Surface soil microbial networks drive organic matter-induced methane emissions in paddy soil

The application of organic materials to improve soil fertility in paddy fields inadvertently stimulates methane (CH 4 ) emissions, a major greenhouse gas. However, the microbial mechanisms, particularly the roles of multi-kingdom interactions and their vertical stratification, remain poorly understood. Through a controlled column experiment with stratified soil sampling, we investigated the impacts of straw, sludge, and manure amendments on CH 4 emissions, methanogenic archaea, and intra- and cross-kingdom microbial interactions in both surface (0–10 cm) and subsurface (10–20 cm) paddy soils. Our results indicated that organic materials significantly stimulated CH 4 emissions, with the most pronounced increase observed under straw treatment (13.1-fold), followed by sludge (4.1-fold) and manure (2.8-fold). This increase was primarily attributed to enhanced methanogenic activity in surface soils, which was corroborated by increased mcrA gene abundance and enrichment of hydrogenotrophic archaea in surface soil after application of organic materials. Furthermore, surface soils exhibited stronger associations between methanogenic archaea and other microbial groups (bacteria, fungi, and non-methanogenic archaea) than subsurface soils, suggesting that multi-kingdom interactions may affect methanogenic activity and thereby control CH 4 production. In addition, organic amendments enhanced microbial network complexity and stability in surface soils compared to subsurface soils, primarily by fostering more frequent intra-kingdom interactions, particularly positive bacterial–bacterial and archaeal–archaeal associations that likely supported functional redundancy and metabolic cooperation. Such network properties were positively correlated with CH 4 emissions, highlighting that intensified cooperative interactions within microbial kingdoms are a key mechanism linking organic amendments to enhanced methanogenesis. Our findings demonstrate that organic matter-induced CH 4 emissions are primarily governed by the restructuring of surface soil microbial communities, which involves a selective enrichment of hydrogenotrophic archaea and a strengthening of within-kingdom cooperative interactions. This study underscores the critical role of vertical stratification and microbial network dynamics in predicting and mitigating greenhouse gas emissions from agroecosystems.