Genome Analysis Suggests that the Soil Oligotrophic Bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) Is a Nitrogen-Fixing Symbiont of Aeschynomene indica

ABSTRACTAgromonas oligotrophica(Bradyrhizobium oligotrophicum) S58Tis a nitrogen-fixing oligotrophic bacterium isolated from paddy field soil that is able to grow in extra-low-nutrient environments. Here, the complete genome sequence of S58 was determined. The S58 genome was found to comprise a circular chromosome of 8,264,165 bp with an average GC content of 65.1% lackingnodABCgenes and the typical symbiosis island. The genome showed a high level of similarity to the genomes ofBradyrhizobiumsp. ORS278 andBradyrhizobiumsp. BTAi1, including nitrogen fixation and photosynthesis gene clusters, which nodulate an aquatic legume plant,Aeschynomene indica, in a Nod factor-independent manner. Although nonsymbiotic (brady)rhizobia are significant components of rhizobial populations in soil, we found that most genes important for nodule development (ndv) and symbiotic nitrogen fixation (nifandfix) withA. indicawere well conserved between the ORS278 and S58 genomes. Therefore, we performed inoculation experiments with fiveA. oligotrophicastrains (S58, S42, S55, S72, and S80). Surprisingly, all five strains ofA. oligotrophicaformed effective nitrogen-fixing nodules on the roots and/or stems ofA. indica, with differentiated bacteroids. Nonsymbiotic (brady)rhizobia are known to be significant components of rhizobial populations without a symbiosis island or symbiotic plasmids in soil, but the present results indicate that soil-dwellingA. oligotrophicagenerally possesses the ability to establish symbiosis withA. indica. Phylogenetic analyses suggest that Nod factor-independent symbiosis withA. indicais a common trait ofnodABC- and symbiosis island-lacking strains within the members of the photosyntheticBradyrhizobiumclade, includingA. oligotrophica.