Submitted to: North American Conference on Symbiotic Nitrogen Fixation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 27, 2004
Publication Date: June 27, 2004
Citation: Van Berkum, P.B., Eardly, B.D., Nour, S.M., Selander, R.K. 2004. Rhizobial 16s and dnak genes: mosaicism and the uncertain phylogenetic placement of rhizobium galegae [abstract]. North American Conference on Symbiotic Nitrogen Fixation. p. 73.
Interpretive Summary: The microbial world profoundly influences agriculture because members either can be beneficial or be harmful. Among microbes, the most predominant are bacteria and archae, which are distinguished from all other life forms by the absence of a membrane bound nucleus containing the genetic material of the cell. Because of their importance in industry, medicine, and agriculture, bacterial molecular and evolutionary biology is a predominant approach used to uncover novel beneficial species and to track virulent pathogens. The most common method of classifying bacteria is to use the small ribosomal gene sequence to portray bacterial genealogy and from this to develop a functional taxonomy from which to extrapolate potential presence of desirable or undesirable characters. The assumption is that genetic traits are passed along by descent from parent to offspring, represented by ribosomal gene inheritance, while genetic variability results from mutation and selection. However, we demonstrate that ribosomal genes in extant bacteria are products of gene exchange and recombination between diverse and sometimes unrelated organisms. Therefore, current methods used to portray bacterial evolutionary relationships are invalid and the evidence in support for the description of taxonomic groups is unsupportable. This information is useful to scientists with interest in bacterial identification, taxonomy and evolutionary biology.
The phylogenetic relatedness among twelve agriculturally important species in the order Rhizobiales were estimated by comparative 16S rRNA and dnaK sequence analyses. Two groups of related species were identified by neighbor joining analysis. One group consisted of the Mesorhizobium loti and M. ciceri, and the other group consisted of
Agrobacterium rhizogenes, Rhizobium tropici, R. etli, and R. leguminosarum. Although bootstrap support for the placement of the remaining six species varied, A. tumefaciens and A. rubi were consistently joined by the same node. The other four species included: A. vitis, R. 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. 1 rhizogenes - Rhizobium cluster in the dnaK nucleotide sequence tree, while it was placed among three Agrobacterium species in the 16S 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 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.