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There are numerous ways in which plants can influence the composition of soil communities. However, it remains unclear whether information on plant community attributes, including taxonomic, phylogenetic, or trait-based composition, can be used to predict the structure of soil communities. We tested, in both monocultures and field-grown mixed temperate grassland communities, whether plant attributes predict soil communities including taxonomic groups from across the tree of life (fungi, bacteria, protists, and metazoa). The composition of all soil community groups was affected by plant species identity, both in monocultures and in mixed communities. Moreover, plant community composition predicted additional variation in soil community composition beyond what could be predicted from soil abiotic characteristics. In addition, analysis of the field aboveground plant community composition and the composition of plant roots suggests that plant community attributes are better predictors of soil communities than root distributions. However, neither plant phylogeny nor plant traits were strong predictors of soil communities in either experiment. Our results demonstrate that grassland plant species form specific associations with soil community members and that information on plant species distributions can improve predictions of soil community composition. These results indicate that specific associations between plant species and complex soil communities are key determinants of biodiversity patterns in grassland soils.

BackgroundIt is now apparent that the complex microbial communities found on and in the human body vary across individuals. What has largely been missing from previous studies is an understanding of how these communities vary over time within individuals. To the extent to which it has been considered, it is often assumed that temporal variability is negligible for healthy adults. Here we address this gap in understanding by profiling the forehead, gut (fecal), palm, and tongue microbial communities in 85 adults, weekly over 3 months.ResultsWe found that skin (forehead and palm) varied most in the number of taxa present, whereas gut and tongue communities varied more in the relative abundances of taxa. Within each body habitat, there was a wide range of temporal variability across the study population, with some individuals harboring more variable communities than others. The best predictor of these differences in variability across individuals was microbial diversity; individuals with more diverse gut or tongue communities were more stable in composition than individuals with less diverse communities.ConclusionsLongitudinal sampling of a relatively large number of individuals allowed us to observe high levels of temporal variability in both diversity and community structure in all body habitats studied. These findings suggest that temporal dynamics may need to be considered when attempting to link changes in microbiome structure to changes in health status. Furthermore, our findings show that, not only is the composition of an individual's microbiome highly personalized, but their degree of temporal variability is also a personalized feature.

More than 200 years ago, Alexander von Humboldt reported that tropical plant species richness decreased with increasing elevation and decreasing temperature. Surprisingly, coordinated patterns in plant, bacterial, and fungal diversity on tropical mountains have not yet been observed, despite the central role of soil microorganisms in terrestrial biogeochemistry and ecology. We studied an Andean transect traversing 3.5 km in elevation to test whether the species diversity and composition of tropical forest plants, soil bacteria, and fungi follow similar biogeographical patterns with shared environmental drivers. We found coordinated changes with elevation in all three groups: species richness declined as elevation increased, and the compositional dissimilarity among communities increased with increased separation in elevation, although changes in plant diversity were larger than in bacteria and fungi. Temperature was the dominant driver of these diversity gradients, with weak influences of edaphic properties, including soil pH. The gradients in microbial diversity were strongly correlated with the activities of enzymes involved in organic matter cycling, and were accompanied by a transition in microbial traits towards slower‐growing, oligotrophic taxa at higher elevations. We provide the first evidence of coordinated temperature‐driven patterns in the diversity and distribution of three major biotic groups in tropical ecosystems: soil bacteria, fungi, and plants. These findings suggest that interrelated and fundamental patterns of plant and microbial communities with shared environmental drivers occur across landscape scales. These patterns are revealed where soil pH is relatively constant, and have implications for tropical forest communities under future climate change. [ABSTRACT FROM AUTHOR]

Identifying the traits that determine spatial distributions can be challenging when studying organisms, like bacteria, for which phenotypic information is limited or non-existent. However, genomic data provide another means to infer traits and determine the ecological attributes that account for differences in distributions. We determined the spatial distributions of ~124 000 soil bacterial taxa across a 3.41 km2 area to determine whether we could use phylogeny and/or genomic traits to explain differences in habitat breadth. We found that occupancy was strongly correlated with environmental range; taxa that were more ubiquitous were found across a broader range of soil conditions. Across the ~500 taxa for which genomic information was available, genomic traits were more useful than phylogeny alone in explaining the variation in habitat breadth; bacteria with larger genomes and more metabolic versatility were more likely to have larger environmental and geographical distributions. Just as trait-based approaches have proven to be so useful for understanding the distributions of animals and plants, we demonstrate that we can use genomic information to infer microbial traits that are difficult to measure directly and build trait-based predictions of the biogeographical patterns exhibited by microbes. [ABSTRACT FROM AUTHOR]

For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes. [ABSTRACT FROM AUTHOR]

Tropical forest conversion to agriculture is a major global change process. Understanding of the ecological consequences of this conversion are limited by poor knowledge of how soil microorganisms respond. We analyzed the response of soil bacteria to conversion from primary rain forest to oil palm plantation and regenerating logged forest in Malaysia. Bacterial diversity increased by approximately 20% with conversion to oil palm because of higher pH due to liming by plantation managers. Phylogenetic clustering indicated that bacterial communities were determined by environmental filtering. Regenerating logged forests did not have significantly different soil chemistry, which did not correspond with significant differences in bacterial richness, diversity, or the relative abundances of particular taxa. However, there were significant differences in the structure of bacterial community networks between regenerating logged forests and primary forests, highlighting previously unobserved effects of these two land uses. Network analysis highlighted taxa that are potentially central to bacterial networks, but have low relative abundances, suggesting that these rare taxa could play an ecological role and therefore warrant further research. [ABSTRACT FROM AUTHOR]