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Puerhibacterium puerhi gen. nov., sp. nov., a novel member of the family Promicromonosporaceae, isolated from Pu-erh tea pile-fermentation

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Abstract

A Gram-staining positive aerobic bacterium, designated TLY-12T, was isolated from the Pu-erh tea pile-fermentation process in Pu'er city, Yunnan, China. Strain TLY-12T grew at 15–37 °C (optimum, 30 °C), pH 6.0–11.0 (optimum, pH 9.0) and 0–9.0% (w/v) NaCl (optimum, 3.0%). The major cellular fatty acids were anteiso-C15:0, C16:0 and iso-C16:0. The respiratory quinone were menaquinones MK-9 (H2) and MK-9 (H4). The polar lipids were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylinositol (PI), phosphoglycolipid (PGL), glycolipid (GL) and an unidentified phospholipid (PL). The peptidoglycan contained glutamic acid, aspartic acid, alanine and lysine, with the last named being the diagnostic diamino acid. Whole-cell sugars of the isolate were ribose, galactose and glucose. Phylogenetic analyses of 16S rRNA gene showed that this strain belonged to the family Promicromonosporaceae, and was most closely related to Isoptericola cucumis DSM 101603 T, which gave sequence similarity of 97.9%. Genome sequencing revealed a genome size of 3.91 Mbp and a G + C content of 75.0%. Average nucleotide identity and digital DNA–DNA hybridization values were all below the species threshold of described Promicromonosporaceae species. Genome phylogenetic analysis showed that strain TLY-12T formed a separate evolutionary branch, and was parallel to other related genera of Promicromonosporaceae. Based on the phylogenetic, phenotypic, chemotaxonomic and genome pairwise data, strain TLY-12T is considered to represent a novel species in a new genus in the family Promicromonosporaceae, for which the name Puerhibacterium puerhi gen. nov, sp. nov. is proposed. The type strain is TLY-12T (= CGMCC 1.17157T = KCTC 49467T).

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Abbreviations

ANI:

Average nucleotide identity

dDDH:

Digital DNA–DNA hybridization

COG:

Cluster of orthologous groups of proteins

CRISPR:

Clustered regularly interspaced short palindromic repeats

RNA:

Ribonucleic acid

tRNA:

Transfer ribonucleic acid

sRNA:

Small ribonucleic acid

LTR:

Long terminal repeat

LINE:

Long interspersed nuclear elements

SINE:

Short interspersed nuclear elements

RC:

Rolling circle

TR:

Terminal repeat

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Acknowledgements

This work was supported by Yunnan Provincial Tea Industry Technical System Construction (Project2017KJTX007) and Yunnan Provincial Key Programs of Yunnan Eco-friendly Food International Cooperation Research Center Project under Grant (Project2019ZG00909-02). We thank Prof. Bernhard Schink and Prof. Aharon Oren for the help of guidance about naming the novel strain.

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Authors and Affiliations

  1. Key Laboratory of Pu-Er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China

    Rui-Juan Yang, Xuan-Jun Wang & Jun Sheng

  2. College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China

    Rui-Juan Yang

  3. College of Tea (Puʼer), West Yunnan University of Applied Sciences, Pu’er, Yunnan, 665000, China

    Rui-Juan Yang, Qiao-Mei Wang, Wen-Shu Peng, Li Liu & Liang Yan

  4. Pu’er Institute of Pu-Erh Tea, Pu’er, Yunnan, 665000, China

    Rui-Juan Yang, Qiao-Mei Wang, Wen-Shu Peng, Li Liu & Liang Yan

  5. College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China

    De Zhou & Jie Lv

  6. MyGenostics Inc., Beijing, 101318, China

    Lu Han

  7. College of Science, Yunnan Agricultural University, Kunming, 650201, China

    Xuan-Jun Wang

  8. State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming, 650201, China

    Xuan-Jun Wang & Jun Sheng

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  1. Rui-Juan Yang
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The GenBank/EMBL/DDBJ accession numbers for the genome and 16S rRNA gene sequence of TLY-12T are WUWN00000000 and MN014098

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Yang, RJ., Zhou, D., Wang, QM. et al. Puerhibacterium puerhi gen. nov., sp. nov., a novel member of the family Promicromonosporaceae, isolated from Pu-erh tea pile-fermentation. Arch Microbiol 203, 1509–1518 (2021). https://doi.org/10.1007/s00203-020-02151-z

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