Genomics of soil microbial communities associated with agricultural and native sites

Teal, T.K., V. Gomez-Alvarez, and T.M. Schmidt

Presented at the All Scientist and GLBRC Sustainability Meeting (2009-05-05 to 2009-05-07 )

Microbial diversity in soils has been studied in diverse locations and soil types, yet there has been little focus on the changes in the microbial communities that result from the conversion of native lands to agricultural use. This conversion has resulted in an increased concentration of greenhouse gases (e.g. CO₂, N₂O, and CH₄). Since bacteria have been proposed to play an important role in the regulation of these gases, it is likely that land management practice is affecting the community composition that contributes to these differences in flux. We studied the taxonomic diversity and functional capabilities of microbial communities in soils under different management practices (native vs agricultural site) at the Kellogg Biological Station LTER at Michigan using metagenomic techniques. Our study generated one billion bp of largely unassembled sequences and one million tags corresponding to the V6 region of bacterial rRNA from 454-pyrosequencing, and an additional 520 1500 bp sequences from 16S clone libraries. Analysis of 16S rRNA gene sequences from the two sites indicated the presence of Acidobacteria, Actinobacteria, α-Proteobacteria, β-Proteobacteria, δ-Proteobacteria, γ-Proteobacteria, Gemmatimonadetes, Planctomycetacia, Sphingobacteria, and Verrucomicrobiae classes. While the diversity of the sites is similar, the structure of the communities differ. Three of the top five phylotypes are the same in both sites, but Sphingomonadaceae is the most abundant group in the agricultural site whereas Acidobacteriaceae and Rhizobiales are the most abundant in native soils. Additional variation in composition is occurring among the taxonomic groups with lower abundances that potentially have a significant functional impact. Comparison of metagenomic libraries using the MG-RAST server shows that most of the functional diversity is similar in both communities, but the relative occurrence of reads connected to a subsystem is higher in the agricultural site. This project will yield new insights into the taxonomic composition and functional potential of microbial communities that contribute to greenhouse gas fluxes under different land management practices.