Microbial Genome Sequencing: Phylogeny to Function: Genomic Analyses of Dominant, Uncultured Soil Bacteria

Michigan State University, East Lansing MI

Investigators

Abstract

Soils constitute a huge reservoir of microbes whose activities have a profound impact on global warming potential, on crop productivity, and on soil fertility and biogeochemistry. However, the vast majority of soil microbes remain uncultured, so knowledge about them is meager. Among the major and consistently present, but not-yet-cultured, microbial groups identified by cultivation-independent molecular methods are members of the Acidobacteria, Verrucomicrobia, Planctomycetes and alpha-Proteobacteria. In an effort to move beyond phylogenetic recognition and enumeration of these groups to their functionality, a genomics approach is being conducted. A novel way was devised to create large (100-150 kb) insert libraries of genomic DNA from soil such that one end of each insert is phylogenetically informative and is flanked by a large portion of genomic sequence. From such libraries, clones are being selected that capture the phylogenetic diversity and breadth of each target microbial group (above) and the inserts are being sequenced to identify genes associated with distinctive modes of nutrition and metabolism, e.g. autotrophy, diazotrophy, denitrification. Between 250-750 kb of genomic information (at * 3X coverage) can be obtained from each of 22 different not-yet-cultured soil microbes with the same effort required to sequence a complete 5 MB genome of a bacterium already in culture. From such information, the metabolic potential of the target organisms and their probable role(s) in soil ecosystems can be realized. The emerging database of sequences will help guide future work on these organisms, as well as ongoing efforts to obtain them in pure culture. Sequence data is being made available through the Ribosomal Database Project (RDP) and through GenBank. In addition to providing the sequences for additional analyses, the RDP server will present the data in a evolutionary context by linkage of sequence data to an organismal phylogeny. This is a Microbial Genome Sequencing Award funded through a collaborative program between the National Science Foundation and the Department of Agriculture Initiative for Future Agriculture and Food Systems.