Ammonium-derived nitrous oxide is a global source in streams.

Global riverine nitrous oxide (NO) emissions have increased more than 4-fold in the last century. It has been estimated that the hyporheic zones in small streams alone may contribute approximately 85% of these NO emissions. However, the mechanisms and pathways controlling hyporheic NO production in stream ecosystems remain unknown. Here, we report that ammonia-derived pathways, rather than the nitrate-derived pathways, are the dominant hyporheic NO sources (69.6 ± 2.1%) in agricultural streams around the world. The NO fluxes are mainly in positive correlation with ammonia. The potential NO metabolic pathways of metagenome-assembled genomes (MAGs) provides evidence that nitrifying bacteria contain greater abundances of NO production-related genes than denitrifying bacteria. Taken together, this study highlights the importance of mitigating agriculturally derived ammonium in low-order agricultural streams in controlling NO emissions. Global models of riverine ecosystems need to better represent ammonia-derived pathways for accurately estimating and predicting riverine NO emissions.