Phytoplankton assimilation and microbial oxidation of ammonium are two critical conversion pathways in the marine nitrogen cycle. The underlying regulatory mechanisms of these two competing processes remain unclear. Here we show that ambient nitrate acts as a key variable to bifurcate ammonium flow through assimilation or oxidation, and the depth of the nitracline represents a robust spatial boundary between ammonium assimilators and oxidizers in the stratified ocean. Profiles of ammonium utilization show that phytoplankton assemblages in nitrate-depleted regimes have higher ammonium affinity than nitrifiers. In nitrate replete conditions, by contrast, phytoplankton reduce their ammonium reliance and thus enhance the success of nitrifiers. This finding helps to explain existing discrepancies in the understanding of light inhibition of surface nitrification in the global ocean, and provides further insights into the spatial linkages between oceanic nitrification and new production.

Nitrogen (N) limits primary productivity in approximately half of the global ocean, with concomitant influences on the magnitude of ocean carbon sequestration (Falkowski, 1997;Moore et al., 2013). Despite the importance of N cycling in global biogeochemistry, our knowledge of the complicated and interactive microbially-mediated transformations among N species remains incomplete. The marine N cycle is structured by a series of redox-driven biological transformations between the major N species, from the most reduced forms of ammonium (NH 4 + ) and organic N to the most oxidized form nitrate (NO 3 − ). As an intermediate in many of these processes, nitrite (NO 2 − ) plays numerous roles in plankton metabolism, including acting

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The removal of carbon dioxide from the atmosphere by the marine biological pump is a key regulator of Earth’s climate; however, the ocean also serves as a large source of nitrous oxide, a potent greenhouse gas and ozone-depleting substance. Although biological carbon sequestration and nitrous oxide production have been individually studied in the ocean, their combined impacts on net greenhouse forcing remain uncertain. Here we show that the magnitude of nitrous oxide production in the epipelagic zone of the subtropical ocean covaries with remineralization processes and thus acts antagonistically to weaken the radiative benefit of carbon removal by the marine biological pump. Carbon and nitrogen isotope tracer incubation experiments and nitrogen isotope natural abundance data indicate enhanced biological activity promotes nitrogen recycling, leading to substantial nitrous oxide production via both oxidative and reductive pathways. These shallow-water nitrous oxide sources account for nearly half of the air–sea flux and counteract 6–27% (median 9%) of the greenhouse warming mitigation achieved by carbon export via the biological pump.

The ocean is a net source of the greenhouse gas and ozone-depleting substance, nitrous oxide (N 2 O), to the atmosphere. Most of that N 2 O is produced as a trace side product during ammonia oxidation, primarily by ammonia-oxidizing archaea (AOA), which numerically dominate the ammonia-oxidizing community in most marine environments. The pathways to N 2 O production and their kinetics, however, are not completely understood. Here, we use 15 N and 18 O isotopes to determine the kinetics of N 2 O production and trace the source of nitrogen (N) and oxygen (O) atoms in N 2 O produced by a model marine AOA species, Nitrosopumilus maritimus . We find that during ammonia oxidation, the apparent half saturation constants of nitrite and N 2 O production are comparable, suggesting that both processes are enzymatically controlled and tightly coupled at low ammonia concentrations. The constituent atoms in N 2 O are derived from ammonia, nitrite, O 2 , and H 2 O via multiple pathways. Ammonia is the primary source of N atoms in N 2 O, but its contribution varies with ammonia to nitrite ratio. The ratio of 45 N 2 O to 46 N 2 O (i.e., single or double labeled N) varies with substrate ratio, leading to widely varying isotopic signatures in the N 2 O pool. O 2 is the primary source for O atoms. In addition to the previously demonstrated hybrid formation pathway, we found a substantial contribution by hydroxylamine oxidation, while nitrite reduction is an insignificant source of N 2 O. Our study highlights the power of dual 15 N- 18 O isotope labeling to disentangle N 2 O production pathways in microbes, with implications for interpretation of pathways and regulation of marine N 2 O sources.