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 °C (optimum, 37 °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 ω6c, summed feature 8 (C_18:1 ω7c), and summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c). 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).