New perspective on uncultured bacterial phylogenetic division OP11 - PubMed (original) (raw)

New perspective on uncultured bacterial phylogenetic division OP11

J Kirk Harris et al. Appl Environ Microbiol. 2004 Feb.

Abstract

Organisms belonging to the OP11 candidate phylogenetic division of Bacteria have been detected only in rRNA-based sequence surveys of environmental samples. Preliminary studies indicated that such organisms represented by the sequences are abundant and widespread in nature and highly diverse phylogenetically. In order to document more thoroughly the phylogenetic breadth and environmental distribution of this diverse group of organisms, we conducted further molecular analyses on environmental DNAs. Using PCR techniques and primers directed toward each of the five described subdivisions of OP11, we surveyed 17 environmental DNAs and analyzed rRNA gene sequences in 27 clonal libraries from 14 environments. Ninety-nine new and unique sequences were determined completely, and approximately 200 additional clones were subjected to partial sequencing. Extensive phylogenetic comparisons of the new sequences to those representing other bacterial divisions further resolved the phylogeny of the bacterial candidate division OP11 and identified two new candidate bacterial divisions, OP11-derived 1 (OD1) and Sulphur River 1 (SR1). The widespread environmental distribution of representatives of the bacterial divisions OD1, OP11, and SR1 suggests potentially conspicuous biogeochemical roles for these organisms in their respective environments. The information on environmental distribution offers clues for attempts to culture landmark representatives of these novel bacterial divisions, and the sequences are specific molecular signatures that provide for their identification in other contexts.

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Figures

FIG. 1.

FIG. 1.

Bootstrap consensus tree showing the well-supported phylogenetic relationships for the bacterial divisions OP11, OD1, and SR1, with division names listed outside the brackets. Nodes within the tree that are supported (bootstrap values of >70%) (9) in all analyses (distance, MP, and ML [see Results]) are indicated by filled circles. Nodes without circles were not strongly supported (bootstrap of <70%) in all analyses. Bootstrap support for the division-level divergences (Table 2) are given for ME (top, 245-taxa data set, HKY85 model of evolution) and MP (bottom, 245-taxa data set). The bar represents 5% sequence divergence.

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