Effects of Nitrification Inhibitor Application on Methanogenic and Methanotrophic Activity in Paddy Soil under Water-Saving Irrigation

The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) modulates methane (CH4) emissions in rice paddies by altering soil biogeochemistry and microbial functionality. This study elucidates the interactive effects of DMPP and water management on methanogen (mcrA) and methanotroph (pmoA) gene abundances across rice growth stages using a rhizobox system. Results revealed that alternate wetting-drying (A) and wetting irrigation (W) suppressed methanogen activity pre-panicle fertilization, whereas DMPP application post-panicle fertilization reduced mcrA abundance by 197–569% across treatments. Methanotroph activity peaked under continuous flooding (C) without DMPP, while DMPP enhanced pmoA abundance by 23.7–35.1% under A. Soil organic carbon (SOC) positively correlated with methanogens, whereas methanotrophs exhibited inverse relationships with SOC and dissolved organic carbon (DOC). These findings demonstrate that optimized water regimes coupled with DMPP application can mitigate CH₄ emissions by restructuring microbial communities and carbon dynamics.The application of 3,4-dimethylpyrazole phosphate (DMPP) can affect paddy soil methane emissions through soil and microbial properties. However, little is know about the effects of DMPP on methanogens and methanotrophs in rice soils under different water management practices. This study utilized the rhizobox method to quantify the gene abundances of these microbial communities across various growth stages. The results showed that water management practices significantly influenced the community structures and gene abundances of methanogens and methanotrophs. Under alternate wetting and drying (A) and continuous flooding (W), methanogen growth was either inhibited or promoted without DMPP application before and after panicle fertilization. However, DMPP application significantly suppressed methanogen activity after panicle fertilization. For methanotrophs, DMPP application enhanced pmoA gene abundance under A, while W and continuous saturation (C) without DMPP promoted methanotroph growth. Additionally, DMPP markedly altered the relationships between SOC, DOC, and the community structures of methanogens and methanotrophs. Methanogens exhibited a significant positive correlation with SOC, while methanotrophs showed negative correlations with both SOC and DOC. Overall, this study demonstrates that water management practices and DMPP application significantly affect methanogen and methanotroph communities in rice soils, with these changes closely linked to soil physicochemical properties.