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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Majority of the world's most abundant creatures live in the far north
Geisen, Stefan ; Putten, Wim van der - \ 2019
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.

A methodological framework to embrace soil biodiversity
Geisen, Stefan ; Briones, Maria J.I. ; Gan, Huijie ; Behan-Pelletier, Valerie M. ; Friman, Ville Petri ; Groot, G.A. de; Hannula, S.E. ; Lindo, Zoë ; Philippot, Laurent ; Tiunov, Alexei V. ; Wall, Diana H. - \ 2019
Soil Biology and Biochemistry 136 (2019). - ISSN 0038-0717
Biodiversity - Fauna - Food-webs - Microorganisms - Molecular methods - Soil functions and health

Soils host the vast majority of life on Earth including microorganisms and animals, and supporting all terrestrial vegetation. While soil organisms are pivotal for ecosystem functioning, the assemblages of different biota from a taxonomic and functional perspective, as well as how these different organisms interact, remains poorly known. We provide a brief overview of the taxonomic and functional diversity of all major groups of soil biota across different scales and organism sizes, ranging from viruses to prokaryotes and eukaryotes. This reveals knowledge gaps in relation to all soil biodiversity groups, which are especially evident for viruses, protists, micro- and meso-fauna. We review currently-available methods to study the taxonomic and functional diversity of soil organisms by grouping all commonly-used methods into morphological, biochemical and molecular approaches. We list potentials and limitations of the methods to reveal that there is, as yet, no single method to fully characterize the biodiversity even of a single group of soil biota. Yet, we stress that we now have the methods available to enable scientists to disentangle the taxonomic and functional diversity of virtually all soil organisms. We provide a user-friendly guide to help researchers address a wider variety of soil biodiversity in their studies by discussing and critically analysing the various potentials and limitations of diverse methods to study distinct groups of soil life. We highlight that integrative methodological approaches, ideally in collaborative interactions, are key to advancing our understanding of soil biodiversity, such as the combination of morphological and molecular approaches to overcome method-specific limitations. Together, integrative efforts can provide information on the abundance, biomass, diversity and function of several groups of soil biota simultaneously. This newly-obtained integrative information on soil biodiversity will help to define the importance of soil biodiversity in ecosystem processes, functions, and services, and serve to refine food-web and earth system models.

Latitudinal variation in soil nematode communities under climate warming-related range-expanding and native plants
Wilschut, Rutger A. ; Geisen, Stefan ; Martens, Henk ; Kostenko, Olga ; Hollander, Mattias de; Hooven, Freddy C. ten; Weser, Carolin ; Snoek, L.B. ; Bloem, Janneke ; Caković, Danka ; Čelik, Tatjana ; Koorem, Kadri ; Krigas, Nikos ; Manrubia, Marta ; Ramirez, Kelly S. ; Tsiafouli, Maria A. ; Vreš, Branko ; Putten, Wim H. van der - \ 2019
Global Change Biology 25 (2019)8. - ISSN 1354-1013 - p. 2714 - 2726.
Centaurea stoebe - enemy release hypothesis - plant-pathogenic nematodes - range expansion - range-expanding plant species - root-feeding nematodes

Current climate change has led to latitudinal and altitudinal range expansions of numerous species. During such range expansions, plant species are expected to experience changes in interactions with other organisms, especially with belowground biota that have a limited dispersal capacity. Nematodes form a key component of the belowground food web as they include bacterivores, fungivores, omnivores and root herbivores. However, their community composition under climate change-driven intracontinental range-expanding plants has been studied almost exclusively under controlled conditions, whereas little is known about actual patterns in the field. Here, we use novel molecular sequencing techniques combined with morphological quantification in order to examine nematode communities in the rhizospheres of four range-expanding and four congeneric native species along a 2,000 km latitudinal transect from South-Eastern to North-Western Europe. We tested the hypotheses that latitudinal shifts in nematode community composition are stronger in range-expanding plant species than in congeneric natives and that in their new range, range-expanding plant species accumulate fewest root-feeding nematodes. Our results show latitudinal variation in nematode community composition of both range expanders and native plant species, while operational taxonomic unit richness remained the same across ranges. Therefore, range-expanding plant species face different nematode communities at higher latitudes, but this is also the case for widespread native plant species. Only one of the four range-expanding plant species showed a stronger shift in nematode community composition than its congeneric native and accumulated fewer root-feeding nematodes in its new range. We conclude that variation in nematode community composition with increasing latitude occurs for both range-expanding and native plant species and that some range-expanding plant species may become released from root-feeding nematodes in the new range.

Soil nematode abundance and functional group composition at a global scale
Hoogen, Johan Van Den; Geisen, Stefan ; Routh, Devin ; Ferris, Howard ; Traunspurger, Walter ; Wardle, David A. ; Goede, Ron G.M. De; Adams, Byron J. ; Ahmad, Wasim ; Andriuzzi, Walter S. ; Korthals, Gerard ; Quist, Casper W. ; Putten, Wim Van Der; Wilschut, Rutger - \ 2019
Nature 572 (2019)7768. - ISSN 0028-0836 - p. 194 - 198.
Soil organisms are a crucial part of the terrestrial biosphere. Despite their importance for ecosystem functioning, few quantitative, spatially explicit models of the active belowground community currently exist. In particular, nematodes are the most abundant animals on Earth, filling all trophic levels in the soil food web. Here we use 6,759 georeferenced samples to generate a mechanistic understanding of the patterns of the global abundance of nematodes in the soil and the composition of their functional groups. The resulting maps show that 4.4 ± 0.64 × 1020 nematodes (with a total biomass of approximately 0.3 gigatonnes) inhabit surface soils across the world, with higher abundances in sub-Arctic regions (38% of total) than in temperate (24%) or tropical (21%) regions. Regional variations in these global trends also provide insights into local patterns of soil fertility and functioning. These high-resolution models provide the first steps towards representing soil ecological processes in global biogeochemical models and will enable the prediction of elemental cycling under current and future climate scenarios
Competition and predation as possible causes of bacterial rarity
Kurm, Viola ; Putten, Wim H. van der; Weidner, Simone ; Geisen, Stefan ; Snoek, Basten L. ; Bakx, Tanja ; Gera Hol, Wilhelmina H. - \ 2019
Environmental Microbiology 21 (2019)4. - ISSN 1462-2912 - p. 1356 - 1368.

We assembled communities of bacteria and exposed them to different nutrient concentrations with or without predation by protists. Taxa that were rare in the field were less abundant at low nutrient concentrations than common taxa, independent of predation. However, some taxa that were rare in the field became highly abundant in the assembled communities, especially under ample nutrient availability. This high abundance points at a possible competitive advantage of some rare bacterial taxa under nutrient-rich conditions. In contrast, the abundance of most rare bacterial taxa decreased at low resource availability. Since low resource availability will be the prevailing situation in most soils, our data suggests that under those conditions poor competitiveness for limiting resources may contribute to bacterial rarity. Interestingly, taxa that were rare in the field and most successful under predator-free conditions in the lab also tended to be more reduced by predation than common taxa. This suggests that predation contributes to rarity of bacterial taxa in the field. We further discuss whether there may be a trade-off between competitiveness and predation resistance. The substantial variability among taxa in their responses to competition and predation suggests that other factors, for example abiotic conditions and dispersal ability, also influence the local abundance of soil bacteria.

Range-expansion effects on the belowground plant microbiome
Ramirez, Kelly S. ; Snoek, L.B. ; Koorem, Kadri ; Geisen, Stefan ; Bloem, L.J. ; Hooven, Freddy ten; Kostenko, Olga ; Krigas, Nikos ; Manrubia, Marta ; Caković, Danka ; Raaij, Debbie van; Tsiafouli, Maria A. ; Vreš, Branko ; Čelik, Tatjana ; Weser, Carolin ; Wilschut, Rutger A. ; Putten, Wim H. van der - \ 2019
Nature Ecology & Evolution 3 (2019)4. - ISSN 2397-334X - p. 604 - 611.

Plant range expansion is occurring at a rapid pace, largely in response to human-induced climate warming. Although the movement of plants along latitudinal and altitudinal gradients is well-documented, effects on belowground microbial communities remain largely unknown. Furthermore, for range expansion, not all plant species are equal: in a new range, the relatedness between range-expanding plant species and native flora can influence plant–microorganism interactions. Here we use a latitudinal gradient spanning 3,000 km across Europe to examine bacterial and fungal communities in the rhizosphere and surrounding soils of range-expanding plant species. We selected range-expanding plants with and without congeneric native species in the new range and, as a control, the congeneric native species, totalling 382 plant individuals collected across Europe. In general, the status of a plant as a range-expanding plant was a weak predictor of the composition of bacterial and fungal communities. However, microbial communities of range-expanding plant species became more similar to each other further from their original range. Range-expanding plants that were unrelated to the native community also experienced a decrease in the ratio of plant pathogens to symbionts, giving weak support to the enemy release hypothesis. Even at a continental scale, the effects of plant range expansion on the belowground microbiome are detectable, although changes to specific taxa remain difficult to decipher.

Root traits and belowground herbivores relate toplant–soil feedback variation among congeners
Wilschut, Rutger ; Putten, W.H. van der; Garbeva, Paolina ; Harkes, Paula ; Konings, W. ; Kulkarni, Purva ; Martens, H.J. ; Geisen, Stefan - \ 2019
Nature Communications 10 (2019). - ISSN 2041-1723
Plant–soil feedbacks contribute to vegetation dynamics by species-specific interactionsbetween plants and soil biota. Variation in plant–soil feedbacks can be predicted by roottraits, successional position, and plant nativeness. However, it is unknown whether closelyrelated plant species develop more similar plant–soil feedbacks than more distantly relatedspecies. Where previous comparisons included plant species from distant phylogeneticpositions, we studied plant–soil feedbacks of congeneric species. Using eight intra-continentally range-expanding and nativeGeraniumspecies, we tested relations betweenphylogenetic distances, chemical and structural root traits, root microbiomes, and plant–soilfeedbacks. We show that root chemistry and specific root length better predict bacterial andfungal community composition than phylogenetic distance. Negative plant–soil feedbackstrength correlates with root-feeding nematode numbers, whereas microbiome dissimilarity,nativeness, or phylogeny does not predict plant–soil feedbacks. We conclude that rootmicrobiome variation among congeners is best explained by root traits, and that root-feedingnematode abundances predict plant–soil feedbacks.
Data from: Integrating quantitative morphological and qualitative molecular methods to analyze soil nematode community responses to plant range expansion
Geisen, Stefan ; Snoek, L.B. ; Hooven, Freddy C. ten; Duyts, Henk ; Kostenko, Olga ; Bloem, J. ; Martens, H.J. ; Quist, C.W. ; Helder, J. ; Putten, W.H. van der - \ 2018
1. Belowground nematodes are important for soil functioning, as they are ubiquitous and operate at various trophic levels in the soil food web. However, morphological nematode community analysis is time consuming and requires ample training. qPCR-based nematode identification techniques are well available, but high throughput sequencing (HTS) might be more suitable for non-targeted nematode community analysis. 2. We compared effectiveness of qPCR and HTS-based approaches with morphological nematode identification while examining how climate warming-induced plant range expansion may influence belowground nematode assemblages. We extracted nematodes from soil of Centaurea stoebe and C. jacea populations in Slovenia, where both plant species are native, and Germany, where C. stoebe is range expander and C. jacea is native. Half of each nematode sample was identified morphologically and the other half was analysed using targeted qPCR and a novel HTS approach. 3. HTS produced the highest taxonomic resolution of the nematode community. Nematode taxa abundances correlated between the methods. Therefore, especially relative HTS and relative morphological data revealed nearly identical ecological patterns. All methods showed lower numbers of plant feeding nematodes in rhizosphere soils of C. stoebe compared to C. jacea. However, a profound difference was observed between absolute and relative abundance data; both sampling origin and plant species affected relative abundances of bacterivorous nematodes, whereas there was no effect on absolute abundances. 4. Taken together, as HTS correlates with relative analyses of soil nematode communities, while providing highest taxonomic resolution and sample throughput, we propose a combination of HTS with microscopic counting to supplement important quantitative data on soil nematode communities. This provides the most cost-effective, in-depths methodology to study soil nematode community responses to changes in the environment. This methodology will also be applicable to nematode analyses in aquatic systems.
Integrating quantitative morphological and qualitative molecular methods to analyze soil nematode community responses to plant range expansion
Geisen, Stefan ; Snoek, L.B. ; Hooven, Freddy C. ten; Duyts, Henk ; Kostenko, Olga ; Bloem, J. ; Martens, H.J. ; Quist, C.W. ; Helder, J. ; Putten, W.H. van der - \ 2018
PRJEB24755 - ERP106607 - Nematode method calibration
Nematodes were extracted from soils of a range expanding and related plant species in the native region of both and the expanded region of the range expanding plant species. we then identified half of the extracted nematodes morphologically and extracted DNA from the other half to apply qPCR with groups specific primers and high throughput amplicon sequencing (HTS). The aim was to compare the methods which overall showed strong correlations. However, different methods had distinct strengths (e.g. providing absolute abundances for morphology, the ease of specific quantification of nematode groups for qPCR and the high resolution of all nematode taxa simultaneously for HTS). Therefore we propose a method combination for in depths studies of soil nematode communities.
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)
Network Analyses Can Advance Above-Belowground Ecology
Ramirez, Kelly S. ; Geisen, Stefan ; Morriën, Elly ; Snoek, Basten L. ; Putten, Wim H. van der - \ 2018
Trends in Plant Science 23 (2018)9. - ISSN 1360-1385 - p. 759 - 768.
community ecology - global change - species interactions - terrestrial ecology

An understanding of above-belowground (AG-BG) ecology is important for evaluating how plant interactions with enemies, symbionts, and decomposers affect species diversity and will respond to global changes. However, research questions and experiments often focus on only a limited number of interactions, creating an incomplete picture of how entire communities may be involved in AG-BG community ecology. Therefore, a pressing challenge is to formulate hypotheses of AG-BG interactions when considering communities in their full complexity. Here we discuss how network analyses can be a powerful tool to progress AG-BG research, link across scales from individual to community and ecosystem, visualize community interactions between the two (AG and BG) subsystems, and develop testable hypotheses.

Soil protists : A fertile frontier in soil biology research
Geisen, Stefan ; Mitchell, Edward A.D. ; Adl, Sina ; Bonkowski, Michael ; Dunthorn, Micah ; Ekelund, Flemming ; Fernández, Leonardo D. ; Jousset, Alexandre ; Krashevska, Valentyna ; Singer, David ; Spiegel, Frederick W. ; Walochnik, Julia ; Lara, Enrique - \ 2018
FEMS Microbiology Reviews 42 (2018)3. - ISSN 0168-6445 - p. 293 - 323.
Biogeography - Functional diversity - Plant performance - Soil food web - Soil microbiome - Taxonomic diversity

Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests. Predatory soil protists release nutrients enhancing plant growth. Soil protists are of key importance for our understanding of eukaryotic evolution and microbial biogeography. Soil protists are also useful in applied research as bioindicators of soil quality, as models in ecotoxicology and as potential biofertilizers and biocontrol agents. In this review, we provide an overview of the enormous morphological, taxonomical and functional diversity of soil protists, and discuss current challenges and opportunities in soil protistology. Research in soil biology would clearly benefit from incorporating more protistology alongside the study of bacteria, fungi and animals.

Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion
Geisen, Stefan ; Snoek, L.B. ; Hooven, Freddy C. ten; Duyts, Henk ; Kostenko, Olga ; Bloem, Janneke ; Martens, Henk ; Quist, Casper W. ; Helder, Johannes A. ; Putten, Wim H. van der - \ 2018
Methods in Ecology and Evolution 9 (2018)6. - ISSN 2041-210X - p. 1366 - 1378.
Biodiversity - High-throughput sequencing - Microscopy - Molecular approaches - Nematodes - QPCR - Soils
Below-ground nematodes are important for soil functioning, as they are ubiquitous and operate at various trophic levels in the soil food web. However, morphological nematode community analysis is time consuming and requires ample training. qPCR-based nematode identification techniques are well available, but high-throughput sequencing (HTS) might be more suitable for non-targeted nematode community analyses. We compared effectiveness of qPCR- and HTS-based approaches with morphological nematode identification while examining how climate warming-induced plant range expansion may influence below-ground nematode assemblages. We extracted nematodes from soil of Centaurea stoebe and C. jacea populations in Slovenia, where both plant species are native, and Germany, where C. stoebe is a range expander and C. jacea is native. Half of each nematode sample was identified morphologically and the other half was analysed using targeted qPCR and a novel HTS approach. HTS produced the highest taxonomic resolution of the nematode community. Nematode taxa abundances correlated between the methods. Therefore, especially relative HTS and relative morphological data revealed nearly identical ecological patterns. All methods showed lower numbers of plant-feeding nematodes in rhizosphere soils of C. stoebe compared to C. jacea. However, a profound difference was observed between absolute and relative abundance data; both sampling origin and plant species affected relative abundances of bacterivorous nematodes, whereas there was no effect on absolute abundances. Taken together, as HTS correlates with relative analyses of soil nematode communities, while providing highest taxonomic resolution and sample throughput, we propose a combination of HTS with microscopic counting to supplement important quantitative data on soil nematode communities. This provides the most cost-effective, in-depth methodology to study soil nematode community responses to changes in the environment. This methodology will also be applicable to nematode analyses in aquatic systems.
Soil protist communities form a dynamic hub in the soil microbiome
Xiong, Wu ; Jousset, Alexandre ; Guo, Sai ; Karlsson, Ida ; Zhao, Qingyun ; Wu, Huasong ; Kowalchuk, George A. ; Shen, Qirong ; Li, Rong ; Geisen, Stefan - \ 2018
ISME Journal 12 (2018)2. - ISSN 1751-7362 - p. 634 - 638.
Soil microbes are essential for soil fertility. However, most studies focus on bacterial and/or fungal communities, while the top-down drivers of this microbiome composition, protists, remain poorly understood. Here, we investigated how soil amendments affect protist communities and inferred potential interactions with bacteria and fungi. Specific fertilization treatments impacted both the structure and function of protist communities. Organic fertilizer amendment strongly reduced the relative abundance of plant pathogenic protists and increased bacterivorous and omnivorous protists. The addition of individual biocontrol bacteria and fungi further altered the soil protist community composition, and eventually function. Network analysis integrating protist, bacterial and fungal community data, placed protists as a central hub in the soil microbiome, linking diverse bacterial and fungal populations. Given their dynamic response to soil management practices and key position in linking soil microbial networks, protists may provide the leverage between soil management and the enhancement of bacterial and fungal microbiota at the service of improved soil health.
The need for standardisation : Exemplified by a description of the diversity, community structure and ecological indices of soil nematodes
Griffiths, B.S. ; Groot, G.A. de; Laros, I. ; Stone, D. ; Geisen, S. - \ 2018
Ecological Indicators 87 (2018). - ISSN 1470-160X - p. 43 - 46.
Biodiversity - DNA extraction - Metabarcoding - Microscopy - Molecular approaches - Nematodes - Standardisation
Molecular approaches are offering a supplement to, or even the possibility of replacing morphological identification of soil fauna, because of advantages for throughput, coverage and objectivity. We determined ecological indices of nematode community data from four sets of duplicate soil cores, based on morphological identification of nematodes after elutriation from 200 g soil and high throughput sequencing (HTS) targeting nematodes both after being elutriated from soils and DNA extracted directly from 10 g soil. HTS (at genus and species level) increased the taxonomic resolution compared to morphology (at family level). DNA extracted from elutriated nematodes identified more nematode taxa than when extracted from soil, due to an enrichment in nematode sequences. Each method also gave a different ecological footprint for the nematode community. Standardisation to previously determined indices based on morphological identification is needed in order to provide more meaningful information about soil quality and for ecological monitoring.
Humusica 2, article 17 : techno humus systems and global change − three crucial questions
Zanella, Augusto ; Geisen, Stefan ; Ponge, Jean François ; Jagers, Gerard ; Benbrook, Charles ; Dilli, Thomas ; Vacca, Andrea ; Kwiatkowska-Malina, Jolanta ; Aubert, Michaël ; Fusaro, Silvia ; Nobili, Maria De ; Lomolino, Giovanna ; Gomiero, Tiziano - \ 2018
Applied Soil Ecology 122 (2018). - ISSN 0929-1393 - p. 237 - 253.
Some soil scientists or biologists (14, one preferring anonymity) answered the three following questions: (1. Introduction) 2. Why is organic food better (tastes better, is healthier, richer in nutrients, contains less pesticide, etc.) than food produced with hydroponic or intensive farming techniques? 3. In a humipedon, are soil functioning, biodiversity and carbon content three interdependent and intersected aspects of a single ecosystem? In other words, can we treat these aspects as if they were inseparable in a humipedon? 4. Are agriculture and civilization (the society, culture, and way of life) interconnected? All scientists expressed affirmative answers. Nuances or in depth information were also furnished. The article allows to understand the real “agronomic challenge” that the predicted Global Change might represent for humanity.
Methodological advances to study the diversity of soil protists and their functioning in soil food webs
Geisen, Stefan ; Bonkowski, Michael - \ 2018
Applied Soil Ecology 123 (2018). - ISSN 0929-1393 - p. 328 - 333.
Biodiversity - Functional diversity - High throughput sequencing - Soil food web - Soil protists

Soils host the most complex communities of organisms, which are still largely considered as an unknown 'black box'. A key role in soil food webs is held by the highly abundant and diverse group of protists. Traditionally, soil protists are considered as the main consumers of bacteria in soils. However, recent insights obtained using new methodologies, provide clear evidence for the trophic diversity of microbial eukaryotes, showing that non-bacterivorous soil protists (fungivores, omnivores, predators of other protists and nematodes), photosynthetic taxa and plant-as well as animal parasites might be equally important.Here we provide an overview of methodologies to study these important soil organisms. Major gaps of knowledge are highlighted, which can be addressed using a combination of now available methods These studies will undeniably reveal an even higher functional diversity of protists and likely raise awareness of their ecological importance in soils.

Soil community functioning in a chronosequence of organically managed farms
Rijssel, Sophie van; Koorneef, G.J. ; Koetsenruijter, Gijs ; Geisen, Stefan ; Korthals, G.W. ; Pulleman, M.M. ; Goede, R.G.M. de; Comans, R.N.J. ; Veen, Ciska G.F. ; Schrama, M. ; Putten, W.H. van der - \ 2017
Seed and root endophytic fungi in a range expanding and a related plant species
Geisen, Stefan ; Kostenko, Olga ; Cnossen, Mark C. ; Hooven, Freddy C. ten; Vreš, Branko ; Putten, Wim H. van der - \ 2017
Frontiers in Microbiology 8 (2017). - ISSN 1664-302X - 11 p.
Cultivation - Endophytes - Fungi - Phylogeny - Range expanding plant species - Seeds - Soil - Soil Sterilization

Climate change is accelerating the spread of plants and their associated species to new ranges. The differences in range shift capacity of the various types of species may disrupt long-term co-evolved relationships especially those belowground, however, this may be less so for seed-borne endophytic microbes. We collected seeds and soil of the range-expanding Centaurea stoebe and the congeneric Centaurea jacea from three populations growing in Slovenia (native range of both Centaurea species) and the Netherlands (expanded range of C. stoebe, native range of C. jacea). We isolated and identified endophytic fungi directly from seeds, as well as from roots of the plants grown in Slovenian, Dutch or sterilized soil to compare fungal endophyte composition. Furthermore, we investigated whether C. stoebe hosts a reduced community composition of endophytes in the expanded range due to release from plant-species specific fungi while endophyte communities in C. jacea in both ranges are similar. We cultivated 46 unique and phylogenetically diverse endophytes. A majority of the seed endophytes resembled potential pathogens, while most root endophytes were not likely to be pathogenic. Only one endophyte was found in both roots and seeds, but was isolated from different plant species. Unexpectedly, seed endophyte diversity of southern C. stoebe populations was lower than of populations from the north, while the seed endophyte community composition of northern C. stoebe populations was significantly different southern C. stoebe as well as northern and southern C. jacea populations. Root endophyte diversity was considerably lower in C. stoebe than in C. jacea independent of plant and soil origin, but this difference disappeared when plants were grown in sterile soils. We conclude that the community composition of fungal endophytes not only differs between related plant species but also between populations of plants that expand their range compared to their native habitat. Our results suggest that fungal endophytes of two Centaurea species are not able to systemically infect plants. We highlight that endophytes remain poorly studied and further work should investigate the functional importance of endophytes.

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