Bacterial and archaeal communities involved in the in situ degradation of 13C-labelled straw in the rice rhizosphere

Rice straw is a major substrate for the production of methane in flooded rice fields and results in increase of CH4 emission into the atmosphere. We investigated the bacteria and archaea involved in straw degradation by adding C-13-labelled straw to the rhizosphere of planted rice microcosms in the greenhouse. The degradation of added straw resulted in the production of C-13-labelled CH4 as end-product, which was detected in the pore water. The incorporation of C-13 into ribosomal RNA of Bacteria and Archaea present in the rhizospheric soil and on the roots was assessed by stable isotope probing ( SIP) followed by terminal restriction fragment polymorphism ( T-RFLP) fingerprinting and cloning/sequencing of RNA fractions with different buoyant densities. Members of the Clostridium cluster I, III and XIVa were actively involved in straw degradation both in rhizospheric soil and on roots. However, on roots, Proteobacteria, Bacilli, Actinobacteria, Bacteroidetes and Chlorobi were also involved in the straw degradation process. Mostly Methanosarcina and to a less degree also Methanobacteriaceae were the dominant Archaea that assimilated straw-derived carbon in the rhizospheric soil. Both Bacteria and Archaea together were most likely responsible for the conversion of rice straw to CH4. In conclusion, this study tackled the important and interesting issue of linking active microorganisms responsible for the straw degradation process to CH4 emission into the atmosphere.