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

Abstract

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 DHUNG17T belonged to the family Sphingomonadaceae, and it showed the highest sequence similarity found with Sphingopyxis panaciterrulae DCY34T (98.4%) and Sphingopyxis granuli TFAT (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 DHUNG17T possessed ubiquinone Q-10 as the predominant respiratory lipoquinone. The predominant fatty acids were C16: 0, C18: 0, summed feature 4 (C16: 1 ω7c and/or C15: 0 iso 2-OH) and summed feature 8 (C19: 1 ω6c 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 DHUNG17T 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 DHUNG17T is 3,129,415bp 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 DHUNG17T. According to the genotypic, phylogenetic and chemotaxonomic data, strain DHUNG17T represents a novel species within the genus Sphingopyxis, for which the name Sphingopyxis lutea sp. nov. is proposed. The type strain is DHUNG17T (= KACC 21746T = NBRC 114643T).