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Methylomonas rhizoryzae sp. nov., a type I methanotroph isolated from the rhizosphere soil of rice

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Abstract

A gammaproteobacterial methanotroph, strain GJ1T, was isolated from a rhizosphere soil sample of rice in Nanjing, China. The cells were Gram-negative, motile rods with a single polar flagellum, and they contained type I intracytoplasmic membranes. The cells formed pink colonies. The strain possessed both the particulate methane monooxygenase enzyme (pMMO) and the soluble methane monooxygenase enzyme (sMMO). pxmABC, encoding a divergent methane monooxygenase (pXMO), and nifH, which encodes dinitrogenase reductase, were also present. Methane and methanol were utilized as sole carbon sources, while other carbon sources, including acetate, pyruvate, succinate, citrate, malate, glucose, urea, methylamine, ethanol and formate, could not be utilized by strain GJ1T. Cell grew optimally at 25–33 °C (range 16–37 °C), pH 6.0–8.0 (range 5.5–8.5) and 0–1.2% NaCl (no growth above 1.5% NaCl). Phylogenetic analyses based on the 16S rRNA gene, pmoA and nifH showed that the isolate belongs to the genus Methylomonas of the family Methylococcaceae within the class Gammaproteobacteria. The major quinone was determined to be MQ-8, and the major fatty acids were observed to be C16:1 and C14:0. The genome size of strain GJ1T is about 4.55 Mb, and the DNA G + C content of the strain was determined to be 53.67 mol% within the range of the genus Methylomonas (47–58 mol%) reported at present. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain GJ1T and Methylomonas koyamae Fw12E-YT among the genus Methylomonas were the highest, and they were only 74.66% and 21.40%, respectively. In consequence, results of phenotypic characterization and phylogenetic analyses support strain GJ1T as a novel species within the genus Methylomonas, namely, Methylomonas rhizoryzae sp. nov.. The type strain is GJ1T (= ACCC 61706).

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Acknowledgements

This work was funded by the National Natural Science Foundation of China (31800095, 31770125, 31970099) and the Natural Science Foundation of Jiangsu Province (BK20180541).

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  1. Pingping Zhu and Minggen Cheng these authors contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

    Pingping Zhu, Minggen Cheng, Dongmei Pei, Yongchuang Liu & Xin Yan

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  1. Pingping Zhu
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  2. Minggen Cheng
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  3. Dongmei Pei
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  4. Yongchuang Liu
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  5. Xin Yan
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PZ, MC, DP and YL performed experiments, PZ and MC performed data analysis and wrote the manuscript, XY designed research and revised the manuscript. All authors read and approved the final manuscript.

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Correspondence to Xin Yan.

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Zhu, P., Cheng, M., Pei, D. et al. Methylomonas rhizoryzae sp. nov., a type I methanotroph isolated from the rhizosphere soil of rice. Antonie van Leeuwenhoek 113, 2167–2176 (2020). https://doi.org/10.1007/s10482-020-01487-2

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