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Actinoplanes aureus sp. nov., a novel protease-producing actinobacterium isolated from soil

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Abstract

A novel protease-producing actinobacterium, designated strain NEAU-A11T, was isolated from soil collected from Aohan banner, Chifeng, Inner Mongolia Autonomous Region, China, and characterised using a polyphasic approach. The hydrolytic enzymes, such as proteases, played critical roles in destruction of fungi by degrading the protein linkages to disrupt integrity in the cell wall. This suggested that the isolate could be a good biocontrol candidate against pathogens to control fungal diseases. On the basis of 16S rRNA gene sequence analysis, strain NEAU-A11T was indicated to belong to the genus Actinoplanes and was most closely related to Actinoplanes rectilineatus JCM 3194 T (98.9%). Cell walls contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell sugars were arabinose, xylose and glucose. The phospholipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and two phosphatidylinositol mannosides. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8). The major fatty acids were C18:0, C16:0, C18:1 ω9c, C17:0 and C15:0. Genome sequencing revealed a genome size of 10,742,096 bp, a G + C content of 70.5% and 9,514 protein-coding genes (CDS), including 102 genes coding for protease. Moreover, Genome analysis showed that strain NEAU-A11T contained 255 glycoside hydrolases (GHs), 152 glycosyl transferases (GTs), 40 carbohydrate esterases (CEs), 26 polysaccharide lyases (PLs), and 12 auxiliary activities (AAs) genes. Genome mining analysis using antiSMASH 5.0 led to the identification of 20 putative gene clusters responsible for the production of diverse secondary metabolites. Phylogenetic analysis using the 16S rRNA gene sequences showed that the strain formed a stable clade with A. rectilineatus JCM 3194 T in the genus Actinoplanes. Whole-genome phylogeny showed strain NEAU-A11T formed a stable phyletic line with Actinoplanes lutulentus DSM 45883 T (97.6%). However, whole-genome average nucleotide identity value between strain NEAU-A11T and its reference strains A. rectilineatus JCM 3194 T and A. lutulentus DSM 45883 T were found to be 81.1% and 81.6%, respectively. The levels of digital DNA-DNA hybridization between them were 24.6% (22.2–27.0%) and 24.8% (22.5–27.3%), respectively. The values were well below the criteria for species delineation of 70% for dDDH and 95–96% for ANI, suggesting that the isolate differed genetically from its closely related type strain. The content of G + C in genomic DNA was 70.5%, within the range of 67–76%. In addition, evidences from phenotypic, chemotaxonomic and genotypic studies indicated that strain NEAU-A11T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes aureus sp. nov. is proposed, with NEAU-A11T (= CCTCC AA 2019063 T = JCM 33971 T) 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-A11T is MW272536. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JADQTO000000000. The version described in this paper is version JADQTO000000000.1.

Abbreviations

ANI:

Average nucleotide identity

BA:

Bennett’s agar

CA:

Czapek’s agar

CCTCC:

China Center for type Culture Collection

dDDH:

Digital DNA:DNA hybridization

DPG:

Diphosphatidylglycerol

DSM:

Deutsche Sammlung von Mikroorganismen und Zellkulturen

GC–MS:

Gas Chromatography-Mass Spectrometer

GY:

Glucose-yeast extract medium

ISCC-NBS:

Inter-society color council-national bureau of standards

ISP:

International Streptomyces Project

JCM:

Japan Collection of Microorganisms

MEGA:

Molecular Evolutionary Genetics Analysis

NA:

Nutrient agar

PE:

Phosphatidylethanolamine

PG:

Phosphatidylglycerol

PI:

Phosphatidylinositol

PIM:

Phosphatidylinositolmannoside

TLC:

Thin-Layer Chromatography

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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. 31972291), 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. Jia Song and Xiujun Sun these authors 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

    Jia Song, Xiujun Sun, Xianxian Luo, Chuan He, Zhenzhen Huang, Junwei Zhao, Beiru He, Xiaowen Du, Xiangjing Wang & 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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  1. Jia Song
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Contributions

JS performed the laboratory experiments, designed the experiments and revised the manuscript. XS performed the laboratory experiments, analysed the data, and drafted the manuscript. XL contributed to the biochemical characterisation. CH and ZH contributed to the polyphasic taxonomy. JZ contributed to the fatty acids determination. BH and XD contributed to the morphological analyses. XW and WX participated to the discussions of each section of experiments, designed the experiments and revised the manuscript.

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Correspondence to Xiangjing Wang or Wensheng Xiang.

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Song, J., Sun, X., Luo, X. et al. Actinoplanes aureus sp. nov., a novel protease-producing actinobacterium isolated from soil. Antonie van Leeuwenhoek 114, 1517–1527 (2021). https://doi.org/10.1007/s10482-021-01617-4

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