Rhizobium dioscoreae sp. nov., a plant growth-promoting bacterium isolated from yam (Dioscorea species)

This study investigated endophytic nitrogen-fixing bacteria isolated from two species of yam (water yam, Dioscorea alata L.; lesser yam, Dioscorea esculenta L.) grown in nutrient-poor alkaline soil conditions on Miyako Island, Okinawa, Japan. Two bacterial strains of the genus Rhizobium, S-93^T and S-62, were isolated. The phylogenetic tree, based on the almost-complete 16S rRNA gene sequences (1476 bp for each strain), placed them in a distinct clade, with Rhizobium miluonense CCBAU 41251^T, Rhizobium hainanense I66^T, Rhizobium multihospitium HAMBI 2975^T, Rhizobium freirei PRF 81^T and Rhizobium tropici CIAT 899^T being their closest species. Their bacterial fatty acid profile, with major components of C_19 : 0 cyclo ω8c and summed feature 8, as well as other phenotypic characteristics and DNA G+C content (59.65 mol%) indicated that the novel strains belong to the genus Rhizobium. Pairwise average nucleotide identity analyses separated the novel strains from their most closely related species with similarity values of 90.5, 88.9, 88.5, 84.5 and 84.4 % for R. multihospitium HAMBI 2975^T, R. tropici CIAT 899^T, R. hainanense CCBAU 57015^T, R. miluonense HAMBI 2971^T and R. freirei PRF 81^T, respectively; digital DNA-DNA hybridization values were in the range of 26-42 %. Considering the phenotypic characteristics as well as the genomic data, it is suggested that strains S-93^T and S-62 represent a new species, for which the name Rhizobium dioscoreae is proposed. The type strain is S-93^T (=NRIC 0988^T=NBRC 114257^T=DSM 110498^T).