Responses of mcrA and pmoA Gene Copies and Methane Fluxes to Soil Temperature Changes in Rice Microcosms

Methane generated from microbial activity in rice fields and wetlands is a major source of atmospheric methane, a potent greenhouse gas. The potency of this gas makes understanding the effect of global warming on methane emissions a key challenge in projecting the impact of future global warming. Methane is actively generated in-situ by methanogens, who use H2 and either CO2 or acetate produced by other organisms that degrade the organics. Our work determined the feedback of global warming on methane emissions from rice agriculture by looking at the links between populations of microbial consortia and increased soil temperature conducive to both methane production and consumption within the rhizosphere. Duplicate vertical soil profile samples were collected from temperature-controlled tubs with rice plants. The four waterbaths, set at different temperatures, each contained four tubs, with one bare tub (control) and three planted with rice. The soil samples were immediately frozen and stored at -80 deg. C, and were homogenized before DNA extraction. Quantitative Polymerase Chain Reaction (qPCR) was used to measure the concentrations of the methyl coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) genes in the extracted soil DNA. The mcrA and pmoA were used as the functional gene probes for methanogens (methane producing bacteria) and methanotrophs (methane oxidizing bacteria), respectively. An FID-equipped Gas Chromatography was used to measure the methane concentration in air samples collected from acrylic flux chambers. Results from our experiments showed that methanogens and methanotrophs were preferentially located to certain regions of the soil profile under different temperature regimes. Our results also indicated that higher global temperatures will increase methanogens populations, but not as much for methanotrophs, and hence increase methane fluxes from rice agriculture. Considering that the mechanisms of methane production in rice paddies are similar to natural wetlands, this feedback may contribute significant additional methane to the atmosphere in a warmer world.