Differences in Methanogenic Pathways and Communities in Paddy Soils Under Three Typical Cropping Modes.

The methane (CH4) production process in paddy fields varies depending on different cropping modes. However, there is limited knowledge on the changes in anaerobically produced CH4 isotopic ratios (δ13CH4), the methanogenic pathways, and the dominant communities of methanogens in paddy soils under different modes. To address this, we conducted experiments using anaerobic incubation methods, stable carbon isotope fractionation through inhibition studies with fluoromethane, and high‐throughput sequencing. These methods allowed us to measure the CH4 production potential (MPP), the relative contribution of acetoclastic methanogenesis to CH4 production (fac), and the composition of the methanogen community in paddy soils under three typical cropping modes: Rice‐Wheat (RW), Rice‐Fallow (RF), and Double‐Rice (DR) in China. The results showed that MPP was 30.7 μg CH4 g−1 d−1 in DR soil, around 57% and 66% higher than that in RW and RF soils, respectively, possibly due to the lower pH, clay content, and higher abundance of the mcrA gene. Moreover, RF soil had the highest value of produced δ13CH4 (−43.9‰) but the lowest value of produced δ13CO2 (−26.3‰). Based on the carbon isotope fractionation associated with methanogenesis via H2/CO2 reduction (1.049–1.062), the values of fac estimated in the RF soil (80%–98%) were much higher than that in the RW (39%–60%) and DR soils (52%–75%). This could be supported by the finding showing that Methanosarcina, the acetoclastic methanogens, were dominant in RF soil, while Methanosarcina and Methanobacterium (the hydrogenotrophic methanogens) dominated in RW and DR soils. Redundancy analysis revealed that the community structure of methanogens was significantly affected by soil pH. The findings suggest that differences in the abundance and composition of methanogens, possibly driven by soil pH, play a key role in regulating methanogenesis in the paddy soils, and further provide valuable insights into the process of CH4 production in different cropping modes. Plain Language Summary: The microbial methanogenesis and its mediated CH4 production potential in paddy soils differs based on various rice‐based cropping modes. However, the methanogenic pathways, microbial mechanisms of methane production, and their responses to key influencing factors under different cropping modes are still poorly documented. We investigated the differences in pathways of CH4 production and methanogenic communities and their responses to the corresponding different soil properties under three typical cropping modes in China, that is, Rice‐Wheat, Rice‐Fallow, and Double‐Rice rotation. Our results demonstrated significant differences in acetoclastic methanogenesis and dominant methanogenic communities in paddy soils under three cropping modes, which might be influenced by soil pH. This study provides a new perspective and further understanding of the methanogenic pathways and their associated microbial mechanisms under different cropping modes. Key Points: The CH4 production potential and methanogenic pathways and communities differ in soils under three cropping modesDifferences in soil properties (mainly soil pH) among three cropping modes mediated methanogenic communities and further regulated methanogenesis [ABSTRACT FROM AUTHOR]