Drivers of Seasonal Variations of Greenhouse Gas Fluxes from Sediment–Water and Water–Atmosphere Interfaces in Different Fish Culture Ponds

Aquaculture ponds constitute critical greenhouse gas (GHG) emission hotspots, yet limited research has concurrently quantified CH4, CO2, and N2O fluxes across sediment–water (SWI) and water–atmosphere (WAI) interfaces and their environmental and microbial controls under different aquaculture regimes. This study explored seasonal and diurnal GHG variations in four subtropical freshwater aquaculture ponds (Crucian carp, CruC; Largemouth bass, LarB; Channel catfish, ChaC; and in-pond raceway system of channel catfish, IPRS) in eastern China. SWI dominated CH4 diffusion, with an average flux of 139.1 ± 120.98 μmol·m–2·h–1, nearly 20 times the WAI CH4 flux. In contrast, WAI contributed 88.3% and 88% of total diffusive CO2 and N2O, respectively. CruC yielded the highest CH4 emissions (20267.06 μmol·m–2·h–1) and N2O emissions (8.73 μmol·m–2·h–1), while the IPRS exhibited the lowest, modulated primarily by temperature and sediment properties. Diurnally, FCH4 peaked in the daytime, whereas CO2 emissions were elevated at night, controlled by dissolved oxygen and pH. NMDS separated CH4 and N2O cycling microbial communities (mcrA, pmoA, nirS, nirK, nosZ) among pond types. PLS–PM verified sediment total nitrogen (STN) as the foremost positive driver of GHG fluxes across all interfaces. Our results confirm SWI predominance in diffusive CH4 production and demonstrate that interface partitioning is essential for refining regional aquatic carbon and nitrogen budgets.