A census of rRNA genes and linked genomic sequences within a soil metagenomic library

Mark R. Liles, Brian F. Manske, Scott B. Bintrim, Jo Handelsman, Robert M. Goodman

Research output: Contribution to journalArticlepeer-review

154 Scopus citations

Abstract

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, α-Proteobacteria, and CFB groups; greater representation among the β- and γ-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.

Original languageEnglish (US)
Pages (from-to)2684-2691
Number of pages8
JournalApplied and environmental microbiology
Volume69
Issue number5
DOIs
StatePublished - May 1 2003
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Applied Microbiology and Biotechnology
  • Food Science
  • Biotechnology
  • Ecology

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