A two-year measurement of methane and nitrous oxide emissions from freshwater aquaculture ponds: Affected by aquaculture species, stocking and water management

Aquaculture ponds are of increasing worldwide concerns as critical sources of atmospheric methane (CH4) and nitrous oxide (N2O), but little is known about these gases emissions as affected by aquaculture species, stocking and water management in aquaculture ponds. Here, a two-year study was carried out to quantify CH4 and N2O emissions from freshwater crab and fish aquaculture ponds in subtropical China. We further explored how the microbial functional genes [CH4: mcrA and pmoA; N2O: archaeal and bacterial amoA (AOA + AOB), nirS, nirK, nosZ] may drive CH4 and N2O release in the crab aquaculture pond typically undergoing flooding-to-drainage alteration. Over the two-year period, annual CH4 and N2O fluxes averaged 0.95 mg m−2 h−1 and 20.94 μg m−2 h−1 in the fish aquaculture, and 0.78 mg m−2 h−1and 28.48 μg m−2 h−1 in the crab aquaculture, respectively. The direct N2O emission factors were estimated to be 0.77% and 0.36% of the total N input by feed or 1.59 g N2O-N kg−1 and 1.06 g N2O-N kg−1 aquaculture yield in the crab and fish ponds, respectively. Among three functional stocking areas, CH4 and N2O emissions were consistently the highest at the feeding area (FA) in the both aquaculture ponds, followed by at the undisturbed area (UA) and aerated area (AA). The shift in sediment soil moisture from waterlogging to drainage conditions significantly increased the abundance of AOB relative to AOA and pmoA, decreased those of denitrifying functional genes (nirS, nirK, nosZ) and mcrA, while did not alter the functional group ratio of nirS + nirK relative to nosZ. Our results highlight that a better understanding of CH4 and N2O emissions from aquaculture ponds requires taking into consideration of data sourced from more diverse aquaculture systems with different management patterns. In addition, a deep analysis of the microbial processes that drive CH4 and N2O production and consumption from aquaculture ponds remains to be addressed in future studies. [Display omitted] •Global CH4 and N2O emissions from aquaculture wetlands remain poorly constrained.•CH4 emissions were greater while N2O emissions were lower in the fish than crab aquaculture.•CH4 and N2O emissions from aquaculture varied with different functional stocking areas.•Bacterial amoA was more sensitive than archaeal amoA to sediment moisture and N input.