Rhizobium smilacinae sp. nov., an endophytic bacterium isolated from the leaf of Smilacina japonica

During a study of endophytic bacteria from traditional Chinese medicinal plants, a bacterial strain, designated PTYR-5T, was isolated from the leaf of Smilacina japonica A. Gray collected from Taibai Mountain in Shaanxi Province, north-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PTYR-5T is a member of the genus Rhizobium, exhibiting the highest sequence similarities to R. cellulosilyticum LMG 23642T (97.2 %), R. huautlense LMG 18254T (97.2 %) and R. alkalisoli CCBAU 01393T (97.1 %). The levels of 16S rRNA gene sequence similarity with respect to other Rhizobium species with validly published names were less than 97.0 %. Phylogenies of the housekeeping genes atpD, recA and glnII confirmed its distinct position, showing low similarity with respect to those of recognized Rhizobium species (no more than 94.1 , 90.0 and 88.0      % similarity, respectively). The DNA–DNA relatedness values of strain PTYR-5T with R. cellulosilyticum LMG 23642T, R. huautlense LMG 18254T and R. alkalisoli CCBAU 01393T were 33.6, 21.4 and 29.5 %, respectively. Based on phenotypic, phylogenetic and genotypic data, strain PTYR-5T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium smilacinae sp. nov. is proposed. The type strain is PTYR-5T (=CCTCC AB 2013016T=KCTC 32300T=LMG 27604T).