Regulation of microbial methane production and oxidation by intermittent drainage in rice field soil

Soil drainage is one of the most promising approaches to mitigate methane (CH4) emission from paddy fields. The microbial mechanism for the drainage effect on CH4 emission, however, remains poorly understood. In the present study, we determined the effect of short (four drainages of 5-6 days each) and long drainage cycles (two drainages of 10-11 days each) on CH4 emission and analyzed the response of the structure and abundance of methanogens and methanotrophs in a Chinese rice field soil at the DNA level. Rice biomass production was similar between drainage and the practice of continuous flooding. The rate of CH4 emission, however, was reduced by 59% and 85% for the long and short drainage cycles, respectively. Quantitative (real-time) PCR analysis revealed that the total abundance of archaeal populations decreased by 40% after multiple drainages, indicating the inhibitory effects on methanogen growth. The structure of the methanogen community as determined by terminal restriction fragment length polymorphism analysis, however, remained unaffected by drainages, although it varied among rhizosphere, bulk and surface soils. Quantitative PCR analysis of the methanotrophic functional pmoA genes revealed that the total abundance of methanotrophs in rhizosphere soil increased two to three times after soil drainages, indicating a stimulation of methanotroph growth. The CH4 oxidation potential in the rhizosphere soil also increased significantly. Furthermore, drainages caused a shift of the methanotrophic community, with a significantly increase of type II methanotrophic bacteria in the rhizosphere and surface soil. Thus, both inhibition of methanogens and stimulation of methanotrophs were partly responsible for the reduction of CH4 emissions. The methanotroph community, however, appeared to react more sensitively to soil drainage compared with the methanogen community.