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Abstract. Oxygen minimum zones (OMZs), due to their large volumes of perennially deoxygenated waters, are critical regions for understanding how the interplay between anaerobic and aerobic nitrogen (N) cycling microbial pathways affects the marine N budget. Here, we present a suite of measurements of the most significant OMZ N cycling rates, which all involve nitrite (NO2-) as a product, reactant, or intermediate, in the eastern tropical North Pacific (ETNP) OMZ. These measurements and comparisons to data from previously published OMZ cruisespresent additional evidence that NO3- reduction is the predominant OMZ N flux, followed by NO2- oxidation back to NO3-. The combined rates of both of these N recycling processes were observed to be much greater (up to nearly 200 times) thanthe combined rates of the N loss processes of anammox and denitrification, especially in waters near the anoxic–oxic interface. We also showthat NO2- oxidation can occur when O2 is maintained near 1 nM by a continuous-purge system, NO2-oxidation and O2 measurements that further strengthen the case for truly anaerobic NO2- oxidation. We also evaluate thepossibility that NO2- dismutation provides the oxidative power for anaerobic NO2- oxidation. The partitioning ofN loss between anammox and denitrification differed widely from stoichiometric predictions of at most 29 % anammox; in fact,N loss rates at many depths were entirely due to anammox. Our new NO3- reduction, NO2- oxidation, dismutation, andN loss data shed light on many open questions in OMZ N cycling research, especially the possibility of truly anaerobicNO2- oxidation.

 

Fixed nitrogen limits primary productivity in most areas of the surface ocean. Nitrite oxidation is the main source of nitrate, the most abundant form of inorganic fixed nitrogen. Even though known as an aerobic process, nitrite oxidation is not always stimulated by increased oxygen concentration, and nitrite oxidation occurs in layers of oxygen minimum zones (OMZs) where oxygen is not detectable. Nitrite‐oxidizing bacteria, known since their original isolation as aerobes, were also detected in these layers. Whether and how nitrite oxidation is occurring in the anoxic seawater is debated. Here, we reassess recent advances in marine nitrite oxidation in OMZ regions using previous work and new data sets we collected in two Pacific OMZs. We analyze the complex relationship between nitrite oxidation and oxygen. We discuss potential mechanisms explaining nitrite oxidation in different layers of OMZs based on recent findings and propose future directions to resolve the controversial question of apparently anaerobic nitrite oxidation in anoxic layers.

 

Abstract. As a key biogeochemical pathway in the marine nitrogen cycle, nitrification (ammonia oxidation and nitrite oxidation) converts the most reduced form of nitrogen – ammonium–ammonia (NH4+–NH3) – into the oxidized species nitrite (NO2-) and nitrate (NO3-). In the ocean, these processes are mainly performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB). By transforming nitrogen speciation and providing substrates for nitrogen removal, nitrification affects microbial community structure; marine productivity (including chemoautotrophic carbon fixation); and the production of a powerful greenhouse gas, nitrous oxide (N2O). Nitrification is hypothesized to be regulated by temperature, oxygen, light, substrate concentration, substrate flux, pH and other environmental factors. Although the number of field observations from various oceanic regions has increased considerably over the last few decades, a global synthesis is lacking, and understanding how environmental factors control nitrification remains elusive. Therefore, we have compiled a database of nitrification rates and nitrifier abundance in the global ocean from published literature and unpublished datasets. This database includes 2393 and 1006 measurements of ammonia oxidation and nitrite oxidation rates and 2242 and 631 quantifications of ammonia oxidizers and nitrite oxidizers, respectively. This community effort confirms and enhances our understanding of the spatial distribution of nitrification and nitrifiers and their corresponding drivers such as the important role of substrate concentration in controlling nitrification rates and nitrifier abundance. Some conundrums are also revealed, including the inconsistent observations of light limitation and high rates of nitrite oxidation reported from anoxic waters. This database can be used to constrain the distribution of marine nitrification, to evaluate and improve biogeochemical models of nitrification, and to quantify the impact of nitrification on ecosystem functions like marine productivity and N2O production. This database additionally sets a baseline for comparison with future observations and guides future exploration (e.g., measurements in the poorly sampled regions such as the Indian Ocean and method comparison and/or standardization). The database is publicly available at the Zenodo repository: https://doi.org/10.5281/zenodo.8355912 (Tang et al., 2023).

 

Obtaining nitrous oxide isotopocule measurements with isotope ratio mass spectrometry (IRMS) involves analyzing the ion current ratios of the nitrous oxide parent ion (N₂O⁺) as well as those of the NO⁺fragment ion. The data analysis requires correcting for “scrambling” in the ion source, whereby the NO⁺fragment ion obtains the outer N atom from the N₂O molecule. While descriptions exist for this correction, and interlaboratory intercalibration efforts have been made, there has yet to be published a package of code for implementing isotopomer calibrations.

We developed a user‐friendly Python package (pyisotopomer) to determine two coefficients (γandκ) that describe scrambling in the IRMS ion source, and then used this calibration to obtain intramolecular isotope deltas in N₂O samples.

With two appropriate reference materials,γandκcan be determined robustly and accurately for a given IRMS system. An additional third reference material is needed to define the zero‐point of the delta scale. We show that IRMS scrambling behavior can vary with time, necessitating regular calibrations. Finally, we present an intercalibration between two IRMS laboratories, using pyisotopomer to calculateγandκ, and to obtain intramolecular N₂O isotope deltas in lake water unknowns.

Given these considerations, we discuss how to use pyisotopomer to obtain high‐quality N₂O isotopocule data from IRMS systems, including the use of appropriate reference materials and frequency of calibration.

 

Nitrous oxide (N 2 O) is a potent greenhouse gas and an ozone destroying substance. Yet, clear step-by-step protocols to measure N 2 O transformation rates in freshwater and marine environments are still lacking, challenging inter-comparability efforts. Here we present detailed protocols currently used by leading experts in the field to measure water-column N 2 O production and consumption rates in both marine and other aquatic environments. We present example 15 N-tracer incubation experiments in marine environments as well as templates to calculate both N 2 O production and consumption rates. We discuss important considerations and recommendations regarding (1) precautions to prevent oxygen (O 2 ) contamination during low-oxygen and anoxic incubations, (2) preferred bottles and stoppers, (3) procedures for 15 N-tracer addition, and (4) the choice of a fixative. We finally discuss data reporting and archiving. We expect these protocols will make 15 N-labeled N 2 O transformation rate measurements more accessible to the wider community and facilitate future inter-comparison between different laboratories. 

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.

 

Marine oxygen‐deficient zones represent a natural source of nitrous oxide (N₂O), a potent greenhouse gas and ozone‐depleting agent. To investigate controls on N₂O production, the responses of ammonia oxidation (AO) to nitrite () and N₂O with respect to oxygen (O₂), ammonium () and concentrations were evaluated using tracer incubations in the Eastern Tropical North Pacific. Within the oxycline, additions of and O₂stimulated N₂O production according to Michaelis–Menten kinetics, indicating that both substrates were limiting, and that N₂O production, even if the exact mechanisms remain uncertain, is mediated by predictable kinetics. Low half‐saturation constants for (12–28 nM) and O₂(460 ± 130 nM) during N₂O production indicate that AO communities are well adapted to low concentrations of both substrates. Hybrid N₂O formation (i.e., from one and one unlabeled nitrogen (N) source, e.g., , NO) accounted for ~ 90% of the N₂O production from and was robust across the different O₂, , and conditions. Lack of response to variable substrate concentrations implies that the unlabeled N source was not limiting for N₂O production. Although both O₂and were key modulators of N₂O production rates, N₂O yield (N₂O produced per produced) seemed to be controlled solely by O₂. The N₂O yield increased when O₂concentrations dropped below the half‐saturation concentration for AO to (< 1.4 μM), the range where production decreased faster than N₂O production. Our study shows that O₂control on N₂O yield from AO is robust across stations and depths.

 

Abstract. Oxygen-deficient zones (ODZs) are major sites of net naturalnitrous oxide (N2O) production and emissions. In order to understandchanges in the magnitude of N2O production in response to globalchange, knowledge on the individual contributions of the major microbialpathways (nitrification and denitrification) to N2O production andtheir regulation is needed. In the ODZ in the coastal area off Peru, thesensitivity of N2O production to oxygen and organic matter wasinvestigated using 15N tracer experiments in combination with quantitative PCR (qPCR) andmicroarray analysis of total and active functional genes targeting archaeal amoAand nirS as marker genes for nitrification and denitrification, respectively.Denitrification was responsible for the highest N2O production with amean 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 productionfrom ammonium oxidation (AO) of 0.16±0.003 nmol L−1 d−1occurred 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 dominantspecies, comprising 70 %–85 % of total produced N2O fromNH4+, regardless of the ammonium oxidation rate or O2concentrations. Oxygen responses of N2O production varied withsubstrate, but production and yields were generally highest below 10 µmol L−1 O2. Particulate organic matter additions increasedN2O production by denitrification up to 5-fold, suggesting increasedN2O production during times of high particulate organic matter export.High N2O yields of 2.1 % from AO were measured, but the overallcontribution by AO to N2O production was still an order of magnitudelower than that of denitrification. Hence, these findings show thatdenitrification is the most important N2O production process in low-oxygen conditions fueled by organic carbon supply, which implies a positivefeedback of the total oceanic N2O sources in response to increasingoceanic deoxygenation. 

Abstract. In the current era of rapid climate change, accuratecharacterization of climate-relevant gas dynamics – namely production,consumption, and net emissions – is required for all biomes, especially thoseecosystems most susceptible to the impact of change. Marine environmentsinclude regions that act as net sources or sinks for numerous climate-activetrace gases including methane (CH4) and nitrous oxide (N2O). Thetemporal and spatial distributions of CH4 and N2O are controlledby the interaction of complex biogeochemical and physical processes. Toevaluate and quantify how these mechanisms affect marine CH4 andN2O cycling requires a combination of traditional scientificdisciplines including oceanography, microbiology, and numerical modeling.Fundamental to these efforts is ensuring that the datasets produced byindependent scientists are comparable and interoperable. Equally critical istransparent communication within the research community about the technicalimprovements required to increase our collective understanding of marineCH4 and N2O. A workshop sponsored by Ocean Carbon and Biogeochemistry (OCB)was organized to enhance dialogue and collaborations pertaining tomarine CH4 and N2O. Here, we summarize the outcomes from theworkshop to describe the challenges and opportunities for near-futureCH4 and N2O research in the marine environment.