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Massilia cellulosiltytica sp. nov., a novel cellulose-degrading bacterium isolated from rhizosphere soil of rice (Oryza sativa L.) and its whole genome analysis

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Abstract

A bacterial strain, Gram-stain negative, rod-shaped, aerobic and cellulose-degrading, designated NEAU-DD11T, was isolated from rhizosphere soil of rice collected from Northeast Agricultural University in Harbin, Heilongjiang Province, North-east China. Base on 16S rRNA gene sequence analysis, strain NEAU-DD11T belongs to the genus Massilia and shared high sequence similarities with Massilia phosphatilytica 12-OD1T (98.46%) and Massilia putida 6NM-7 T (98.41%). Phylogenetic analysis based on the 16S rRNA gene and whole genome sequences indicated that strain NEAU-DD11T formed lineage related to M. phosphatilytica 12-OD1T and M. putida 6NM-7 T. The major fatty acids of the strain were C16:0, C17:0-cyclo and C16:1ω7c. The respiratory quinone was Q-8. The polar lipids profile of the strain showed the presence of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified polar lipid and an unidentified phospholipid. In addition, the digital DNA-DNA hybridization values between strain NEAU-DD11T and M. phosphatilytica 12-OD1T and M. putida 6NM-7 T were 45.4 and 35.6%, respectively, which are lower than the accepted threshold value of 70%. The DNA G + C content of strain NEAU-DD11T was 66.2%. The whole genome analysis showed the strain contained carbohydrate enzymes such as glycoside hydrolase and polysaccharide lyase, which enabled the strain to have the function of degrading cellulose. On the basis of the phenotypic, genotypic and chemotaxonomic characteristics, we conclude that strain NEAU-DD11T represents a novel species of the genus Massilia, for which the name Massilia cellulosiltytica sp. nov. is proposed. The type strain is NEAU-DD11T (= CCTCC AB 2019141 T = DSM 109721 T).

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Data availability

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain NEAU-DD11T is MN784464. The Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession WSES00000000. The version described in this paper is version WSES00000000.1.

Abbreviations

CCTCC:

China Center for Type Culture Collection

DSM:

Deutsche Sammlung von Mikroorganismen und Zellkulturen

GDMCC:

Guangdong Microbial Culture Collection Center

DPG:

Diphosphatidylglycerol

PE:

Phosphatidylethanolamine

PG:

Phosphatidylglycerol

MEGA:

Molecular Evolutionary Genetics Analysis

ANI:

Average nucleotide identity

dDDH:

Digital DNA-DNA hybridization

GGDC:

Genome-to-Genome Distance Calculator

TYGS:

Type strain Genome Server

ISCC-NBS:

Inter-society color council-national bureau of standards

GO:

Gene Ontology

KEGG:

Kyoto Encyclopedia of Genes and Genome

CAZy:

Carbohydrate-Active enZYmes Database

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Acknowledgements

The authors would like to thank Prof. Aharon Oren (Department of Plant and Environmental Sciences, the Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem) for helpful advice on the specific epithet.

Funding

This work was supported in part by grants from the Key Program of the National Natural Science Foundation of China (No. 32030090), the China Postdoctoral Science Foundation (2018M631907) and the Heilongjiang Postdoctoral Fund (LBH-Z17015).

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Authors and Affiliations

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

    Chuanjiao Du, Chenxu Li, Peng Cao, Tingting Li, Dandan Du, Xiangjing Wang, Junwei Zhao & 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. Chuanjiao Du
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  2. Chenxu Li
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  3. Peng Cao
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  4. Tingting Li
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  5. Dandan Du
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  6. Xiangjing Wang
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Contributions

Chuanjiao Du performed the laboratory experiments, analyzed the data, and drafted the manuscript. Chenxu Li contributed to the biochemical characterization. Peng Cao contributed to the morphological analyzes. Tingting Li contributed to the fatty acids determination. Dandan Du contributed to the polyphasic taxonomy. Xiangjing Wang participated to the discussions of each section of experiments. Junwei Zhao and Wensheng Xiang designed the experiments and revised the manuscript.

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Correspondence to Junwei Zhao or Wensheng Xiang.

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Du, C., Li, C., Cao, P. et al. Massilia cellulosiltytica sp. nov., a novel cellulose-degrading bacterium isolated from rhizosphere soil of rice (Oryza sativa L.) and its whole genome analysis. Antonie van Leeuwenhoek 114, 1529–1540 (2021). https://doi.org/10.1007/s10482-021-01618-3

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