Responses of MethanogenmcrAGenes and Their Transcripts to an Alternate Dry/Wet Cycle of Paddy Field Soil

Abstract

ABSTRACTIntermittent drainage can substantially reduce methane emission from rice fields, but the microbial mechanisms remain poorly understood. In the present study, we determined the rates of methane production and emission, the dynamics of ferric iron and sulfate, and the abundance of methanogenmcrAgenes (encoding the alpha subunit of methyl coenzyme M reductase) and their transcripts in response to alternate dry/wet cycles in paddy field soil. We found that intermittent drainage did not affect the growth of rice plants but significantly reduced the rates of both methane production and emission. The dry/wet cycles also resulted in shifts of soil redox conditions, increasing the concentrations of ferric iron and sulfate in the soil. Quantitative PCR analysis revealed that bothmcrAgene copies andmcrAtranscripts significantly decreased after dry/wet alternation compared to continuous flooding. Correlation and regression analyses showed that the abundance ofmcrAgenes and transcripts positively correlated with methane production potential and soil water content and negatively correlated with the concentrations of ferric iron and sulfate in the soil. However, the transcription ofmcrAgenes was reduced to a greater extent than the abundance ofmcrAgenes, resulting in very lowmcrAtranscript/gene ratios after intermittent drainage. Furthermore, terminal restriction fragment length polymorphism analysis revealed that the composition of methanogenic community remained stable under dry/wet cycles, whereas that of metabolically active methanogens strongly changed. Collectively, our study demonstrated a stronger effect of intermittent drainage on the abundance ofmcrAtranscripts than ofmcrAgenes in rice field soil.