Denitrification in paddy soil as a cooperative process of different nitrogen oxide reducers, revealed by metatranscriptomic analysis of denitrification-induced soil microcosm

Denitrification in paddy soils is an environmentally important reaction, which reduces leaching or emission of nitrogen pollutants. This reaction has long been considered to be driven by typical denitrifiers mostly belonging to <i>Alpha-, Beta-</i>, and <i>Gammaproteobacteria</i>. Our recent metatranscriptomic analysis of rice paddy field soil suggested that paddy soil denitrification is a cooperative process of different nitrogen oxide reducers, i.e., NO₂⁻, NO, and N₂O reducers. However, it was not clear whether denitrification actually occurred in the soil samples examined, which was not easy to confirm under field conditions. Therefore, we carried out this study (1) to establish a soil microcosm with the steady activity of denitrification, and (2) to identify microbial communities, which drive each step of denitrification in the soil microcosm by metatranscriptomic analysis. As a result, a chemostat-type soil microcosm with steady denitrification activity was successfully established. Metatranscriptomic analysis of the denitrification-induced soils, together with supportive PCR-based clone library analysis, indicated that the community compositions of microbial drivers at each step of denitrification are different from each other. The results verified our above-mentioned suggestion of denitrification in paddy soil being a cooperative process of different nitrogen oxide reducers. Microbial communities of the cooperative denitrification in paddy soil might be established, and might have advantages to eliminate/detoxify microbiologically and/or chemically generated nitrogen oxides smoothly under changing paddy soil environments.