A topomonas sediminilitoris sp. nov., isolated from beach sediment of Zhairuo Island, China

A novel bacterium designated A3.4 T was isolated from the beach sediment of Zhairuo Island, which is located in the East China Sea. Strain A3.4 T was found to be Gram-stain negative, cream coloured, rod-shaped, aerobic and motile via a single monopolar flagellum. The isolate grows at 20–37 °C (optimum 25–30 °C), at pH 6.0–8.0 (optimum pH 7.0–8.0), and in the presence of 0–5.0% (w/v) NaCl (optimum 0.5–1%). A3.4 T has catalase and oxidase activity. The predominant fatty acids (≥ 10%) of the strain were identified as C 16:0 , summed feature 3 (C 16:1 ω 7 c /C 16:1 ω 6 c ) and summed feature 8 (C 18:1 ω 7 c /C 18:1 ω 6 c ). Q-9 was identified as the major isoprenoid quinone, with trace levels of Q-8 present. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The draft genome size is 3.55 Mb, with a DNA G + C content of 57.7 mol%. Analysis of the 16S rRNA gene sequence of strain A3.4 T indicates that it belongs to the genus Atopomonas and shares high sequence similarity with Atopomonas hussainii JCM 19513 T (97.60%). This classification was also supported by phylogenetic analysis using rpoB and several core genes. The genome of strain A3.4 T shows an average nucleotide identity of 82.3%, an amino acid identity of 83.0%, and a digital DNA–DNA hybridization value of 22.1% with A . hussainii . In addition, 20 conserved signature indels (CSIs) were identified to be specific for A3.4 T and A . hussainii , demonstrating that the strain A3.4 T is closely related to A. hussainii rather than other species of family Pseudomonadaceae . Hundreds of unique genes were identified in the genomes of A3.4 T and A . hussainii , which may underly multiple phenotypic differences between these strains. Based on phenotypic, chemotaxonomic, phylogenetic, and genomic investigations, strain A3.4 T is concluded to represent a novel species of the genus Atopomonas , for which the name Atopomonas sediminilitoris sp. nov. is proposed. The type strain is A3.4 T (= LMG 32563 T = MCCC 1K07166 T ).