis was performed. Data were analyzed from August 2016 to July 2017. Exposures: Residing in the United States. Main outcomes ans measures: Cardiovascular disease disability-Adjusted life-years (DALYs). Results: Between 1990 and 2016, age-standardized CVD DALYs for all states decreased. Several states had large rises in their relative rank ordering for total CVD DALYs among states, including Arkansas, Oklahoma, Alabama, Kentucky, Missouri, Indiana, Kansas, Alaska, and Iowa. The rate of decline varied widely across states, and CVD burden increased for a small number of states in the most recent years. Cardiovascular disease DALYs remained twice as large among men compared with women. Ischemic heart disease was the leading cause of CVD DALYs in all states, but the second most common varied by state. Trends were driven by 12 groups of risk factors, with the largest attributable CVD burden due to dietary risk exposures followed by high systolic blood pressure, high body mass index, high total cholesterol level, high fasting plasma glucose level, tobacco smoking, and low levels of physical activity. Increases in risk-deleted CVD DALY rates between 2006 and 2016 in 16 states suggest additional unmeasured risks beyond these traditional factors. Conclusions and relevance: Large disparities in total burden of CVD persist between US states despite marked improvements in CVD burden. Differences in CVD burden are largely attributable to modifiable risk exposures.
    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
    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.
    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.
    Disturbance–diversity relationships for soil fauna are explained by faunal community biomass in a salt marsh
    Thakur, M.P. ; Berg, M.P. ; Eisenhauer, N. ; Langevelde, F. van - \ 2014
    Soil Biology and Biochemistry 78 (2014). - ISSN 0038-0717 - p. 30 - 37.
    species-diversity - intermediate disturbance - richness - productivity - coexistence - succession - patterns - competition - collembola - dynamics
    Disturbance–diversity relationships have long been studied in ecology with a unimodal relationship as the key prediction. Although this relationship has been widely contested, it is rarely tested for soil invertebrate fauna, an important component of terrestrial biodiversity. We tested disturbance–diversity relationships for soil meso- and macrofauna in a salt marsh where periodic sea water inundation and cattle grazing occur as stressors. We hypothesized a unimodal inundation frequency–diversity relationship, whereas we expected grazing to overrule the effects of inundation frequency due to its large effects on the habitat of soil fauna. We found a negative relationship between inundation frequency and diversity at the ungrazed sites and no relationship at the grazed sites. Moreover, we found a negative relationship between community biomass and diversity for soil fauna that may have caused this negative disturbance–diversity relationship. Community biomass at the intermediate inundation frequency increased due to the dominance of Orchestia gammarellus (a macro-detritivore species), which could exploit low quality litters at the ungrazed sites. We highlight that the negative relationship between faunal community biomass and faunal diversity may influence disturbance–diversity relationships and illustrate that total biomass distribution of feeding guilds of soil fauna can improve our understanding of the soil fauna response to stressors in salt marshes.
    Productivity affects the density-body mass relationship of soil fauna communities
    Comor, V.N.R. ; Thakur, M.P. ; Berg, M.P. ; Bie, S. de; Prins, H.H.T. ; Langevelde, F. van - \ 2014
    Soil Biology and Biochemistry 72 (2014). - ISSN 0038-0717 - p. 203 - 211.
    intermediate disturbance hypothesis - energetic equivalence rule - plant-species richness - population-density - size relationships - food webs - salt-marsh - forest mull - rain-forest - abundance
    The productivity of ecosystems and their disturbance regime affect the structure of animal communities. However, it is not clear which trophic levels benefit the most from higher productivity or are the most impacted by disturbance. The density-body mass (DBM) relationship has been shown to reflect changes in the structure of communities subjected to environmental modifications, so far, mainly in aquatic systems. We tested how different seawater inundation frequencies and cattle grazing, which both disturbed and impacted the productivity of a terrestrial system, a salt marsh, affected the size structure of soil fauna communities, expressed by their DBM relationship. We hypothesized that either: (1) all the trophic levels of soil fauna would benefit from higher productivity (i.e., amount of litter mass), reflected by a higher Y-intercept of the DBM relationship; (2) only smaller animals would benefit, reflected by a lower slope of the relationship; (3) or only larger animals would benefit, reflected by a higher slope of the relationship. We collected a large range of soil fauna from different elevation levels in grazed and ungrazed areas, thence subjected to different levels of productivity, represented by litter mass, with the most inundated and grazed area as the least productive one. Considering that pore size must be smaller in inundated and grazed areas, productivity seemed to be a greater factor influencing species distribution than soil structure. We found slopes lower than 0.75, showing that large animals dominated the community. However, a difference between the DBM relationships of the most and least frequently inundated ungrazed sites indicated that higher productivity benefited the smaller animals. Our findings show that high productivity does not equally affect the different trophic levels of this soil fauna community, suggesting inefficient transfers of energy from one trophic level to another, as smaller species benefitted more from higher productivity.
    Interactions between microbial-feeding and predatory soil fauna trigger N2O emissions
    Thakur, M.P. ; Groenigen, J.W. van; Kuiper, I. ; Deyn, G.B. de - \ 2014
    Soil Biology and Biochemistry 70 (2014). - ISSN 0038-0717 - p. 256 - 262.
    nitrogen mineralization - enchytraeid worms - trophic cascades - food webs - raw humus - decomposition - biodiversity - nitrification - oligochaeta - microarthropods
    Recent research has shown that microbial-feeding invertebrate soil fauna species can significantly contribute to N2O emissions. However, in soil food webs microbial-feeding soil fauna interact with each other and with their predators, which affects microbial activity. To date we lack empirical tests of whether or not these interactions play a significant role in N2O emissions from soil. Therefore we studied how interactions between soil microbes, two groups of microbial-feeding soil fauna (enchytraeids and fungivorous mites) and their predators (predatory mites) affect soil N2O emissions. We hypothesized that: 1) the presence of two microbial-feeding fauna groups (enchytraeids and fungivorous mites) together increase N2O emissions more than when only a single group is present; and 2) the addition of predatory mites further enhances N2O emissions. We assembled soil food webs consisting of soil microbes, enchytraeids, fungivorous and predatory mites in microcosms with sandy loamy soil and sterilised hay as a substrate for the soil microbes. N2O emissions were measured during 56 days. We found no support for our first yet support for our second hypothesis. Addition of predatory mites to microcosms with enchytraeids and fungivorous mites increased N2O emissions significantly from 135.3 to 482.1 mg N m-2, which was also significantly higher than the control without fauna (83 mg N m-2) (P <0.001). In presence of enchytraeids, fungivorous and predatory mites, we found much higher nitrate availability at the time of the N2O peak on Day 35 (10.9 versus 5.5 mg N per kg soil without soil fauna), indicating that the major increase in N2O emissions in this treatment may be due to increased nitrification. Increased nitrification may be attributed to higher availability of N from the dead tissues of fungivorous mites and increased activity of the enchytraeids that might also have affected soil structure and contributed to increased N2O emissions. This study demonstrates the importance of interactions between microbial-feeding invertebrate soil fauna and their predators in understanding N2O emissions.
    Soil invertebrate fauna affect N2O emissions from soil
    Kuiper, I. ; Deyn, G.B. de; Thakur, M.P. ; Groenigen, J.W. van - \ 2013
    Global Change Biology 19 (2013)9. - ISSN 1354-1013 - p. 2814 - 2825.
    greenhouse-gas emissions - nitrous-oxide - nutrient mineralization - n mineralization - forest soil - carbon - ecosystems - denitrification - decomposition - enchytraeids
    Nitrous oxide (N2O) emissions from soils contribute significantly to global warming. Mitigation of N2O emissions is severely hampered by a lack of understanding of its main controls. Fluxes can only partly be predicted from soil abiotic factors and microbial analyses – a possible role for soil fauna has until now largely been overlooked. We studied the effect of six groups of soil invertebrate fauna and tested the hypothesis that all of them increase N2O emissions, although to different extents. We conducted three microcosm experiments with sandy soil and hay residue. Faunal groups included in our experiments were as follows: fungal-feeding nematodes, mites, springtails, potworms, earthworms and isopods. In experiment I, involving all six faunal groups, N2O emissions declined with earthworms and potworms from 78.4 (control) to 37.0 (earthworms) or 53.5 (potworms) mg N2O-N m-2. In experiment II, with a higher soil-to-hay ratio and mites, springtails and potworms as faunal treatments, N2O emissions increased with potworms from 51.9 (control) to 123.5 mg N2O-N m-2. Experiment III studied the effect of potworm density; we found that higher densities of potworms accelerated the peak of the N2O emissions by 5 days (P <0.001), but the cumulative N2O emissions remained unaffected. We propose that increased soil aeration by the soil fauna reduced N2O emissions in experiment I, whereas in experiment II N2O emissions were driven by increased nitrogen and carbon availability. In experiment III, higher densities of potworms accelerated nitrogen and carbon availability and N2O emissions, but did not increase them. Overall, our data show that soil fauna can suppress, increase, delay or accelerate N2O emissions from soil and should therefore be an integral part of future N2O studies.
    Conserved C-Terminal Motifs Required for Avirulence and Suppression of Cell Death by Phytophthora sojae effector Avr1b
    Dou, D. ; Kale, S.D. ; Wang, X. ; Chen, Y. ; Wang, Q. ; Jiang, R.H.Y. ; Arredondo, F.D. ; Anderson, R.G. ; Thakur, P.B. ; McDowell, J.M. ; Wang, Y. ; Tyler, B.M. - \ 2008
    The Plant Cell 20 (2008). - ISSN 1040-4651 - p. 1118 - 1133.
    broad-spectrum resistance - plant-disease-resistance - nucleotide-binding-site - late blight resistance - host-targeting signal - e3 ubiquitin ligase - phytopathogenic bacteria - solanum-bulbocastanum - innate immunity - downy mildew
    The sequenced genomes of oomycete plant pathogens contain large superfamilies of effector proteins containing the protein translocation motif RXLR-dEER. However, the contributions of these effectors to pathogenicity remain poorly understood. Here, we show that the Phytophthora sojae effector protein Avr1b can contribute positively to virulence and can suppress programmed cell death (PCD) triggered by the mouse BAX protein in yeast, soybean (Glycine max), and Nicotiana benthamiana cells. We identify three conserved motifs (K, W, and Y) in the C terminus of the Avr1b protein and show that mutations in the conserved residues of the W and Y motifs reduce or abolish the ability of Avr1b to suppress PCD and also abolish the avirulence interaction of Avr1b with the Rps1b resistance gene in soybean. W and Y motifs are present in at least half of the identified oomycete RXLR-dEER effector candidates, and we show that three of these candidates also suppress PCD in soybean. Together, these results indicate that the W and Y motifs are critical for the interaction of Avr1b with host plant target proteins and support the hypothesis that these motifs are critical for the functions of the very large number of predicted oomycete effectors that contain them
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