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

Abstract

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.shotgun metagenomics | soil microbial ecology | 16S rRNA gene sequencing | biogeography

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

“…To do so, we quantified the abundance of DA101 16S rRNA genes within previously published soil shotgun metagenomes 17,18 . The relative abundance of DA101 in amplicon data was well correlated with the relative abundance of DA101 in shotgun metagenomic data (P < 0.0001, ρ = 0.50, n = 102).…”

“…As a second measure to verify this genome is a representative of the DA101 clade, we compared the abundance of three housekeeping genes assembled within the Ca. U. copiosus genome (dnaK, rpoB and secY) to the abundance of the DA101 16S rRNA gene in >100 metagenomic samples from two separate studies 17,18 . All three genes show a very strong significant correlation with the DA101 16S rRNA gene (P < 0.0001, ρ > 0.87, n = 102, Pearson correlation, Supplementary Fig.…”

“…15) was clearly dominant. We searched previously published soil data sets for representative sequences with 100% identity to this DA101 phylotype, including 31 soils from US native tallgrass prairies 10 , 64 soils from matched forest and grassland sites across North America 51 , 595 soils collected from Central Park in New York City 1 , 367 grassland soils collected from North America, Europe, Australia and Africa 17 , and a cross-biome collection of 15 desert and non-desert soils from across the globe 18 . We also included a data set from a grassland terrace near Boulder, Colorado (105.23W, 40.12N, Table Mountain) where 29 soils were collected from a depth of 25 cm within a 100 m 2 area on 28 January 2015.…”

“…We used Metaxa2 with default settings 22 to extract bacterial 16S rRNA gene sequences from shotgun metagenomic data compiled from previous analyses of 75 different soils after rarefaction 17,18 . Extracted 16S rRNA gene fragments were matched to Greengenes full-length sequences at 99% ID using the usearch7 command usearch_global.…”

Responses of Soil Fungi to Logging and Oil Palm Agriculture in Southeast Asian Tropical Forests

“…Compositional changes in fungal communities have been linked to altered plant dynamics [20], changes in nutrient cycling [21,22], and shifts in soil carbon pools and fluxes [23]. However, few belowground studies have evaluated the responses of soil fungi to landuse conversion in tropical forests and more work has focused on how bacterial communities are structured by the biotic and abiotic soil properties that can be altered with land-use change [15,[24][25][26]. However, fungi and bacteria have different physiologies [11,27] and display differential responses and feedbacks to factors such as pH [28] and soil C [29], so fungal responses cannot necessarily be inferred from the responses of soil bacteria.…”