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Micromonospora rubida sp. nov., a novel actinobacterium isolated from soil of Harbin

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Abstract

A novel actinobacterium, designated strain NEAU-HG-1T, was isolated from soil collected from Harbin, Heilongjiang Province, Northeast China and characterised using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NEAU-HG-1T belonged to the genus Micromonospora, and shared high sequence similarities with Micromonospora auratinigra DSM 44815T (98.9%) and Micromonospora coerulea DSM 43143T (98.7%). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Micromonospora. Cell wall contained meso-diaminopimelic acid and the whole-cell sugars were arabinose and xylose. The polar lipid contained diphosphatidylglycerol, phosphatidylethanolamine, glycolipid and phosphatidylinositol. The predominant menaquinones were MK-10(H2), MK-10(H4) and MK-10(H6). The major fatty acids were C17:0 cycle, iso-C15:0, and iso-C16:0. Furthermore, strain NEAU-HG-1T displayed a DNA–DNA relatedness of 33.8 ± 2.2% with M. coerulea DSM 43143T. The level of digital DNA–DNA hybridization between strain NEAU-HG-1T and M. auratinigra DSM 44815T was 27.2% (24.8–29.7%). The value was well below the criteria for species delineation of 70% for dDDH. Whole-genome average nucleotide identity analyses result also indicated that the isolate should be assigned to a new species under the genus Micromonospora. Therefore, it is concluded that strain NEAU-HG-1T represents a novel species of the genus Micromonospora, for which the name Micromonospora rubida sp. nov. is proposed, with NEAU-HG-1T (= CGMCC 4.7479T = JCM 32386T) as the type strain.

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Data availability

The GenBank/EMBL/DDBJ Accession Number for the 16S rRNA gene sequence of strain NEAU-HG-1T is MG753996. The GenBank/EMBL/DDBJ accession number for the partial gyrB gene sequence of strain NEAU-HG-1T is MW091032. The Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAAALO000000000. The version described in this paper is version JAAALO000000000.1.

Abbreviations

ANI:

Average nucleotide identity

MEGA:

Molecular evolutionary genetics analysis

ISCC-NBS:

Inter-society color council-national bureau of standards

TLC:

Thin-layer chromatography

GC–MS:

Gas chromatography–mass spectrometer

ISP:

International Streptomyces project

BA:

Bennett’s agar

NA:

Nutrient agar

CGMCC:

China general microbiological culture collection center

DSM:

Deutsche Sammlung von Mikroorganismen und Zellkulturen

dDDH:

Digital DNA:DNA hybridization

DPG:

Ddiphosphatidylglycerol

PE:

Phosphatidylethanolamine

PG:

Phosphatidylglycerol

PI:

Phosphatidylinositol

GL:

Glycolipid

GY:

Glucose–yeast extract medium

JCM:

Japan collection of microorganisms

SSC:

Saline-sodium citrate

UPL:

Unknown phosphoglycolipid

PIM:

Phosphatidylinositol mannosides

UL:

Unidentified lipid

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Acknowledgements

We thank Prof. Aharon Oren for his valuable help with naming the species.

Funding

This work was supported in part by grants from the National Natural Science Foundation of China (No. 31700067), the China Postdoctoral Science Foundation (2015M580255), the Heilongjiang Provincial Postdoctoral Science Foundation (LBH-Z15016), and the “Academic Backbone” Project of Northeast Agricultural University (19XG18).

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  1. Xiujun Sun and Shiwen Qiu have contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People’s Republic of China

    Xiujun Sun, Shiwen Qiu, Xianxian Luo, Pinjiao Jin, Junwei Zhao, Xianyao Wu, Jize Yang, Xiangjing Wang, Jia Song & Wensheng Xiang

  2. State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China

    Wensheng Xiang

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Contributions

Xiujun Sun and Shiwen Qiu performed the laboratory experiments, analysed the data, and drafted the manuscript. Xianxian Luo contributed to the biochemical characterization. Pinjiao Jin contributed to the polyphasic taxonomy. Junwei Zhao contributed to the fatty acids determination. Xianyao Wu and Jize Yang contributed to the morphological analyses. Xiangjing Wang participated to the discussions of experiments and revised the manuscript. Jia Song and Wensheng Xiang designed the experiments and revised the manuscript.

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Sun, X., Qiu, S., Luo, X. et al. Micromonospora rubida sp. nov., a novel actinobacterium isolated from soil of Harbin. Antonie van Leeuwenhoek 114, 697–708 (2021). https://doi.org/10.1007/s10482-021-01550-6

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