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Tropicibacter oceani sp. nov., a novel sulfur-metabolizing bacteria isolated from the intertidal zone sediment of Chinese Yellow Sea

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Abstract

In this study, we reported a Gram-stain-negative, rod-shaped, atrichous, and aerobic bacterial strain named YMD87T, which was isolated from the intertidal zone sediment of Chinese Yellow Sea. Growth of strain YMD87T occurred at 10.0–40.0 °C (optimum, 25–30 °C), pH 4.0–12.0 (optimum, 8.0) and with 0–6.0% (w/v) NaCl (optimum, 0.0–2.0%). Phylogenetic tree analysis based on 16S rRNA gene sequence indicated that strain YMD87T belonged to the genus Tropicibacter and was closely related to Tropicibacter alexandrii LMIT003T (97.2% sequence similarity). Genomic analysis indicated that strain YMD87T contains a circular chromosome of 3,932,460 bp with G + C content of 63.8% and three circular plasmids of 116,492 bp, 49,209 bp and 49,673 bp, with G + C content of 64.3%. Genomic functional analysis revealed that strain YMD87T is potential a novel sulfur-metabolizing bacteria. The predominant respiratory quinone of YMD87T was ubiquinone-10 (Q-10). The major polar lipids of YMD87T contained phosphatidylglycerol, phosphatidylethanolamine, five unidentified lipids, five unidentified phospholipids, phosphatidylcholine, unidentified glycolipid and five unidentified aminolipids. The major fatty acids of strain YMD87T contained C12:1 3-OH, C16:0, and summed feature 8 (C18:1 ω7c or/and C18:1 ω6c). Phylogenetic, physiological, biochemical and morphological analyses suggested that strain YMD87T represents a novel species of the genus Tropicibacter, and the name Tropicibacter oceani sp. nov is proposed. The type strain is YMD87T (= MCCC 1K08473T = KCTC 92856 T).

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Data availability

The 16S rRNA gene and the complete genome sequences of strain YMD87T have been deposited under the GenBank accession numbers OP942226 and CP124616, respectively.

Abbreviations

KCTC:

Korean collection for type cultures

FAME:

Fatty acid methyl esters

ANIP:

Average nucleotide identity

GGDC:

Genome-to-genome distance calculator

DSMZ:

Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

DDH:

DNA-DNA hybridizations

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Funding

This work is supported by the Key Laboratory of Mariculture of Ministry of Education, Ocean University of China, Development Plan of Youth Innovation Team in Colleges and Universities of Shandong Province (2022KJ269) and Yantai University Doctoral Start-up Foundation (HX20B34).

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Authors and Affiliations

  1. School of Ocean, Yantai University, 30 QingQuan Road, Yantai, 264005, China

    Dan-dan Zhou, Xiu-dan Xu, Bin-zhe Zhang, Ji-xing Feng & Jian Zhang

Authors
  1. Dan-dan Zhou
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  2. Xiu-dan Xu
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  3. Bin-zhe Zhang
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  4. Ji-xing Feng
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  5. Jian Zhang
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Contributions

DDZ: investigation, conceptualization, writing original draft. XDX: isolated the bacterium. BZZ and JXF: phylogenetic and genomic characterisation. JZ: supervision and writing-reviewing and editing, funding acquisition. All authors read and approved the manuscript.

Corresponding author

Correspondence to Jian Zhang.

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The authors declare that they have no competing interests.

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This article does not contain any studies with animals performed by any of the authors.

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The GenBank accession number of the 16S rRNA gene sequence of strain YMD87T is OP942226. The GenBank accession number of complete genome and plasmid sequences of strain YMD87T are CP124616-CP124619.

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Zhou, Dd., Xu, Xd., Zhang, Bz. et al. Tropicibacter oceani sp. nov., a novel sulfur-metabolizing bacteria isolated from the intertidal zone sediment of Chinese Yellow Sea. Antonie van Leeuwenhoek 116, 1337–1344 (2023). https://doi.org/10.1007/s10482-023-01890-5

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