Intensive flooding enhances methane but reduces carbon dioxide and nitrous oxide emissions in reservoir drawdown areas

Riparian ecosystems, vital interfaces for soil-atmosphere greenhouse gases (GHG) exchange, are increasingly subject to perturbations from extreme flooding events and artificial hydrological alterations. The resultant effects on soil microbiomes and GHG emissions, particularly under varying flooding regimes, remain poorly elucidated. Here, we conducted an in-situ flooding manipulation experiment across three elevation gradients in a reservoir drawdown area, applying continuous flooding (Extreme), 3-day flooding alternating with 3-day drainage (Moderate), and no flooding (Control) to evaluate responses of CH₄, CO₂, and N₂O emissions and associated microbiomes. Flooding exerted stronger control than elevation on GHG fluxes. CH₄ emissions increased dramatically under both extreme and moderate flooding (24-fold and 25-fold, respectively), whereas CO₂ and N₂O emissions decreased: extreme flooding reducing CO₂ by 51 % and N₂O by 108 %, and moderate flooding reducing N₂O by 67 % with minimal effect on CO₂ emissions. CH₄ emissions increased primarily due to elevated water tables and enhanced soil anaerobic conditions, stimulating methanogenic activity via methylotrophic pathways (up-regulated mtaC gene) and greater availability of labile plant litter. CO₂ emissions declined as flooding reduced aboveground plant biomass, thereby lowering plant respiration. N₂O emissions decreased because higher soil moisture promoted complete denitrification, converting N₂O to N₂. Using co-occurrence network analysis, the bacterial order Xanthomonadales emerged as keystone taxa, showing strong associations with microbial functional groups involved in GHG-related metabolic pathways. Overall, our findings indicate that riparian ecosystems may become CH₄ emission hotspots under future climatic extremes and highlight the critical role of hydrological dynamics–microbiome interactions in shaping riparian carbon and nitrogen cycles.