Sphingomonas edaphi sp. nov., a novel species isolated from beach soil in the Republic of Korea

Abstract

A yellow-coloured, Gram-negative, motile, strictly aerobic bacterial strain, designated strain DAC4T, was isolated from a soil sample collected at Ahnmok Beach (Busan, Republic of Korea). The cells of strain DAC4(T) were rod-shaped and the colonies that formed were round and convex. The results of phylogenetic analysis based on the 16S rRNA gene sequence of strain DAC4(T) revealed that the bacterium belongs to the genus Sphingomonas, family Sphingomonadaceae, and that it was most closely related to Sphingomonas jaspsi DSM 18422(T) (98.01 %), Sphingomonas rhizophila KACC 19189T (97.76 %), Sphingomonas mesophila KCTC 62179T(97.30%), Sphingomonas sedimincola KCTC 12629(T) (97.16 %) and Sphingomonas oryziterrae KCTC 22476T (97.05 %). The major respiratory quinone was Q-10, and the major cellular fatty acids were summed feature 8 (C 18 :1.7c) and summed feature 3 (C (16:1)omega 7c/C-16:1 omega 6c). The whole genome DNA G+C content of strain DAC4(T) was 62.16 mol%. Phosphatidylethanolamine, diphosphatidylglycerol, sphingoglycolipids, phosphatidylglycerol, phosphatidylcholine, four undefined glycolipids and an undefined lipid were detected in strain DAC4(T), and the strain had sym-homospermidine as a major polyamine. The in silico DNA-DNA hybridization and average nucleotide identity values between strain DAC4(T) and the closely related taxa S. jaspsi and S. mesophila were 75.5/23.5% and 73.5 /18.5%, respectively. The fluorimetric DNA-DNA hybridization results showed that strain DAC4(T) and S. rhizophila, S. sediminicola and S. oryziterrae have 37.1, 35.2 and 32.2 % DNA similarity, respectively. Based on phylogenetic, phenotypic and chemotaxonomic distinctiveness, strain DAC4(T) (=KCTC 62107(T)=JCM 32377(T)) is classified as a novel species of the genus Sphingomonas, for which the name Sphingomonas edaphi sp. nov. is proposed.