Transcriptional response of methanogen mcrA genes to oxygen exposure of rice field soil

Methane production in paddy soil is substantially suppressed after even a brief exposure of soil to oxygen. We hypothesized that the strong response of methanogen activity is reflected in the transcription of functional genes rather than in the composition of the community of methanogens. Therefore, we determined the community composition and the transcriptional response of methanogens in a rice field soil by targeting the mcrA gene (encoding the α subunit of methyl-coenzyme M reductase). Transcription of mcrA genes measured by quantitative PCR decreased by an order of magnitude after brief exposure to O2 . Terminal restriction fragment length polymorphism of mcrA genes and gene transcripts showed that although the community structure of methanogens did not change, the composition of transcripts dramatically responded to O2 exposure. In the beginning, transcripts of Methanocellales were the relatively most abundant, indicating resistance of these hydrogenotrophic methanogens against O2 stress. Later on, mcrA transcripts of acetoclastic methanogens became relatively more abundant coinciding with the turnover of acetate. The transcription of Methanosarcinaceae was relatively greater when acetate accumulated while Methanosaetaceae became more active when acetate concentrations decreased. In the presence of methyl fluoride, a specific inhibitor of acetoclastic methanogenesis, mcrA transcription by Methanosaetaceae was greatly suppressed while that of Methanosarcinaceae was less affected. Our study showed that in contrast to constant community structure as revealed by DNA-based fingerprinting the transcription of functional mcrA genes strongly responded to O2 stress and the presence of inhibitor CH3 F. The response patterns reflected the genomic and physiological traits of individual methanogens.