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 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 degrees 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: 1 omega 7c and/or C-15: 0 iso 2-OH) and summed feature 8 (C-19: 1 omega 6c 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)).