Sphingomonas xanthus sp. nov., Isolated from Beach Soil

• Published in: Current microbiology Vol. 78; no. 1; pp. 403 - 410
• Main Authors: Kim, Hyungdong, Chhetri, Geeta, Seo, Taegun
• Format: Journal Article
• Language: English
• Published: New York Springer US 2021; Springer Nature B.V
• Subjects: Bacterial Typing Techniques; Biomedical and Life Sciences; Biotechnology; Catalase; Deoxyribonucleic acid; DNA; DNA, Bacterial - genetics; Fatty acids; Fatty Acids - analysis; Genomes; Genomic analysis; Gram stain; Hybridization; Life Sciences; Lipids; Microbiology; New species; Nucleotides; pH effects; Phosphatidylethanolamine; Phospholipids; Phylogenetics; Phylogeny; Quinones; RNA, Ribosomal, 16S - genetics; rRNA 16S; Sequence Analysis, DNA; Sodium chloride; Soil; Soil Microbiology; Soils; Sphingoglycolipids; Sphingomonas; Sphingomonas - genetics; Taxonomy
• ISSN: 0343-8651; 1432-0991
• DOI: 10.1007/s00284-020-02273-z

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
ω
6
c
, summed feature 8 (C
18:1
ω
7
c
), and summed feature 3 (C
16:1
ω
7
c
and/or C
16:1
ω
6
c
). 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
).