Rhizobium lichense sp. nov., a novel rhizobial species lacking nodC and nifH genes, isolated from a lichen sample Xanthoparmelia orientalis

A Gram-stain-negative, pinkish-white, non-spore-forming, catalase-positive, oxidase-positive, motile with flagella, rod-shaped and aerobic bacterium, denominated strain YIM 134829 ^T , was isolated from a lichen Xanthoparmelia orientalis collected from the rock surface soil in Chayu County, Linzhi City, Tibet Autonomous Region, China. The novel strain grew at pH 5.0–10.0 (optimum, pH 7.0–8.0), 4–40 ℃ (optimum, 20–40℃, including 28℃, 37℃), and with the existence of 0–3% (w/v) NaCl. The predominant polar lipids in strain YIM 134829 ^T consisted of phosphatidylcholines and phosphatidylmethylethanolamine. Q-10 was identified as the predominant ubiquinone. The major fatty acids (> 4%) of the strain contained C _18:1 ω 9 c (31.3%), C _17:1 ω 7 c (21.4%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain isolate was related to species of the genus Rhizobium , sharing the highest 16S rRNA gene sequence similarity with Rhizobium helianthi CGMCC 1.12192 ^T (97%), followed by Rhizobium capsici CC-SKC2 ^T (96.6%), and Rhizobium rhizoryzae J3-AN59 ^T (96.4%). There were low similarities (< 93%) between the recA , atpD and glnII gene sequences of the novel strain and those of members of the genus Rhizobium . The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain YIM 134829 ^T and its closely related type strains were 72.6–76.6% and 19.3–20.7%, respectively, which were below the species delineation thresholds. Genomic analysis revealed the absence of the nodulation ( nodC ) and nitrogen fixation ( nifH ) genes. On the basis of physiological and biochemical characteristics, together with genotypic data obtained in this study, strain YIM 134829 ^T represents a novel species of the genus Rhizobium , for which the name Rhizobium lichense sp. nov. is proposed. The type strain is YIM 134829 ^T (= CGMCC1.61955 ^T =XXXXX).