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 (delta(CH4)-C-13), 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 (f(ac)), 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 mu g 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 delta(CH4)-C-13 (-43.9 parts per thousand) but the lowest value of produced delta(CO2)-C-13 (-26.3 parts per thousand). Based on the carbon isotope fractionation associated with methanogenesis via H-2/CO2 reduction (1.049-1.062), the values of f(ac) 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.