The current classification of the rhizobia (root-nodule symbionts) assigns them to six genera. It is strongly influenced by the small subunit (16S, SSU) rRNA molecular phylogeny, but such single-gene phylogenies may not reflect the evolution of the genome as a whole. To test this, parts of the atpD and recA genes have been sequenced for 25 type strains within the α-Proteobacteria, representing species in Rhizobium, Sinorhizobium, Mesorhizobium, Bradyrhizobium, Azorhizobium, Agrobacterium, Phyllobacterium, Mycoplana and Brevundimonas. The current genera Sinorhizobium and Mesorhizobium are well supported by these genes, each forming a distinct phylogenetic clade with unequivocal bootstrap support. There is good support for a Rhizobium clade that includes Agrobacterium tumefaciens, and the very close relationship between Agrobacterium rhizogenes and Rhizobium tropici is confirmed. There is evidence for recombination within the genera Mesorhizobium and Sinorhizobium, but the congruence of the phylogenies at higher levels indicates that the genera are genetically isolated. rRNA provides a reliable distinction between genera, but genetic relationships within a genus may be disturbed by recombination. Rhizobium, Sinorhizobium, Mesorhizobium, recA, atpD
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INTRODUCTIONThe rhizobia are root-nodulating bacteria responsible for a significant part of the global fixation of nitrogen. The ability of rhizobia to nodulate plants and reduce N # is conferred by genes that are plasmid-borne in many species (Pueppke, 1996), and the lateral transfer The atpD and recA sequences and details of the SimPlot analyses are available as supplementary material in IJSEM Online (http :// ijs.sgmjournals.org/ ).Abbreviations : HKY85, Hasegawa-Kishino-Yano model ; K2P, Kimura's two-parameter model ; SSU, small subunit rRNA.The EMBL accession numbers for the sequences reported in this study are AJ294386-AJ294409 (atpD) and AJ294363-AJ294385 (recA). of these genes is the most likely explanation for their occurrence within several distinct clades of subgroup 2 of the α-Proteobacteria (Dobert et al., 1994 ; Kaijalainen & Lindstro$ m, 1989 ;Lindstro$ m et al., 1995 ;Young, 1998 ;Young & Johnston, 1989). The phylogeny of the nodulation genes is quite different from that of the small subunit rRNA (SSU or 16S rRNA) genes in these bacteria. As in other bacterial groups, the SSU phylogeny has had a major influence on our current perception of evolutionary relationships among rhizobia ( Willems & Collins, 1993 ;Young, 1996 ;Young et al., 1991). More than 20 species have been described, and they are classified into the genera Rhizobium, Sinorhizobium, Allorhizobium, Mesorhizobium, Bradyrhizobium and Azorhizobium as well as ' Methylobacterium nodulans ' (de Lajudie et al., 1994' (de Lajudie et al., , 1998b Dreyfus et al., 1988 ; Jarvis et al., 1997 ; Jordan, 1982 ;Sy et al., 2001 M. W. Gaunt and others ing much slower growth on laboratory media (Dreyfus et al., 1988 ; Fred et al., 1932 ; Jordan, 1982). They are also fairly distant in the SSU p...
