Response of fermenting bacterial and methanogenic archaeal communities in paddy soil to progressing rice straw degradation

Rice straw is one of the major organic materials introduced to rice field soils and its incorporation strongly enhances the emission of CH4. We incubated unamended and straw-amended Italian paddy soil under anaerobic conditions and studied the functional (carbon source, rate, pathway) and structural (abundance, taxonomic composition) responses of methanogenic microbial communities progressively in samples taken after 0, 30, 60, 90, and 120 days. Initially, rice straw significantly enhanced CH4 production rates. Later on, the values strongly decreased with the progress of rice straw degradation. The contribution of rice straw to CH4 production decreased with progressing anaerobic incubation. This decrease was paralleled by an increase of the contribution of hydrogenotrophic methanogenesis to CH4 production indicating a change in the network of bacterial and archaeal microbial communities. The methanogenic and bacterial communities indeed strongly responded to rice straw amendment and exhibited a distinct succession over the subsequent degradation periods. Network analysis of both 16S rRNA and Methyl coenzyme M reductase (mcrA) genes showed apparent co-occurrence of fermenting bacteria and CH4-producing archaea belonging to distinct operational taxonomic units (OTU) demonstrating strong functional and structural responses of methanogenic microbial communities to progressing rice straw degradation. Clostridiales, Fibrobacterales, and two Bacteroidetes groups (WCHB1-32 and Sphingobacteriales), as well as Anaerolineales and Bacteroidetes environmental group vadinHA17 were important bacterial taxa. Acetoclastic Methanosarcina and Methanothrix ('Methanosaeta') as well as hydrogentrophic Methanocella were important archaeal taxa involved in rice straw degradation.