Raw data on pond characteristics and GHG fluxes from three fishing ponds in the Netherlands.

Aquaculture is a fast-growing industry that provides affordable protein for a growing human population. Most production occurs in freshwater ponds, which can emit nitrous oxide (N₂O) through microbial nitrogen transformations. Despite increasing attention to greenhouse gas emissions from aquaculture, N₂O dynamics in fishponds remain poorly constrained. Fish excrete ammonia, which can be a source for N₂O or N₂ production under suboxic and anoxic conditions, respectively. We previously showed that gill-associated nitrogen-cycling bacteria in common carp (Cyprinus carpio) can convert fish-derived ammonia to N₂. We examined the role of gill- and sediment-associated microbiota in nitrogen-cycling of three fishponds. We quantified N₂O fluxes at the pond level and from individual fish and characterized microbial communities and nitrogen-cycling potential of carp gills, pond water and sediments, using 16S rRNA amplicon sequencing and functional gene analysis. Potential N₂O formation was assessed in incubations of pond water and sediments. Sediments exhibited high potential N₂O production and consumption, indicating microbial regulation of N₂O within the ponds. Accordingly, diffusive N₂O emissions were low or indicated net uptake of N₂O from the water column. N2O present in gas bubbles likely bypassed microbial consumption leading to ebullitive N₂O emissions (up to 7.3 mg m-2 day-1). No N₂O release was detected from individual fish. Microbial community analyses showed that gill microbiota shared more taxa with pond water than with sediments. These findings indicate that N-cycling in fishponds involves microbial communities in sediment, water and fish, and that the formation of gas bubbles is a key driver of N₂O emission intensity.