Urea-driven nitrification contributes to N2O production in the oligotrophic euphotic ocean

Urea is an important alternative nitrogen source to ammonium for nitrification in oligotrophic oceans, yet its role in substrate-driven nitrous oxide (N2O) production remains poorly constrained. Here, we combined N2O isotopomer profiling, 15N-tracer incubations, and metagenomics to quantify and mechanistically resolve substrate-specific archaeal nitrification in the western tropical Pacific euphotic zone. Isotopomer-based mixing and fractionation model indicated that archaeal nitrification accounted for 69.6% ± 14.1% of microbial sources of N2O in oxygenated epipelagic waters. Depth-integrated urea-driven nitrification contributed 14%-41% of total nitrification and 21%-39% of nitrification-derived N2O, with contributions regulated by substrate proportions. Acidification experiments showed that pH decline inhibited ammonium-driven nitrification (median 21.9%) and enhanced urea oxidation (median 61.9%), whereas N2O production increased for both substrates (median 35.9% and 38.0%). In addition, experimental acidification induced opposite shifts in hybrid versus double-labeled N2O, suggesting pH-driven shifts N-intermediate chemistry and intracellular partitioning. Metagenomic results support the globally widespread urea-type AOA. Together, these results indicate that urea-driven nitrification constitutes a non-negligible, substrate-dependent source of N2O in oligotrophic euphotic zones. We recommend that Earth-system N-cycle models represent urea and ammonium oxidation as distinct pathways with pH-sensitive yields to improve projections of marine nitrification and N2O fluxes under acidification.