LAUSR

Abstract Anaerobic methane production from paddy soils plays an important role in global methane emissions. Syntrophic-methanogenic associations have been viewed as a key regulator of methane generation in paddy fields. However, the effects of rice phenology on the diversity and abundance of syntrophic and methanogenic communities remain largely unknown. This study investigated the changes in syntrophic-methanogenic associations at different rice growth by comparing the 16S RNA sequences of total (DNA-based) and active (RNA-based) microbial communities in rhizosphere and bulk soils. Moreover, the concentrations of specific syntrophs and methanogens were quantified using qPCR assay. Statistical significant differences in the alpha and beta diversities were observed between DNA-based and RNA-based syntrophic communities. The relative abundance of syntrophs in rhizosphere soil was significantly higher at RNA level compared to that at DNA level, indicating that syntrophs display considerably high specific activities. Syntrophic bacteria accounted for 6.23–6.81% of the active communities in rhizosphere soil and 6.12–6.71% in bulk soil. Besides, the quantities of methanogens increased over the entire period of rice growth, and peaked at flowering stage. Such changing pattern was consistent with the total number of short-chain fatty acids-degrading syntrophs at flowering stage, suggesting that rice phenology can affect both syntrophic and methanogenic activities. Furthermore, not only environmental factors (e.g., pH and SOC), but also organic acids (e.g., citrate and succinate), shaped the composition and abundance of syntrophic and methanogenic communities in paddy soils.