Sphingorhabdus lutea sp. Nov., isolated from sea water

Min Gyung Baek; Su Kyoung Shin; Hana Yi

doi:10.1099/ijsem.0.003662

Sphingorhabdus lutea sp. Nov., isolated from sea water

Min Gyung Baek, Su Kyoung Shin, Hana Yi

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

Abstract

A Gram-stain-negative, yellow-pigmented, aerobic bacterial strain, designated LPB0140^T, was isolated from sea water. The 16S rRNA gene sequence similarity analysis demonstrated that the closest relative of the isolate is Sphingorhabdus contaminans (96.4 %), but the new isolate formed an independent phyletic line within the genus Sphingorhabdus. Its genome is composed of a circular chromosome of 2.53 Mb with DNA G+C content of 46.1 mol%. The genome includes 2359 protein-coding genes, and two copies of rRNA operons. Strain LPB0140^T possessed C_{14: 0} 2-OH, C_{16: 1}!7c and/or C_{16: 1} !6c, and C_{18: 1} !7c and/or C_{18: 1}!6c as the major cellular fatty acids and Q-10 as the isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, and sphingoglycolipid, but phosphatidylmonomethylethanolamine and phosphatidyldimethylethanolamine were also detected as minor polar lipids. The chemotaxonomic properties and enzymatic activities of the novel isolate clearly differed from those of its closest relatives. Thus, based on the phylogenetic and phenotypic data presented in this study, strain LPB0140^T should be classified as a novel species in the genus Sphingorhabdus. The type strain is LPB0140^T (=KACC18891^T =JCM31568^T ).

Original language	English
Article number	003662
Pages (from-to)	3593-3598
Number of pages	6
Journal	International Journal of Systematic and Evolutionary Microbiology
Volume	69
Issue number	11
DOIs	https://doi.org/10.1099/ijsem.0.003662
Publication status	Published - 2019

Bibliographical note

Funding Information:
Author affiliations: 1Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea; 2Institute for Biomaterials, Korea University, Seoul, Republic of Korea; 3School of Biosystem, and Biomedical Science, Korea University, Seoul, Republic of Korea. *Correspondence: Hana Yi, [email protected] Keywords: Sphingorhabdus lutea; Sphingorhabdus; sphingolipid. Abbreviations: AL, unidentified aminolipid; DPG, diphosphatidylglycerol; GL, unidentified glycolipid; L, unidentified lipid; PC, phosphatidylcholine; PDME, phosphatidyldimethylethanolamine; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PL, unidentified phospholipid; PMME, phosphati-dylmonomethylethanolamine; SGL, sphingoglycolipid. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence and the complete genome sequence of Sphingorhabdus lutea LPB0140T are KX066860 and CP018154, respectively. Four supplementary figures are available with the online version of this article.

Funding Information:
This study was funded by the Survey of Korean Indigenous Species Program through the National Institute of Biological Resources funded by the Korean Ministry of Environment and the Basic Science Research Programs through the National Research Foundation of Korea (NRF) funded by the Korean Ministry of Education (2015R1D1A1A01057527).

Publisher Copyright:
© 2019, Microbiology Society. All rights reserved.

Keywords

Sphingolipid
Sphingorhabdus
Sphingorhabdus lutea

ASJC Scopus subject areas

Microbiology
Ecology, Evolution, Behavior and Systematics

Access to Document

10.1099/ijsem.0.003662

Cite this

@article{437f4f65af304ec8866ba26fdfd41090,

title = "Sphingorhabdus lutea sp. Nov., isolated from sea water",

abstract = "A Gram-stain-negative, yellow-pigmented, aerobic bacterial strain, designated LPB0140T, was isolated from sea water. The 16S rRNA gene sequence similarity analysis demonstrated that the closest relative of the isolate is Sphingorhabdus contaminans (96.4 %), but the new isolate formed an independent phyletic line within the genus Sphingorhabdus. Its genome is composed of a circular chromosome of 2.53 Mb with DNA G+C content of 46.1 mol%. The genome includes 2359 protein-coding genes, and two copies of rRNA operons. Strain LPB0140T possessed C14: 0 2-OH, C16: 1!7c and/or C16: 1 !6c, and C18: 1 !7c and/or C18: 1!6c as the major cellular fatty acids and Q-10 as the isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, and sphingoglycolipid, but phosphatidylmonomethylethanolamine and phosphatidyldimethylethanolamine were also detected as minor polar lipids. The chemotaxonomic properties and enzymatic activities of the novel isolate clearly differed from those of its closest relatives. Thus, based on the phylogenetic and phenotypic data presented in this study, strain LPB0140T should be classified as a novel species in the genus Sphingorhabdus. The type strain is LPB0140T (=KACC18891T =JCM31568T ).",

keywords = "Sphingolipid, Sphingorhabdus, Sphingorhabdus lutea",

author = "Baek, {Min Gyung} and Shin, {Su Kyoung} and Hana Yi",

note = "Funding Information: Author affiliations: 1Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea; 2Institute for Biomaterials, Korea University, Seoul, Republic of Korea; 3School of Biosystem, and Biomedical Science, Korea University, Seoul, Republic of Korea. *Correspondence: Hana Yi, [email protected] Keywords: Sphingorhabdus lutea; Sphingorhabdus; sphingolipid. Abbreviations: AL, unidentified aminolipid; DPG, diphosphatidylglycerol; GL, unidentified glycolipid; L, unidentified lipid; PC, phosphatidylcholine; PDME, phosphatidyldimethylethanolamine; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PL, unidentified phospholipid; PMME, phosphati-dylmonomethylethanolamine; SGL, sphingoglycolipid. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence and the complete genome sequence of Sphingorhabdus lutea LPB0140T are KX066860 and CP018154, respectively. Four supplementary figures are available with the online version of this article. Funding Information: This study was funded by the Survey of Korean Indigenous Species Program through the National Institute of Biological Resources funded by the Korean Ministry of Environment and the Basic Science Research Programs through the National Research Foundation of Korea (NRF) funded by the Korean Ministry of Education (2015R1D1A1A01057527). Publisher Copyright: {\textcopyright} 2019, Microbiology Society. All rights reserved.",

year = "2019",

doi = "10.1099/ijsem.0.003662",

language = "English",

volume = "69",

pages = "3593--3598",

journal = "International Journal of Systematic and Evolutionary Microbiology",

issn = "1466-5026",

publisher = "Microbiology Society",

number = "11",

}

TY - JOUR

T1 - Sphingorhabdus lutea sp. Nov., isolated from sea water

AU - Baek, Min Gyung

AU - Shin, Su Kyoung

AU - Yi, Hana

N1 - Funding Information: Author affiliations: 1Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea; 2Institute for Biomaterials, Korea University, Seoul, Republic of Korea; 3School of Biosystem, and Biomedical Science, Korea University, Seoul, Republic of Korea. *Correspondence: Hana Yi, [email protected] Keywords: Sphingorhabdus lutea; Sphingorhabdus; sphingolipid. Abbreviations: AL, unidentified aminolipid; DPG, diphosphatidylglycerol; GL, unidentified glycolipid; L, unidentified lipid; PC, phosphatidylcholine; PDME, phosphatidyldimethylethanolamine; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PL, unidentified phospholipid; PMME, phosphati-dylmonomethylethanolamine; SGL, sphingoglycolipid. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence and the complete genome sequence of Sphingorhabdus lutea LPB0140T are KX066860 and CP018154, respectively. Four supplementary figures are available with the online version of this article. Funding Information: This study was funded by the Survey of Korean Indigenous Species Program through the National Institute of Biological Resources funded by the Korean Ministry of Environment and the Basic Science Research Programs through the National Research Foundation of Korea (NRF) funded by the Korean Ministry of Education (2015R1D1A1A01057527). Publisher Copyright: © 2019, Microbiology Society. All rights reserved.

PY - 2019

Y1 - 2019

N2 - A Gram-stain-negative, yellow-pigmented, aerobic bacterial strain, designated LPB0140T, was isolated from sea water. The 16S rRNA gene sequence similarity analysis demonstrated that the closest relative of the isolate is Sphingorhabdus contaminans (96.4 %), but the new isolate formed an independent phyletic line within the genus Sphingorhabdus. Its genome is composed of a circular chromosome of 2.53 Mb with DNA G+C content of 46.1 mol%. The genome includes 2359 protein-coding genes, and two copies of rRNA operons. Strain LPB0140T possessed C14: 0 2-OH, C16: 1!7c and/or C16: 1 !6c, and C18: 1 !7c and/or C18: 1!6c as the major cellular fatty acids and Q-10 as the isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, and sphingoglycolipid, but phosphatidylmonomethylethanolamine and phosphatidyldimethylethanolamine were also detected as minor polar lipids. The chemotaxonomic properties and enzymatic activities of the novel isolate clearly differed from those of its closest relatives. Thus, based on the phylogenetic and phenotypic data presented in this study, strain LPB0140T should be classified as a novel species in the genus Sphingorhabdus. The type strain is LPB0140T (=KACC18891T =JCM31568T ).

AB - A Gram-stain-negative, yellow-pigmented, aerobic bacterial strain, designated LPB0140T, was isolated from sea water. The 16S rRNA gene sequence similarity analysis demonstrated that the closest relative of the isolate is Sphingorhabdus contaminans (96.4 %), but the new isolate formed an independent phyletic line within the genus Sphingorhabdus. Its genome is composed of a circular chromosome of 2.53 Mb with DNA G+C content of 46.1 mol%. The genome includes 2359 protein-coding genes, and two copies of rRNA operons. Strain LPB0140T possessed C14: 0 2-OH, C16: 1!7c and/or C16: 1 !6c, and C18: 1 !7c and/or C18: 1!6c as the major cellular fatty acids and Q-10 as the isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, and sphingoglycolipid, but phosphatidylmonomethylethanolamine and phosphatidyldimethylethanolamine were also detected as minor polar lipids. The chemotaxonomic properties and enzymatic activities of the novel isolate clearly differed from those of its closest relatives. Thus, based on the phylogenetic and phenotypic data presented in this study, strain LPB0140T should be classified as a novel species in the genus Sphingorhabdus. The type strain is LPB0140T (=KACC18891T =JCM31568T ).

KW - Sphingolipid

KW - Sphingorhabdus

KW - Sphingorhabdus lutea

UR - http://www.scopus.com/inward/record.url?scp=85074445075&partnerID=8YFLogxK

U2 - 10.1099/ijsem.0.003662

DO - 10.1099/ijsem.0.003662

M3 - Article

C2 - 31460859

AN - SCOPUS:85074445075

SN - 1466-5026

VL - 69

SP - 3593

EP - 3598

JO - International Journal of Systematic and Evolutionary Microbiology

JF - International Journal of Systematic and Evolutionary Microbiology

IS - 11

M1 - 003662

ER -

Sphingorhabdus lutea sp. Nov., isolated from sea water

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this