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Molecular identification of methane oxidizing bacteria in a Japanese rice field soil

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Abstract

By using cultivation-independent techniques, community changes of methane-oxidizing bacteria (MOB) in rice bulk soils were investigated under field conditions in a Japanese rice field. The representative soil samples were collected during the typical rice growing season and nonrice growing period all year round. Statistical characterization of denaturing gradient gel electrophoresis (DGGE) community patterns of MOB pmoA/amoA functional gene fragments showed that MOB community structures in the rice bulk soils remained largely unchanged throughout the investigated period. The total intensity of six common DGGE bands that appeared consistently throughout the investigated period accounted for 64% of the total intensity of all 18 different DGGE bands detected. The low squared distance of the Ward cluster analysis of the DGGE pattern and the high Sorensen similarity coefficient (81%) also implied the high similarity of the MOB community structures. The stable MOB community structure did not couple well with the wide variation of soil water contents all year round. Sequencing analysis of the nine characteristic bands including six common bands revealed the presence of Type I, Type II methanotrophs, and β-proteobacterial ammonia oxidizers in rice bulk soils. In comparison with MOB type species, three DGGE bands showed a wide variation of the highly conserved amino acid residues, implying the presence of novel MOB bacteria inhabiting the rice bulk soil. The high diversity of MOB composition suggested that rice bulk soils might serve as an ideal reservoir for the dynamic changes of MOB in a rice field ecosystem in response to environment changes.

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Acknowledgment

The authors are grateful to the staffs of the Anjo Research and Extension Center for field management and sampling assistance. Zhongjun Jia also wants to extend his gratitude to the Japan Society for the Promotion of Science (JSPS) for financial support.

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Authors and Affiliations

  1. Laboratory of Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya, 464-8601, Japan

    Zhongjun Jia, Takeshi Watanabe, Susumu Asakawa & Makoto Kimura

  2. Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße, 35043, Marburg, Germany

    Zhongjun Jia

  3. Aichi Steel Corporation, Arao, Tokai, 476-8666, Japan

    Hiroyasu Kikuchi

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  1. Zhongjun Jia
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  2. Hiroyasu Kikuchi
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  4. Susumu Asakawa
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  5. Makoto Kimura
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Correspondence to Zhongjun Jia.

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Jia, Z., Kikuchi, H., Watanabe, T. et al. Molecular identification of methane oxidizing bacteria in a Japanese rice field soil. Biol Fertil Soils 44, 121–130 (2007). https://doi.org/10.1007/s00374-007-0186-x

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  • DOI: https://doi.org/10.1007/s00374-007-0186-x

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