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Sphingomonas xanthus sp. nov., Isolated from Beach Soil

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Abstract

A light yellow-colored, Gram-stain-negative, aerobic, oxidase- and catalase-positive, flagellated bacterium with motility, designated as strain AE3T was isolated from soil. Cells of strain AE3T are rod-shaped, and the colonies are round and convex. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain AE3T 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 AE3T 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 AE3T contains Q-10 as a predominant respiratory quinone, and the major fatty acids are C17:1 ω6c, summed feature 8 (C18:1 ω7c), and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The major polar lipids are sphingoglycolipids, unidentified phospholipids, and phosphatidylethanolamine. The DNA G + C content of strain AE3T is 63.6 mol%. The nearly complete genome of strain AE3T 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 AE3T from other species of the genus Sphingomonas with values below the thresholds for species delineation. Based on phenotypic, genotypic, and phylogenetic analyses, strain AE3T 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 AE3T (= KCTC 620106 T = JCM 32376 T).

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Abbreviations

RAST:

Rapid Annotation using Subsystem Technology

ANI:

Average nucleotide identity

DDH:

DNA–DNA hybridization

GGDC:

Genome-to-Genome Distance Calculator

SGL:

Sphingoglycolipid

PL:

Phospholipid

PE:

Phosphatidylethanolamine

GPL:

Glycerophospholipids

GL:

Glycolipids

NJ:

Neighbor-joining

MP:

Maximum-parsimony

ML:

Maximum-likelihood

ME:

Minimum-evolution

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Acknowledgements

The authors thank Dr. Bernhard Schink (University of Konstanz, Konstanz, Germany) for the suggested genus and species names. This work was supported by a grant from the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR202002203), and by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (2020R1F1A1072647).

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  1. Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea

    Hyungdong Kim, Geeta Chhetri & Taegun Seo

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  1. Hyungdong Kim
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HK isolated the bacterium, designed the study, performed the phenotypic and biochemical characterization, and wrote the original draft; GC helped with the analysis of taxonomic data; TS designed and supervised the study, and edited the original draft.

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Correspondence to Taegun Seo.

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Kim, H., Chhetri, G. & Seo, T. Sphingomonas xanthus sp. nov., Isolated from Beach Soil. Curr Microbiol 78, 403–410 (2021). https://doi.org/10.1007/s00284-020-02273-z

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