Rubrobacter tropicus sp. nov. and Rubrobacter marinus sp. nov., isolated from deep-sea sediment of the South China Sea

Two novel Gram-stain-positive bacteria, designated as SCSIO 52909(T) and SCSIO 52915(T), were isolated from a deep-sea sediment sample collected at about 3448 m water depth of the South China Sea. Phenotypic, chemotaxonomic and genomic characteristics were investigated. These strains were aerobic and tested positive for catalase activity, oxidase activity and nitrate reduction. Optimal growth occurred at 28 degrees C, pH 7 and 3% salinity over 14 days cultivation. Its peptidoglycan structure was type A3 alpha (l-Lys-l-Ala) and the only menaquinone was MK-8. Both strains possessed diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid, an unidentified glycolipid and an unidentified phospholipid. Their major fatty acids differed, but both contained iso-branched components of C-16:0 12-methyl. Genome sequencing revealed two large genomes of 4.58 Mbp with G+C content of 67.0 mol% in SCSIO 52909(T) and of 4.42 Mbp with G+C content of 69.1% in SCSIO 52915(T). The two novel strains encoded genes for metabolism that are absent in most other Rubrobacter species, and possessed many more gene copy numbers of alkaline phosphatase and thioredoxin reductase. Results of gANI and 16S rRNA gene analyses suggested that the two strains represent two new species, with 74.9, 95.0% pairwise similarity between each other, and less than 74.3 and 93.5 % to other recognized Rubrobacter species, respectively. In the phylogenetic analysis, strains SCSIO 52909(T) and SCSIO 52915(T) were separately clustered together and formed a well-separated phylogenetic branch distinct from the other known species in the genus Rubrobacter. Based on the data presented here, these two strains should be recognized as two new species in the genus Rubrobacter, for which the names Rubrobacter tropicus sp. nov., with the type strain SCSIO 52909(T) (=KCTC 49412(T)=CGMCC 1.13853(T)), and Rubrobacter marinus sp. nov., with the type strain SCSIO 52915(T) (=KCTC 49411(T)=CGMCC 1.13852(T)), are proposed.