Isolation, Identification and Characterization of Endophytic Bacterium Rhizobium oryzihabitans sp. nov., from Rice Root with Biotechnological Potential in Agriculture

A flagellate, rod–shaped bacterium designated strain M15(T) was isolated from rice roots. Phylogenetic analysis based on the sequences of the 16S rRNA, housekeeping genes and genomes showed that the isolate belonged to the genus Rhizobium, with the highest 16S rRNA similarity to Rhizobium radiobacter LMG140(T) (99.64%) and Rhizobium pusense NRCPB10(T) (99.36%), respectively. The complete genome of the strain M15(T) has a 59.28% G+C content, and the highest average nucleotide identity (ANI) and DNA-DNA relatedness (DDH) values were obtained with R. radiobacter LMG140(T) (88.11%, 54.80%), R. pusense NRCPB10(T) (86.00%, 53.00%) and R. nepotum 39/7(T) (88.80%, 49.80%), respectively. Plant growth-promoting characteristics tests showed that the strain M15(T) produced siderophore, 1–aminocyclopropane–1–carboxylate (ACC) deaminase and indole-3-acetic acid (IAA) and also produced some secondary metabolites according to the analysis of the comparative genomes. Based on the data mentioned above, we proposed that the strain M15(T) represented a novel species of the genus Rhizobium, named Rhizobium oryzihabitans sp. nov. The type strain is M15(T) (=JCM 32903(T) = ACCC 60121(T)), and the strain M15(T) can be a novel biofertilizer Rhizobium to reduce the use of synthetic fertilizers for plant growth promotion.