Nitrous oxide (N₂O) is a potent greenhouse gas and ozone-depleting substance, and the ocean represents one of its major natural sources. However, current ocean biogeochemical models still show substantial discrepancies with observation-based estimates, suggesting that key microbial source and sink processes remain insufficiently constrained, particularly in oxygenated epipelagic waters. Here, we investigated overlooked N₂O cycling pathways in oligotrophic tropical oceans, with a focus on the western tropical Pacific and the eastern Indian Ocean.
Using multi-substrate isotope tracer incubations, N₂O isotopomer analysis, functional gene quantification, microbial community profiling, metagenomics and metatranscriptomics, we identified urea-driven nitrification as an important N₂O source in the oligotrophic euphotic zone. In the western tropical Pacific, ammonium and urea occurred at comparable nanomolar concentrations, while archaeal nitrification dominated N₂O production. Urea-driven nitrification contributed 14.2% to 40.7% of total ammonium plus urea nitrification, with a median contribution of 27.4%. Its contribution to N₂O production reached 20.6% to 38.8%, with a median of 31.6%. Archaeal amoA and ureC gene abundances were significantly correlated with substrate-specific nitrification and N₂O production rates, and urea-type ammonia-oxidizing archaea were broadly distributed across global ocean regions. Experimental acidification further revealed contrasting responses between ammonium and urea oxidation: lowered pH suppressed ammonium oxidation but enhanced urea oxidation and stimulated N₂O production from both substrates, supporting direct urea utilization by ammonia-oxidizing archaea.
We further examined potential N₂O biological sinks in oxygenated epipelagic waters of the eastern Indian Ocean using ¹⁵N-N₂O and NaH¹³CO₃ tracer incubations. Both N₂O reduction to N₂ and N₂O assimilation into particulate organic nitrogen were detected. N₂O assimilation was relatively more important in surface waters, whereas N₂O reduction dominated at the deep chlorophyll maximum. Diazotrophic cyanobacteria, especially photoautotrophic diazotrophs, were associated with surface N₂O assimilation, while nosZ clade II microorganisms showed active transcription and appeared to mediate high-affinity N₂O reduction in oxygenated waters. A regional budget indicated that biological consumption could remove approximately 55% of epipelagic N₂O, substantially weakening N₂O accumulation and sea-to-air emission.
Together, these results extend the conventional marine N₂O framework by incorporating urea-driven nitrification as an important epipelagic N₂O source and identifying N₂O assimilation and nosZ-mediated reduction as underestimated biological sinks in oxygenated upper waters. These findings highlight the epipelagic ocean as an active regulatory layer for marine N₂O cycling and call for the inclusion of these microbial pathways in future ocean N₂O models.