Patulibacter endophyticus sp. nov., an endophytic actinobacterium isolated from root of Acanthus ilicifolius

A Gram-stain-positive, aerobic, non-motile, non-sporulating and rod-shaped actinobacterium, designated strain S7RM1-6^T, was isolated from a root of the mangrove plant Acanthus ilicifolius collected from Beihai City in Guangxi Zhuang Autonomous Region, China. The cells of strain S7RM1-6^T were catalase-positive and oxidase-negative and grew at temperatures of 15‒40 °C (optimum, 37 °C), at pH 6.0‒9.0 (optimum, pH 7.0-8.0) and in the presence of 0‒5% (wt/v) NaCl (optimum, 1%). Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain S7RM1-6^T was affiliated with members of the genus Patulibacter and shared the highest 16S rRNA gene sequence similarities with Patulibacter minatonensis DSM 18081^T (97.9%) and Patulibacter americanus DSM 16676^T (97.9%). The draft genome of strain S7RM1-6^T displayed a size of 3.7 Mbp with a DNA G+C content of 75.0 mol%. Phylogenomic analysis based on whole-genome sequences indicated strain S7RM1-6^T should be assigned to the genus Patulibacter. The highest average nucleotide identity and digital DNA-DNA hybridization values between strain S7RM1-6^T and its closest type strain P. americanus DSM 16676^T were 80.9 and 24.7%, respectively. The chemotaxonomic characteristics supported its placement within the genus Patulibacter, with meso-diaminopimelic acid as the diagnostic peptidoglycan diamino acid, demethylmenaquinone 7 as the predominant respiratory quinone and C_18:1 ω9c and anteiso-C_15:0 as the major fatty acids. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylglycerol, five unknown glycolipids, two unidentified phospholipids and one unidentified aminolipid. Genomic and phenotypic analyses revealed adaptive traits consistent with an endophytic lifestyle associated with A. ilicifolius, including enhanced osmotic stress tolerance, a reduced secondary metabolome and versatile carbon utilization capacity. These results support the classification of strain S7RM1-6^T as a novel species of the genus Patulibacter, for which the name Patulibacter endophyticus sp. nov. is proposed. The type strain is S7RM1-6^T (= KCTC 59613^T = CPCC 206827^T).