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Title: CONFLICTING PHYLOGEOGRAPHIC PATTERNS IN RRNA AND NIFD INDICATE REGIONALLY RESTRICTED GENE TRANSFER IN BRADYRHIZOBIUM

Author
item Van Berkum, Peter
item PARKER, MATTHEW
item LAFAY, BENEDICTE
item BURDON, JEREMY

Submitted to: Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/26/2002
Publication Date: N/A
Citation: N/A

Interpretive Summary: Globally, soybean is the most important grain legume. Because soybean is a legume it benefits from biological nitrogen fixation through a symbiosis with soil bacteria of two different genera. In agriculture, the benefit is in the form of enhanced efficiency of crop production. Management of biological nitrogen fixation involves the inoculation of the appropriate bacterial cultures at the time of sowing. These bacterial cultures are available to the farmer as inoculants manufactured by industry. The problem is that many different bacteria are available, but comprehensive investigations for evolutionary differences have not been done. Also, factors that contribute to bacterial diversity are for the most part not known. Here we report that the bacterial symbionts vary genetically but results are influenced by the specific gene that is analyzed. We report that nitrogen fixation gene variation is influenced by geographic origin of the bacteria. We concluded that this variation may be due to genetic transfer of these genes and that the resulting recombinant gene structures are the product of the geographic location. Our results will be useful to scientists who are interested in evolutionary biology, taxonomy and strain identification of bacteria that fix nitrogen in symbioses with soybean.

Technical Abstract: Major differences in evolutionary relationships of the 16S rRNA gene and the nitrogenase alpha-subunit gene (nifD) were observed among 38 strains of Bradyrhizobium sp. nodule bacteria from North America, Central America, Asia and Australia. Two lineages were evident in the 16S rRNA phylogeny representing strains related to Bradyrhizobium japonicum (29 isolates) or Bradyrhizobium elkanii (9 isolates). Both clades were distributed across most or all of the geographic regions sampled. By contrast, in the nifD tree almost all isolates were placed into one of three groups each exclusively composed of taxa from a single geographic region (North Temperate, Central America or Australia). Isolates that were closely related or identical in gene sequence at one locus often had divergent sequences at the other locus and a partition homogeneity test indicated that the 16S rRNA and nifD phylogenies were significantly incongruent. No evidence for any gene duplication of nifD was found by Southern hybridization analysis on a subset of the strains, so unrecognized paralogy is not likely to be responsible for the discrepancy between 16S rRNA and nifD tree topologies. These results are consistent with a model whereby geographic areas were initially colonized by several diverse 16S rRNA lineages, with subsequent horizontal gene transfer of nifD leading to increased nifD sequence homogeneity within each regional population.