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Applied and Environmental Microbiology, May 2003, p. 2684-2691, Vol. 69, No. 5
0099-2240/03/$08.00+0     DOI: 10.1128/AEM.69.5.2684-2691.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

A Census of rRNA Genes and Linked Genomic Sequences within a Soil Metagenomic Library

Mark R. Liles,1 Brian F. Manske,1 Scott B. Bintrim,1,{dagger} Jo Handelsman,1 and Robert M. Goodman1,2*

Department of Plant Pathology,1 Gaylord Nelson Institute of Environmental Studies, University of Wisconsin—Madison, Madison, Wisconsin 537062

Received 15 October 2002/ Accepted 30 January 2003

We have analyzed the diversity of microbial genomes represented in a library of metagenomic DNA from soil. A total of 24,400 bacterial artificial chromosome (BAC) clones were screened for 16S rRNA genes. The sequences obtained from BAC clones were compared with a collection generated by direct PCR amplification and cloning of 16S rRNA genes from the same soil. The results indicated that the BAC library had substantially lower representation of bacteria among the Bacillus, {alpha}-Proteobacteria, and CFB groups; greater representation among the ß- and {gamma}-Proteobacteria, and OP10 divisions; and no rRNA genes from the domains Eukaryota and Archaea. In addition to rRNA genes recovered from the bacterial divisions Proteobacteria, Verrucomicrobia, Firmicutes, Cytophagales, and OP11, we identified many rRNA genes from the BAC library affiliated with the bacterial division Acidobacterium; all of these sequences were affiliated with subdivisions that lack cultured representatives. The complete sequence of one BAC clone derived from a member of the Acidobacterium division revealed a complete rRNA operon and 20 other open reading frames, including predicted gene products involved in cell division, cell cycling, folic acid biosynthesis, substrate metabolism, amino acid uptake, DNA repair, and transcriptional regulation. This study is the first step in using genomics to reveal the physiology of as-yet-uncultured members of the Acidobacterium division.

* Corresponding author. Mailing address: Department of Plant Pathology, University of Wisconsin—Madison, Room 689A, Russell Laboratories, 1630 Linden Dr., Madison, WI 53706. Phone: (608) 262-9162. Fax: (608) 262-8643. E-mail: RGoodman{at}wisc.edu.

{dagger} Present address: Dow AgroSciences LLC, Indianapolis, IN 46268.

Applied and Environmental Microbiology, May 2003, p. 2684-2691, Vol. 69, No. 5
0099-2240/03/$08.00+0     DOI: 10.1128/AEM.69.5.2684-2691.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



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