Slow-growing Rhizobium japonicum comprises two highly divergent symbiotic types.

We examined the interrelationships of the genomes of 10 slow-growing strains of Rhizobium japonicum to provide a foundation for molecular genetic studies of these agriculturally important endosymbiotic bacteria of commercial soybeans. The degree of base substitution in and around known symbiotic genes (nif and presumptive nod), constitutively expressed genes (glnA and recA), and two other cloned sequences was estimated from restriction site variation by using cloned DNAs as hybridization probes to genomic Southern blots. Two highly divergent patterns of conservation of nifDH genes and nod-homologous sequences were found. On this basis, we classified the strains as the symbiotic genotypes sTI or sTII. Existing maps of the nif genes of R. japonicum apply only to strains of the sTI genotype. This division was further characterized by four other probes which also distinguished two sublines within sTI. Phenograms were constructed depicting interrelationships according to DNA sequence divergence. sTI and sTII are two highly divergent evolutionary lines consistent with the status of individual species. Neither is related to fast-growing Rhizobium strains (PRC strains) nodulating soybeans.