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Conflicting phylogeographic patterns in rRNA and nifD indicate regionally restricted gene transfer in Bradyrhizobium^a

Department of Biological Sciences, State University of New York, Binghamton, NY 13902, USA¹
Centre for Plant Biodiversity Research, CSIRO Plant Industry, Canberra ACT 2601, Australia²
Soybean and Alfalfa Research Laboratory, USDA, ARS, HH-4, Bldg010, BARC-West, 10300 Baltimore Blvd, Beltsville, MD 20705, USA³

Author for correspondence: Matthew A. Parker. Tel: +1 607 777 6283. Fax: +1 607 777 6521. e-mail: mparker{at}binghamton.edu

Major differences in evolutionary relationships of the 16S rRNA gene and the nitrogenase -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.

Keywords: geographic variation, nitrogenase, nodule bacteria, Rhizobiaceae

Abbreviations: ML, maximum-likelihood; MP, maximum-parsimony; NJ, neighbour-joining

^a The GenBank accession numbers for the nifD sequences determined in this work are AF484254–AF484287.

^b Present address: Centre d’Etudes sur le Polymorphisme des Micro-Organismes, UMR CNRS-IRD 9926, 911 Avenue Agropolis – BP 64501, 34394 Montpellier Cedex 5, France.

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