Slow-growing and oligotrophic soil bacteria phylogenetically close to Bradyrhizobium japonicum

Eleven isolates of slow-growing oligotrophic bacteria from grassland soil were found to be closely related by partial 16S rRNA sequence similarity and many common taxonomic traits. Analysis of full 16S rRNA gene sequences of four representative isolates and Agromonas oligotrophica S58 indicated that they were more closely related to Bradyrhizobium japonicum, a symbiotic nitrogen-fixing bacterium, (similarity values: 98.1–98.8%) than other strains such as Bradyrhizobium elkanii, Nitrobacter spp., Rhodopseudomonas palustris, and Afipia spp. This result was supported by analysis of phenotypic traits and DNA-DNA hybridization analysis. No strain showed hybridization to nodD1YABC of B. japonicum, and only strain G14130 exhibited hybridization to nifDK- and hupSL-specific DNA. These latter genotypes are involved in the phenotypes of nodulation and nitrogen fixation under microaerobic conditions. These results suggest that the isolates possess a unique phylogenetic position since they are closely related to B. japonicum though they do not have characteristics of symbiotic nitrogen fixation.