Distinct members of a stable methanogenic archaeal community transcribe mcrA genes under flooded and drained conditions in Japanese paddy field soil

The composition and succession of methanogenic archaea in a Japanese paddy field were investigated during an annual cycle by analyses of methyl-coenzyme M reductase α subunit (mcrA) genes and their mRNA transcripts, which encode a key enzyme for methanogenesis. The paddy field was managed with a double-cropping cultivation, i.e. rice grown in summer under a flooded condition and wheat cultivated in winter under a drained condition. The mcrA genes and their transcripts were amplified from genomic DNA and total RNA extracted from soil samples, respectively. Numbers of the mcrA genes estimated by the most probable number-PCR showed little variation among the samples, whereas those of the transcripts and the transcripts/mcrA gene ratios increased in the late period of the rice cultivation under flooded condition. In addition, band patterns of denaturing gradient gel electrophoresis of the mcrA gene PCR products were similar among the samples, while those from the transcripts were different between the samples under flooded and drained conditions. Methanogenic activities of the paddy soils were higher under flooded conditions than drained conditions. Clones belonging to Methanomicrobiales, Methanosarcinales, Methanocellales (Rice cluster I), mrtA cluster (isoenzyme genes) and Methanobacteriaceae were detected in the soils by the clone library analysis. However, the relative proportions in the libraries from the transcripts were completely different, i.e. transcripts derived from members of unidentified Methanosarcinales and Rice cluster I were predominantly detected in the soils under flooded and drained conditions, respectively. These results suggested that distinct members in a well-established methanogenic archaeal community transcribed mcrA genes and contributed to methane production corresponding to soil conditions.