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.

Soils represent a significant reservoir of biological diversity that underpins a broad range of key processes and moderate ecosystem service provision. Our understanding of the role that soil organisms play in ecosystems is still developing, but the increased investigation into biodiversity-ecosystem functioning relationships in soils over the past couple of decades has provided insights that have greatly enhanced our ability to sustainably manage soil biodiversity. In this review, we synthesize emerging knowledge of soil biodiversity as a natural resource that supports the functioning of terrestrial ecosystems and their delivery of ecosystem services. We explore how environmental changes alter soil biodiversity and how this in turn can affect ecosystem processes as well as resistance and resilience to environmental changes. We then discuss ways to include soil biodiversity in management strategies for sustainable production and biodiversity conservation. We conclude by highlighting key research challenges to further improve our knowledge of soil biodiversity and its management.