Mechanisms and factors controlling greenhouse gases production in agricultural drains and ponds

Agricultural drains and ponds are underexplored but potentially significant sources of greenhouse gases (GHGs). Yet, the microbial pathways responsible for CH₄, CO₂, and N₂O production, and their responses to hydrological events, remain poorly understood. Here, we applied a multi-isotope framework (δ¹³C-CH₄, δ¹³C-CO₂, δ¹⁵N-N₂O, δ¹⁸O-N₂O, and N₂O site preference) to quantify GHG production processes in agricultural drains and ponds in south-eastern Australia during rainfall and irrigation events. GHG concentrations and fluxes were consistently higher in ponds than in drains, with CH₄ contributing most emissions. δ¹³C-CH₄ values suggested the predominance of hydrogenotrophic methanogenesis under irrigation. In contrast, during rainfall events, higher δ¹³C-CH₄ values suggested partial CH₄ oxidation under transiently oxygenated conditions with a possible increase in acetoclastic methanogenesis. The ¹⁵N SP values of N₂O showed that heterotrophic denitrification dominated production, with evidence of partial N₂O reduction in ponds. CO₂ concentrations were elevated but comparatively more variable and linked to hydrological events. Together, these findings reveal that agricultural ponds are hotspots of GHG emissions and act as dynamic biogeochemical reactors where nutrient inputs, redox conditions, and hydrological events jointly regulate GHG cycling. From a management perspective, small, high-emitting ponds and drains contribute disproportionately to farm-scale emissions, highlighting the urgent need to incorporate these water bodies into national GHG inventories.