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Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil

Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado,¹ Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado,² College of Marine Science, University of South Florida, St. Petersburg, Florida,³ Department of Mathematics and Statistics, San Diego State University, San Diego, California,⁴ Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado,⁵ Center for Microbial Sciences, San Diego State University, San Diego, California,⁶ Department of Biology, San Diego State University, San Diego, California,⁷ Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado,⁸ Department of Biology, Duke University, Durham, North Carolina,⁹ Nicholas School of the Environment and Earth Sciences, Duke University, Durham, North Carolina,¹⁰

Received 13 February 2007/ Accepted 29 August 2007

Recent studies have highlighted the surprising richness of soil bacterial communities; however, bacteria are not the only microorganisms found in soil. To our knowledge, no study has compared the diversities of the four major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an individual soil sample. We used metagenomic and small-subunit RNA-based sequence analysis techniques to compare the estimated richness and evenness of these groups in prairie, desert, and rainforest soils. By grouping sequences at the 97% sequence similarity level (an operational taxonomic unit [OTU]), we found that the archaeal and fungal communities were consistently less even than the bacterial communities. Although total richness levels are difficult to estimate with a high degree of certainty, the estimated number of unique archaeal or fungal OTUs appears to rival or exceed the number of unique bacterial OTUs in each of the collected soils. In this first study to comprehensively survey viral communities using a metagenomic approach, we found that soil viruses are taxonomically diverse and distinct from the communities of viruses found in other environments that have been surveyed using a similar approach. Within each of the four microbial groups, we observed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse.

Published ahead of print on 7 September 2007.

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