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Root-associated fungi could play a role in determining both the positive relationship between plant diversity and productivity in experimental grasslands, and its strengthening over time. This hypothesis assumes that specialized pathogenic and mutualistic fungal communities gradually assemble over time, enhancing plant growth more in species-rich than in species-poor plots. To test this hypothesis, we used high-throughput amplicon sequencing to characterize root-associated fungal communities in experimental grasslands of 1 and 15 years of age with varying levels of plant species richness. Specifically, we tested whether the relationship between fungal communities and plant richness and productivity becomes stronger with the age of the experimental plots. Our results showed that fungal diversity increased with plant diversity, but this relationship weakened rather than strengthened over the two time points. Contrastingly, fungal community composition showed increasing associations with plant diversity over time, suggesting a gradual build-up of specific fungal assemblages. Analyses of different fungal guilds showed that these changes were particularly marked in pathogenic fungi, whose shifts in relative abundance are consistent with the pathogen dilution hypothesis in diverse plant communities. Our results suggest that root-associated fungal pathogens play more specific roles in determining the diversity–productivity relationship than other root-associated plant symbionts.

Recent studies on root traits have shown that there are two axes explaining trait variation belowground: the collaboration axis with mycorrhizal partners and the conservation (‘fast – slow’) axis. However, it is yet unknown whether these trait axes affect the assembly of soilborne fungi. We expect saprotrophic fungi to link to the conservation axis of root traits, whereas pathogenic and arbuscular mycorrhizal fungi link to the collaboration axis, but in opposite directions, as arbuscular mycorrhizal fungi might provide pathogen protection.To test these hypotheses, we sequenced rhizosphere fungal communities and measured root traits in monocultures of 25 grassland plant species, differing in age. Within the fungal guilds, we evaluated fungal species richness, relative abundance and community composition.Contrary to our hypotheses, fungal diversity and relative abundance were not strongly related to the root trait axes. However, saprotrophic fungal community composition was affected by the conservation gradient and pathogenic community composition by the collaboration gradient. The rhizosphere AMF community composition did not change along the collaboration gradient, even though the root trait axis was in line with the root mycorrhizal colonization rate.Overall, our results indicate that in the long term, the root trait axes are linked with fungal community composition.

Plants impact the development of their rhizosphere microbial communities. It is yet unclear to what extent the root cap and specific root zones contribute to microbial community assembly. To test the roles of root caps and root hairs in the establishment of microbiomes along maize roots (Zea mays), we compared the composition of prokaryote (archaea and bacteria) and protist (Cercozoa and Endomyxa) microbiomes of intact or decapped primary roots of maize inbred line B73 with its isogenic root hairless (rth3) mutant. In addition, we tracked gene expression along the root axis to identify molecular control points for an active microbiome assembly by roots. Absence of root caps had stronger effects on microbiome composition than the absence of root hairs and affected microbial community composition also at older root zones and at higher trophic levels (protists). Specific bacterial and cercozoan taxa correlated with root genes involved in immune response. Our results indicate a central role of root caps in microbiome assembly with ripple-on effects affecting higher trophic levels and microbiome composition on older root zones.

Climate and agricultural practice interact to influence both crop production and soil microbes in agroecosystems. Here, we carried out a unique experiment in Central Germany to simultaneously investigate the effects of climates (ambient climate vs. future climate expected in 50–70 years), agricultural practices (conventional vs. organic farming), and their interaction on arbuscular mycorrhizal fungi (AMF) inside wheat (Triticum aestivum L.) roots. AMF communities were characterised using Illumina sequencing of 18S rRNA gene amplicons. We showed that climatic conditions and agricultural practices significantly altered total AMF community composition. Conventional farming significantly affected the AMF community and caused a decline in AMF richness. Factors shaping AMF community composition and richness at family level differed greatly among Glomeraceae, Gigasporaceae, and Diversisporaceae. An interactive impact of climate and agricultural practices was detected in the community composition of Diversisporaceae. Organic farming mitigated the negative effect of future climate and promoted total AMF and Gigasporaceae richness. AMF richness was significantly linked with nutrient content of wheat grains under both agricultural practices.

Aim Quantify direct and indirect relationships between soil microbial community properties (potential basal respiration, microbial biomass) and abiotic factors (soil, climate) in three major land-cover types. Location Europe. Time period 2018. Major taxa studied Microbial community (fungi and bacteria). Methods We collected 881 soil samples from across Europe in the framework of the Land Use/Land Cover Area Frame Survey (LUCAS). We measured potential soil basal respiration at 20 oC and microbial biomass (substrate-induced respiration) using an O-2-microcompensation apparatus. Soil and climate data were obtained from the same LUCAS survey and online databases. Structural equation models (SEMs) were used to quantify relationships between variables, and equations extracted from SEMs were used to create predictive maps. Fatty acid methyl esters were measured in a subset of samples to distinguish fungal from bacterial biomass. Results Soil microbial properties in croplands were more heavily affected by climate variables than those in forests. Potential soil basal respiration and microbial biomass were correlated in forests but decoupled in grasslands and croplands, where microbial biomass depended on soil carbon. Forests had a higher ratio of fungi to bacteria than grasslands or croplands. Main conclusions Soil microbial communities in grasslands and croplands are likely carbon-limited in comparison with those in forests, and forests have a higher dominance of fungi indicating differences in microbial community composition. Notably, the often already-degraded soils of croplands could be more vulnerable to climate change than more natural soils. The provided maps show potentially vulnerable areas that should be explicitly accounted for in future management plans to protect soil carbon and slow the increasing vulnerability of European soils to climate change.

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Goldmann, K., Boeddinghaus, R. S., Klemmer, S., Regan, K. M., Heintz-Buschart, A., Fischer, M., Prati, D., Piepho, H., Berner, D., Marhan, S., Kandeler, E., Buscot, F., & Wubet, T. Unraveling spatiotemporal variability of arbuscular mycorrhizal fungi in a temperate grassland plot. Environmental Microbiology, 22(3),(2020): 873-888, doi:10.1111/1462-2920.14653., Soils provide a heterogeneous environment varying in space and time; consequently, the biodiversity of soil microorganisms also differs spatially and temporally. For soil microbes tightly associated with plant roots, such as arbuscular mycorrhizal fungi (AMF), the diversity of plant partners and seasonal variability in trophic exchanges between the symbionts introduce additional heterogeneity. To clarify the impact of such heterogeneity, we investigated spatiotemporal variation in AMF diversity on a plot scale (10 × 10 m) in a grassland managed at low intensity in southwest Germany. AMF diversity was determined using 18S rDNA pyrosequencing analysis of 360 soil samples taken at six time points within a year. We observed high AMF alpha‐ and beta‐diversity across the plot and at all investigated time points. Relationships were detected between spatiotemporal variation in AMF OTU richness and plant species richness, root biomass, minimal changes in soil texture and pH. The plot was characterized by high AMF turnover rates with a positive spatiotemporal relationship for AMF beta‐diversity. However, environmental variables explained only ≈20% of the variation in AMF communities. This indicates that the observed spatiotemporal richness and community variability of AMF was largely independent of the abiotic environment, but related to plant properties and the cooccurring microbiome., We thank the managers of the three Exploratories, Kirsten Reichel‐Jung, Swen Renner, Katrin Hartwich, Sonja Gockel, Kerstin Wiesner, and Martin Gorke for their work in maintaining the plot and project infrastructure; Christiane Fischer and Simone Pfeiffer for giving support through the central office, Michael Owonibi and Andreas Ostrowski for managing the central data base, and Eduard Linsenmair, Dominik Hessenmöller, Jens Nieschulze, Ernst‐Detlef Schulze, Wolfgang W. Weisser and the late Elisabeth Kalko for their role in setting up the Biodiversity Exploratories project. The work has been funded by the DFG Priority Program 1374 ‘Infrastructure‐Biodiversity‐Exploratories’ (BU 941/22‐1, BU 941/22‐3, KA 1590/8‐2, KA 1590/8‐3). Field work permits were issued by the responsible state environmental office of Baden‐Württemberg (according to § 72 BbgNatSchG). Likewise, we kindly thank Beatrix Schnabel, Melanie Günther and Sigrid Härtling for 454 sequencing in Halle. AHB gratefully acknowledges the support of the German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig funded by the German Research Foundation (FZT 118). Authors declare no conflict of interests.

At the global scale, most forest research on biodiversity focuses on aboveground organisms. However, understanding the structural associations between aboveground and belowground communities provides relevant information about important functions linked to biogeochemical cycles. Microorganisms such as soil fungi are known to be closely coupled to the dominant tree vegetation, and we hypothesize that tree traits affect fungal guilds and soil functionality in multiple ways. By analyzing fungal diversity of 64 plots from four European forest types using Illumina DNA sequencing, we show that soil fungal communities respond to tree community traits rather than to tree species diversity. To explain changes in fungal community structure and measured soil enzymatic activities, we used a trait‐based ecological approach and community‐weighted means of tree traits to define “fast” (acquisitive) vs. “slow” (conservative) tree communities. We found specific tree trait effects on different soil fungal guilds and soil enzymatic activities: Tree traits associated with litter and absorptive roots correlated with fungal, especially pathogen diversity, and influenced community composition of soil fungi. Relative abundance of the symbiotrophic and saprotrophic guilds mirrored the litter quality, while the root traits of fast tree communities enhanced symbiotroph abundance. We found that forest types of higher latitudes, which are dominated by fast tree communities, correlated with high carbon‐cycling enzymatic activities. In contrast, Mediterranean forests with slow tree communities showed high enzymatic activities related to nitrogen and phosphorous. Our findings highlight that tree trait effects of either “fast” or “slow” tree communities drive different fungal guilds and influence biogeochemical cycles.

Ecologists have had a very good foundational knowledge of the global distribution of plants and aboveground animals for many decades. But despite the immense diversity of soil organisms, our knowledge of the global distribution, drivers and threats to soil biodiversity is very limited.

The recent past has seen a tremendous surge in soil macroecological studies and new insights into the global drivers of one‐quarter of the biodiversity of the Earth. Building on these important developments, a recent paper in Global Ecology and Biogeography outlined promising methods and approaches to advance soil macroecology. Among other recommendations, White and colleagues introduced the concept of a spatial three‐dimensionality in soil macroecology by considering the different spheres of influence and scales, as soil organism size ranges vary from bacteria to macro‐ and megafauna. Here, we extend this concept by discussing three additional dimensions (biological, physical, and societal) that are crucial to steer soil macroecology from pattern description towards better mechanistic understanding. In our view, these are the requirements to establish it as a predictive science that can inform policy about relevant nature and management conservation actions. We highlight the need to explore temporal dynamics of soil biodiversity and functions across multiple temporal scales, integrating different facets of biodiversity (i.e., variability in body size, life‐history traits, species identities, and groups of taxa) and their relationships to multiple ecosystem functions, in addition to the feedback effects between humans and soil biodiversity. We also argue that future research needs to consider effective soil conservation policy and management in combination with higher awareness of the contributions of soil‐based nature's contributions to people. To verify causal relationships, soil macroecology should be paired with local and globally distributed experiments. The present paper expands the multidimensional perspective on soil macroecology to guide future research contents and funding. We recommend considering these multiple dimensions in projected global soil biodiversity monitoring initiatives.

Soils provide a heterogeneous environment varying in space and time; consequently, the biodiversity of soil microorganisms also differs spatially and temporally. For soil microbes tightly associated with plant roots, such as arbuscular mycorrhizal fungi (AMF), the diversity of plant partners and seasonal variability in trophic exchanges between the symbionts introduce additional heterogeneity. To clarify the impact of such heterogeneity, we investigated spatiotemporal variation in AMF diversity on a plot scale (10 × 10 m) in a grassland managed at low intensity in southwest Germany. AMF diversity was determined using 18S rDNA pyrosequencing analysis of 360 soil samples taken at six time points within a year. We observed high AMF alpha‐ and beta‐diversity across the plot and at all investigated time points. Relationships were detected between spatiotemporal variation in AMF OTU richness and plant species richness, root biomass, minimal changes in soil texture and pH. The plot was characterized by high AMF turnover rates with a positive spatiotemporal relationship for AMF beta‐diversity. However, environmental variables explained only ≈20% of the variation in AMF communities. This indicates that the observed spatiotemporal richness and community variability of AMF was largely independent of the abiotic environment, but related to plant properties and the cooccurring microbiome.