Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia

The current classification of the rhizobia (root-nodule symbionts) assigns them to six genera. It is strongly influenced by the small subunit (16S, SS U) rRNA molecular phylogeny, but such single-gene phylogenies may not refle ct 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 alpha -Pr oteobacteria, representing species in Rhizobium, Sinorhizobium, Mesorhizobi um, 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 w ith unequivocal bootstrap support. There is good support for a Rhizobium cl ade that includes Agrobacterium tumefaciens, and the very close relationshi p between Agrobacterium rhizogenes and Rhizobium tropici is confirmed. Ther e is evidence for recombination within the genera Mesorhizobium and Sinorhi zobium, but the congruence of the phylogenies at higher levels indicates th at the genera are genetically isolated. rRNA provides a reliable distinctio n between genera, but genetic relationships within a genus may be disturbed by recombination.