Sphingomonas xanthus sp. nov., Isolated from Beach Soil

Abstract

A light yellow-colored, Gram-stain-negative, aerobic, oxidase- and catalase-positive, flagellated bacterium with motility, designated as strain AE3(T) was isolated from soil. Cells of strain AE3(T) are rod-shaped, and the colonies are round and convex. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain AE3(T) forms a lineage within the genus Sphingomonas of the family Sphingomonadaceae and is most closely related to Sphingomonas edaphi KCTC 62107( T) (98.6%), Sphingomonas oryziterrae KCTC 22476( T) (97.9%), and Sphingomonas jaspsi DSM 18422( T) (97.4%). The growth of the strain AE3(T) was observed under 18-42 degrees C (optimum, 37 degrees C), pH 6.0-9.0 (optimum, pH 6.5-7.0), and in the absence of NaCl. Strain AE3(T) contains Q-10 as a predominant respiratory quinone, and the major fatty acids are C-17:1 omega 6c, summed feature 8 (C-18:1 omega 7c), and summed feature 3 (C-16:1 omega 7c and/or C-16:1 omega 6c). The major polar lipids are sphingoglycolipids, unidentified phospholipids, and phosphatidylethanolamine. The DNA G + C content of strain AE3(T) is 63.6 mol%. The nearly complete genome of strain AE3(T) consists of 2.2 Mbp, (2,168 total protein-coding genes, 45 tRNAs, 4 ncRNAs, and 3 rRNAs). Genomic taxonomy analysis demonstrates that the novel strain has < 75.9% average nucleotide identity value, and also shows < 24.9% in silico DNA-DNA hybridization value compared to related taxa, which clearly separates strain AE3(T) from other species of the genus Sphingomonas with values below the thresholds for species delineation. Based on phenotypic, genotypic, and phylogenetic analyses, strain AE3(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas xanthus sp. nov. is proposed. The type strain of Sphingomonas xanthus is AE3(T) (= KCTC 620106( T) = JCM 32376( T)).