Revisiting nitrification in the Eastern Tropical South Pacific: A focus on controls

Nitrification, the oxidation of ammonium (NH4+) to nitrite (NO2-) and to nitrate (NO3-), is a component of the nitrogen (N) cycle internal to the fixed N pool. In oxygen minimum zones (OMZs), which are hotspots for oceanic fixed N loss, nitrification plays a key role because it directly supplies substrates for denitrification and anaerobic ammonia oxidation (anammox), and may compete for substrates with these same processes. However, the control of oxygen and substrate concentrations on nitrification are not well understood. We performed onboard incubations with ¹⁵N-labeled substrates to measure rates of NH4+ and NO2- oxidation in the eastern tropical South Pacific (ETSP). The spatial and depth distributions of NH4+ and NO2- oxidation rates were primarily controlled by NH4+ and NO2- availability, oxygen concentration, and light. In the euphotic zone, nitrification was partially photoinhibited. In the anoxic layer, NH4+ oxidation was negligible or below detection, but high rates of NO2- oxidation were observed. NH4+ oxidation displayed extremely high affinity for both NH4+ and oxygen. The positive linear correlations between NH4+ oxidation rates and in situ NH4+ concentrations and ammonia monooxygenase subunit A (amoA) gene abundances in the upper oxycline indicate that the natural assemblage of ammonia oxidizers responds to in situ NH4+ concentrations or supply by adjusting their population size, which determines the NH4+ oxidation potential. The depth distribution of archaeal and bacterial amoA gene abundances and N₂O concentration, along with independently reported simultaneous direct N₂O production rate measurements, suggests that AOA were predominantly responsible for NH4+ oxidation, which was a major source of N₂O production at oxygen concentrations > 5 μM.