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Methanogenic archaeal communities developed in paddy fields in the Kojima Bay polder, estimated by denaturing gradient gel electrophoresis, real-time PCR and sequencing analyses

Authors

  • Takeshi WATANABE,

    1. Laboratory of Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan;
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  • Vita Ratri CAHYANI,

    1. Laboratory of Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan;
    2. Faculty of Agriculture, Sebelas Maret University, Surakarta 57126, Indonesia; and
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  • Jun MURASE,

    1. Laboratory of Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan;
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  • Eiji ISHIBASHI,

    1. Agricultural Experiment Station, Okayama Prefectural General Agricultural Center, Okayama 709-0801, Japan
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  • Makoto KIMURA,

    1. Laboratory of Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan;
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  • Susumu ASAKAWA

    1. Laboratory of Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan;
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: T. WATANABE, Laboratory of Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan. Email: watanabe.t@nagoya-u.jp

Abstract

Methanogenic archaeal communities inhabiting the paddy field soils in the Kojima Bay polder were investigated using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), real-time PCR and sequencing analyses. Soil samples of the plow and subsoil layers were collected in 2006 from four paddy fields that were reclaimed between 1692 and 1954. The DGGE band patterns of the targeted 16S rRNA genes amplified from the extracted DNA from the samples were different from the patterns from the paddy field soils in diluvial and alluvial areas. The numbers of targeted 16S rRNA genes, which were involved with methanogenic archaeal and other archaeal sequences, were approximately 107–108 and 106 g−1 dry soil in the plow and subsoil layers, respectively. Sequences of methanogenic archaeal 16S rRNA genes belonging to Methanocellales (Rice cluster I), Methanosarcinales and Methanobacteriales were obtained from the major DGGE bands. Whereas sequences in Methanomicrobiales, which were predominant methanogens in the diluvial and alluvial paddy fields, were not recovered. Known halophilic and methylotrophic methanogens, which are characteristic of saline and marine environments, were not detected. These results indicate that distinctive methanogenic archaeal communities have developed in the paddy field soils in the Kojima Bay polder.

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