S phingopyxis lutea sp. nov., a novel moderately halotolerant bacterium isolated from pebbles

A Gram-stain-negative, aerobic, motile and rod-shaped bacterium was isolated from pebbles collected from the coast near Taejongdae Park, Busan, South Korea. Phylogenetic analysis based on 16S rRNA gene sequence analysis revealed that strain DHUNG17^T belonged to the family Sphingomonadaceae, and it showed the highest sequence similarity found with Sphingopyxis panaciterrulae DCY34^T (98.4%) and Sphingopyxis granuli TFA^T (98.4%). The strain grew at 10–45 °C, at pH 5.0–9.0 and with 0–12% (w/v) NaCl. Chemotaxonomic data revealed that strain DHUNG17^T possessed ubiquinone Q-10 as the predominant respiratory lipoquinone. The predominant fatty acids were C_16: 0, C_18: 0, summed feature 4 (C_16: 1ω7c and/or C_15: 0 iso 2-OH) and summed feature 8 (C_19: 1ω6c and/or unknown 18.864). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and a sphingoglycolipid and spermidine were detected as the major polyamines. Strain DHUNG17^T was able to produce carotenoid-type pigment. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values with its closest neighbors were 79.3–81.7% and 22.0–24.4%, respectively. The genome of strain DHUNG17^T is 3,129,415 bp long with a DNA G + C content of 64.7% and encodes 2,951 predicted proteins, 3 rRNAs and 47 tRNAs. Gene related to transportation of polycyclic aromatic hydrocarbons (PAHs) was found in the genome of strain DHUNG17^T. According to the genotypic, phylogenetic and chemotaxonomic data, strain DHUNG17^T represents a novel species within the genus Sphingopyxis, for which the name Sphingopyxis lutea sp. nov. is proposed. The type strain is DHUNG17^T (= KACC 21746^T = NBRC 114643^T).