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Journal of Bacteriology, May 2003, p. 2988-2998, Vol. 185, No. 10
0021-9193/03/$08.00+0     DOI: 10.1128/JB.185.10.2988-2998.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Discordant Phylogenies within the rrn Loci of Rhizobia

Soybean Genomics and Improvement Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland 20705,¹ Department of Applied Chemistry and Microbiology, Biocenter 1, Viikinkaari 9,² Institute of Biotechnology, Biocenter 1, Viikinkaari 6, University of Helsinki, Helsinki, Finland,³ Penn State Berks-Lehigh Valley College, Berks Campus, Reading, Pennsylvania 19610⁴

Received 25 October 2002/ Accepted 3 March 2003

It is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes. Since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of -Proteobacteria by sequencing analysis of three loci within their rrn operons. Tree topologies generated with 16S rRNA gene sequences were significantly different from corresponding trees assembled with 23S rRNA gene and internally transcribed space region sequences. Besides the incongruence in tree topologies, evidence that distinct segments along the 16S rRNA gene sequences of bacteria currently classified within the genera Bradyrhizobium, Mesorhizobium and Sinorhizobium have a reticulate evolutionary history was also obtained. Our data have important implications for bacterial taxonomy, because currently most taxonomic decisions are based on comparative 16S rRNA gene sequence analysis. Since phylogenetic placement based on 16S rRNA gene sequence divergence perhaps is questionable, we suggest that the proposals of bacterial nomenclature or changes in their taxonomy that have been made may not necessarily be warranted. Accordingly, a more conservative approach should be taken in the future, in which taxonomic decisions are based on the analysis of a wider variety of loci and comparative analytical methods are used to estimate phylogenetic relationships among the genomes under consideration.

For a commentary on this article, see page 2975 in this issue.

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