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Pelagibacterium flavum sp. nov., Isolated from Soil Sample

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Abstract

A Gram-stain-negative, yellow, moist and circular, aerobic, motile, and rod-shaped bacterium, designated YIM 151497T, was isolated from soil sample collected from Blue-Bridge, Weizhou Island, Guangxi province, China. Classification using a polyphasic approach suggested that strain YIM 151497T belonged to the genus Pelagibacterium, and was closely relevant to Pelagibacterium nitratireducens JLT2005T (98.8%), Pelagibacterium halotolerans CGMCC 1.7692T (98.7%), Pelagibacterium lixinzhangensis H64T (98.1%), and Pelagibacterium luteolum CGMCC 1.10267T (97.1%). The growth ranges of temperature, pH, and NaCl were 4–40 ℃, pH 4.0–10.0, and 0–7% NaCl, respectively. It was positive for catalase and oxidase. The primary respiratory quinone was Q-10. The elemental fatty acids were Summed Feature 8 (constituting C18:1ω7c and/or C18:1ω6c), C19:0 cyclo ω8c, C16:0, and C18:1ω7c 11-methyl. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and three unidentified glycolipids. The DNA G+C content based on the complete genome sequence was 60.7 mol%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) between strain YIM 151497T and species of Pelagibacterium were in the ranges of 73.9–86.3% and 19.7–31.3%, respectively. The Average Amino Acid Identity (AAI) between strain YIM 151497T and species of Pelagibacterium were in the ranges of 68.8–88.8%. On the basis of these data, strain YIM 151497T is considered to represent a novel species of the genus Pelagibacterium with the name of Pelagibacterium flavum sp. nov. Type strain is strain YIM 151497T (= KCTC 49826T = CGMCC 1.61521T = MCCC 1K08053T).

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Fig. 1

Data Availability

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence and the whole genome sequence of strain YIM 151497T were OP603122 and CP107716, respectively.

Abbreviations

ANI:

Average nucleotide identity

dDDH:

Digital DNA–DNA hybridization

ISP:

International Streptomyces Project

TSA:

Tryptic soy agar

R2A:

Reasoner’s 2A

NA:

Nutrient agar

LB:

Luria–Bertani agar

MA:

Marine broth 2216

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Acknowledgements

The authors thank Prof. Dr. Bernhard Schink for consenting prokaryotic names.

Funding

This experiment was supported by three projects, namely National Natural Science Foundation of China (32060001), The Government Project of Yunnan Province (YNWR-QNBJ-2018-085) and Major research project of Guangxi for science and technology (AA18242026).

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Authors and Affiliations

  1. School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People’s Republic of China

    Xue-Mei Chen, Zu-Zhen Yang, Si-Rong He, Lian-Shuang Xiong, Qing Yuan, Shu-Ya Zuo, Cheng-Lin Jiang & Yi Jiang

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  1. Xue-Mei Chen
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Contributions

XMC conducted relevant experiments and wrote the paper. ZZY, SRH, and LSX assisted in conducting experiments and revised the paper together. QY and SYZ searched for literature and analyzed the data. CLJ designed the experiments. YJ designed the experiments and revised the paper.

Corresponding author

Correspondence to Yi Jiang.

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All authors declare that there are no conflicts of interest.

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All authors contributed to the manuscript and agreed to publish.

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

Repositories

The type strain for new taxa have been deposited in China General Microbiological Culture Collection Center (CGMCC), Marine Culture Collection of China (MCCC) and Korean Collection for Type Cultures (KCTC), the preservation number were CGMCC 1.61521T, MCCC 1K08053T and KCTC 49826T, respectively.

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Chen, XM., Yang, ZZ., He, SR. et al. Pelagibacterium flavum sp. nov., Isolated from Soil Sample. Curr Microbiol 81, 72 (2024). https://doi.org/10.1007/s00284-023-03583-8

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