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Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

Fierer, Noah, Leff, Jonathan W., Adams, Byron J., Nielsen, Uffe N., Bates, Scott Thomas, Lauber, Christian L., Owens, Sarah, Gilbert, Jack A., Wall, Diana H., Caporaso, J. Gregory
Proceedings of the National Academy of Sciences of the United States of America 2012 v.109 no.52 pp. 21390-21395
animal communities, antibiotic resistance, biogeochemical cycles, biomass, cold, desert soils, deserts, dormancy, ecologists, forests, functional diversity, genes, grasslands, metabolism, metagenomics, microbial communities, organic compounds, osmoregulation, phylogeny, soil microorganisms, soil surveys, species diversity, terrestrial ecosystems, tundra
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.