DNA sequence of the common nodulation genes of Bradyrhizobium elkanii and their phylogenetic relationship to those of other nodulating bacteria

Abstract

A 6.6-kb BamHI fragment containing the common nodulation genes of Bradyrhizobium elkanii USDA94 was identified by southern hybridization using the common nod genes of B. japonicum as a probe. This fragment was cloned and sequenced. Analysis of the sequence showed open reading frames highly homologous to nolA, nodD2, nodD1, and nodKABC from other bradyrhizobial sources. The sequence showed higher homology to the common nod genes of Bradyrhizobium sp. (Parasponia) than to those from B. japonicum. The open reading frame identified between nodD1 and nodA in the B. elkanii sequence was far more similar to nodK from Bradyrhizobium sp. (Parasponia) than to nodY from B. japonicum. The molecular phylogeny of nodD and nodAB from many sources was analyzed. The genetic distance between the nod genes is far greater than the distance between the 16S rRNA and nifH genes. The differences between the nod genes among the species of Rhizobium is as great as that between Bradyrhizobium and Rhizobium. The host range of the microsymbiont was found to be a better predictor of the similarities of the common nod genes than the 16S rRNA or nifH genes. We propose two groups of nod genes among the rhizobia and bradyrhizobia, based on molecular phylogenetic analysis: those which nodulate legumes of temperate origin in the tribes Vicieae or Trifolieae and those which nodulate legumes of tropical origin in the tribe Phaseoleae.