Description of Neorhizobium ytuae sp. nov., a non-symbiotic bacterium isolated from the deep-sea cold seep sediment of South China Sea

Abstract In this study, we reported a Gram-stain-negative, rod-shaped, flagellated, and aerobic bacterial strain named CSC1952T, which was isolated from the deep-sea cold seep sediment of South China Sea. Growth of strain CSC1952T occurred at 10–40°C (optimum, 30°C), pH 5.0–11.0 (optimum, 6.0–7.0) and with 0–5.0% (w/v) NaCl (optimum, 0–1.0%). Phylogenetic tree analysis based on 16S rRNA gene or genomic sequence indicated that strain CSC1952T belonged to the genus Neorhizobium and was closely related to Neorhizobium petrolearium SL-1T (97.35% sequence similarity), and Rhizobium deserti SPY-1T (97.28%). Genomic analysis indicated that strain CSC1952T contains a circular chromosome of 4,909,874 bp with G + C content of 62.8%. The polar lipids of CSC1952T include phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unidentified aminolipid, phosphatidylmethylethanolamine; diphosphatidylglycerol; unidentified glycolipid; unidentified phospholipids. The major fatty acids of strain CSC1952T contained C16:0, C19:0 cyclo ω 8c, summed feature 2 and 8. In addition, none of the symbiotic and nitrogen-fixing genes were detected in the in the genomic of strain CSC1952T, indicating strain CSC1952T is a non-symbiotic bacterium. Phylogenetic, physiological, biochemical and morphological analyses suggested that strain CSC1952T represents a novel genus and a novel species of the genus Neorhizobium, and the name Neorhizobium ytuae sp. nov. is proposed. The type strain is CSC1952T (= MCCC 1K08370T = LMG 33224T). The GenBank accession number of complete genome sequence of strain CSC1952T is CP128416 The 16S rRNA gene GenBank accession number of the strain CSC1952T is OP441406.