Abstract. Oxygen-deficient zones (ODZs) are major sites of net natural nitrous oxide (N2O) production and emissions. In order to understand changes in the magnitude of N2O production in response to global change, knowledge on the individual contributions of the major microbial pathways (nitrification and denitrification) to N2O production and their regulation is needed. In the ODZ in the coastal area off Peru, the sensitivity of N2O production to oxygen and organic matter was investigated using 15N tracer experiments in combination with quantitative PCR (qPCR) and microarray analysis of total and active functional genes targeting archaeal amoA and nirS as marker genes for nitrification and denitrification, respectively. Denitrification was responsible for the highest N2O production with a mean of 8.7 nmol L−1 d−1 but up to 118±27.8 nmol L−1 d−1 just below the oxic–anoxic interface. The highest N2O production from ammonium oxidation (AO) of 0.16±0.003 nmol L−1 d−1 occurred in the upper oxycline at O2 concentrations of 10–30 µmol L−1 which coincided with the highest archaeal amoA transcripts/genes. Hybrid N2O formation (i.e., N2O with one N atom from NH4+ and the other from other substrates such as NO2-) was the dominant species, comprising 70 %–85 % of total produced N2O from NH4+, regardless of the ammonium oxidation rate or O2 concentrations. Oxygen responses of N2O production varied with substrate, but production and yields were generally highest below 10 µmol L−1 O2. Particulate organic matter additions increased N2O production by denitrification up to 5-fold, suggesting increased N2O production during times of high particulate organic matter export. High N2O yields of 2.1 % from AO were measured, but the overall contribution by AO to N2O production was still an order of magnitude lower than that of denitrification. Hence, these findings show that denitrification is the most important N2O production process in low-oxygen conditions fueled by organic carbon supply, which implies a positive feedback of the total oceanic N2O sources in response to increasing oceanic deoxygenation.

Chemolithoautotrophic denitrification is an important mechanism of nitrogen loss in the water column of euxinic basins, but its isotope fractionation factor is not known. Sulfurimonas gotlandica GD1(T), a recently isolated bacterial key player in Baltic Sea pelagic redoxcline processes, was used to determine the isotope fractionation of nitrogen and oxygen in nitrate during denitrification. Under anoxic conditions, nitrate reduction was accompanied by nitrogen and oxygen isotope fractionation of 23.8 ± 2.5‰ and 11.7 ± 1.1‰, respectively. The isotope effect for nitrogen was in the range determined for heterotrophic denitrification, with only the absence of stirring resulting in a significant decrease of the fractionation factor. The relative increase in δ(18)ONO3 to δ(15)NNO3 did not follow the 1:1 relationship characteristic of heterotrophic, marine denitrification. Instead, δ(18)ONO3 increased slower than δ(15)NNO3, with a conserved ratio of 0.5:1. This result suggests that the periplasmic nitrate reductase (Nap) of S. gotlandica strain GD1(T) fractionates the N and O in nitrate differently than the membrane-bound nitrate reductase (Nar), which is generally prevalent among heterotrophic denitrifiers and is considered as the dominant driver for the observed isotope fractionation. Hence in the Baltic Sea redoxcline, other, as yet-unidentified factors likely explain the low apparent fractionation.

Nitrite is a pivotal component of the marine nitrogen cycle. The fate of nitrite determines the loss or retention of fixed nitrogen, an essential nutrient for all organisms. Loss occurs via anaerobic nitrite reduction to gases during denitrification and anammox, while retention occurs via nitrite oxidation to nitrate. Nitrite oxidation is usually represented in biogeochemical models by one kinetic parameter and one oxygen threshold, below which nitrite oxidation is set to zero. Here we find that the responses of nitrite oxidation to nitrite and oxygen concentrations vary along a redox gradient in a Pacific Ocean oxygen minimum zone, indicating niche differentiation of nitrite-oxidizing assemblages. Notably, we observe the full inhibition of nitrite oxidation by oxygen addition and nitrite oxidation coupled with nitrogen loss in the absence of oxygen consumption in samples collected from anoxic waters. Nitrite-oxidizing bacteria, including novel clades with high relative abundance in anoxic depths, were also detected in the same samples. Mechanisms corresponding to niche differentiation of nitrite-oxidizing bacteria across the redox gradient are considered. Implementing these mechanisms in biogeochemical models has a significant effect on the estimated fixed nitrogen budget.