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Applied and Environmental Microbiology, March 2005, p. 1328-1335, Vol. 71, No. 3
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.3.1328-1335.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Rhizobial 16S rRNA and dnaK Genes: Mosaicism and the Uncertain Phylogenetic Placement of Rhizobium galegae

B. D. Eardly,1* S. M. Nour,2 P. van Berkum,3 and R. K. Selander4

Pennsylvania State University, Berks Campus, Reading,1 Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, Pennsylvania,4 Soybean Genomics and Improvement Laboratory, USDA Agricultural Research Service, Beltsville, Maryland,3 Agriculture and Agri-food Canada, London, Ontario, Canada2

Received 22 June 2004/ Accepted 13 October 2004

The phylogenetic relatedness among 12 agriculturally important species in the order Rhizobiales was estimated by comparative 16S rRNA and dnaK sequence analyses. Two groups of related species were identified by neighbor-joining and maximum-parsimony analysis. One group consisted of Mesorhizobium loti and Mesorhizobium ciceri, and the other group consisted of Agrobacterium rhizogenes, Rhizobium tropici, Rhizobium etli, and Rhizobium leguminosarum. Although bootstrap support for the placement of the remaining six species varied, A. tumefaciens, Agrobacterium rubi, and Agrobacterium vitis were consistently associated in the same subcluster. The three other species included Rhizobium galegae, Sinorhizobium meliloti, and Brucella ovis. Among these, the placement of R. galegae was the least consistent, in that it was placed flanking the A. rhizogenes-Rhizobium cluster in the dnaK nucleotide sequence trees, while it was placed with the other three Agrobacterium species in the 16S rRNA and the DnaK amino acid trees. In an effort to explain the inconsistent placement of R. galegae, we examined polymorphic site distribution patterns among the various species. Localized runs of nucleotide sequence similarity were evident between R. galegae and certain other species, suggesting that the R. galegae genes are chimeric. These results provide a tenable explanation for the weak statistical support often associated with the phylogenetic placement of R. galegae, and they also illustrate a potential pitfall in the use of partial sequences for species identification.

* Corresponding author. Mailing address: Pennsylvania State University, Berks Campus, P.O. Box 7009, Reading, PA 19610. Phone: (610) 396-6131. Fax: (610) 396-6024. E-mail: bde1{at}psu.edu.

Applied and Environmental Microbiology, March 2005, p. 1328-1335, Vol. 71, No. 3
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.3.1328-1335.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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