NifH and NifD sequences of heliobacteria: a new lineage in the nitrogenase phylogeny.
Partial sequences of farnesyl diphosphate (FPP) synthase genes derived from the Rhodobacter-Rhodovulum group and from the Rhodopseudomonas palustris-Bradyrhizobium japonicum group of the alpha-Proteobacteria were subjected to phylogenetic analysis to investigate the relationships of phototrophic and non-phototrophic bacteria in the alpha-Proteobacteria . The four Rhodovulum species formed a monophyletic group within the Rhodobacter cluster, and Agrobacterium ferrugineum IAM 12616(T) intermingled with the Rhodobacter species. This topology is in good agreement with the 16S rRNA phylogeny, although the FPP synthase gene was more divergent than the 16S rRNA. On the other hand, strains of the phototrophic Rps. palustris formed a cluster far from that of the non-phototrophic Bradyrhizobium japonicum strains. Moreover, Rps. palustris strains were differentiated from the nodule-forming B. japonicum, Mezorhizobium loti MAFF 303099 and Sinorhizobium sp. NGR 234 in the FPP synthase phylogeny. This relationship does not agree with the 16S rRNA phylogeny, wherein Rps. palustris was more closely related to B. japonicum than to strains of the Rhodobacter-Rhodovulum group. These results suggest that the FPP synthase gene of Rps. palustris diverged from that of B. japonicum.