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Nitrous oxide (N2O) is a powerful greenhouse gas and a major cause of stratospheric ozone depletion, yet its sources and sinks remain poorly quantified in the oceans. We used isotope tracers to directly measure N2O reduction rates in the eastern tropical North Pacific. Because of incomplete denitrification, N2O cycling rates are an order of magnitude higher than predicted by current models in suboxic regions, and the spatial distribution suggests strong dependence on both organic carbon and dissolved oxygen concentrations. Furthermore, N2O turnover is 20 times higher than the net atmospheric efflux. The rapid rate of this cycling coupled to an expected expansion of suboxic ocean waters implies future increases in N2O emissions., (Copyright © 2015, American Association for the Advancement of Science.)

Nitrogen (N) bioavailability affects phytoplankton growth and primary production in the aquatic environment. N bioavailability is partly determined by biological N cycling processes that either transform N species or remove fixed N. Reliable estimates of their kinetic parameters can help understand the distribution of N cycling processes. However, available estimates of kinetic parameters are often derived from microbial isolates and may not be representative of the natural environment. Observations are particularly lacking in estuarine and coastal waters. We conducted isotope tracer addition incubations to evaluate substrate affinities of nitrification, denitrification and anammox in the Chesapeake Bay water column. The half‐saturation constant for ammonia oxidation ranged from 0.38 to 0.75 μM ammonium, substantially higher than observed in the open oceans. Half‐saturation constants for denitrification—0.92–1.86 μM nitrite or 1.15 μM nitrate—were within the lower end or less than those reported for other aquatic environments and for denitrifier isolates. Interestingly, water column denitrification potential was comparable to that of sedimentary denitrification, highlighting the contribution of the water column to N removal during anoxia. Mostly undetectable anammox rates prevented us from deriving the half‐saturation constants, suggesting a low affinity of anammox. Using these substrate kinetics, we were able to predict in situ N cycling rates and explain the vertical distribution of N nutrient concentrations. Our newly derived substrate kinetics parameters can be useful for improving model representation of N nutrient dynamics in estuarine and coastal waters, which is critical for assessing the ecosystem productivity and function. [ABSTRACT FROM AUTHOR]

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 (NH 4+ –NH 3) – into the oxidized species nitrite (NO 2-) and nitrate (NO 3-). 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 (N 2 O). 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 N 2 O 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: 10.5281/zenodo.8355912 (Tang et al., 2023). [ABSTRACT FROM AUTHOR]

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 2187 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; method comparison/standardization). The database is publicly available at Zenodo repository: https://doi.org/10.5281/zenodo.7942922 (Tang et al., 2023). [ABSTRACT FROM AUTHOR]

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. Plain Language Summary: No organism can survive without nitrogen. The scarcity of fixed nitrogen in large surface areas of the ocean limits the capacity of phytoplankton to fix carbon dioxide. Oxygen minimum zones (OMZs) are critical oceanic regions for marine nitrogen inventory because the full spectrum of oxygen conditions in OMZs allows the retention and the loss of fixed nitrogen. The anoxic layer in OMZs was thought to host only anaerobic nitrogen loss processes. However, nitrite oxidation, conventionally known as an aerobic process that retains fixed nitrogen, was also detected in the anoxic zone. We revisit the complex relationship between nitrite oxidation and oxygen, and present mechanisms explaining nitrite oxidation in different layers of the ocean. We also chart a way forward for deciphering the mystery of anaerobic nitrite oxidation. Key Points: The detection of nitrite oxidation in anoxic seawater suggests the necessity to reevaluate our understanding of the nitrogen budgetDifferent mechanisms explaining nitrite oxidation in different oceanic layers are discussedThe complex relationship between nitrite oxidation and O2 indicates the importance of rigorous O2 control during experimental manipulations [ABSTRACT FROM AUTHOR]

Across the Southern Ocean in winter, nitrification is the dominant mixed-layer nitrogen cycle process, with some of the nitrate produced therefrom persisting to fuel productivity during the subsequent growing season. Because this nitrate constitutes a regenerated rather than a new nutrient source to phytoplankton, it will not support the net removal of atmospheric CO 2. To better understand the controls on Southern Ocean nitrification, we conducted nitrite oxidation kinetics experiments in surface waters across the western Indian sector in winter. While all experiments (seven in total) yielded a Michaelis–Menten relationship with substrate concentration, the nitrite oxidation rates only increased substantially once the nitrite concentration exceeded 115±2.3 to 245±18 nM, suggesting that nitrite-oxidizing bacteria (NOB) require a minimum (i.e., "threshold") nitrite concentration to produce nitrate. The half-saturation constant for nitrite oxidation ranged from 134±8 to 403±24 nM, indicating a relatively high affinity of Southern Ocean NOB for nitrite, in contrast to results from culture experiments. Despite the high affinity of NOB for nitrite, its concentration rarely declines below 150 nM in the Southern Ocean's mixed layer, regardless of season. In the upper mixed layer, we measured ammonium oxidation rates that were two- to seven-fold higher than the coincident rates of nitrite oxidation, indicating that nitrite oxidation is the rate-limiting step for nitrification in the winter Southern Ocean. The decoupling of ammonium and nitrite oxidation, combined with a possible nitrite concentration threshold for NOB, may explain the non-zero nitrite that persists throughout the Southern Ocean's mixed layer year-round. Additionally, nitrite oxidation may be limited by dissolved iron, the availability of which is low across the upper Southern Ocean. Our findings have implications for understanding the controls on nitrification and ammonium and nitrite distributions, both in the Southern Ocean and elsewhere. [ABSTRACT FROM AUTHOR]

As a key intermediate in the nitrogen cycle, nitrite is involved in multiple biological pathways that regulate the distribution and availability of nitrogen in the ocean. In the oligotrophic gyres, nitrite accumulates near the base of the euphotic zone, demonstrating a subsurface maximum, termed the primary nitrite maximum; while in subpolar regions, nitrite concentrations are elevated in the near-surface ocean. As yet, the mechanisms controlling this meridional pattern remain unclear. Here, we present vertically resolved profiles of rates of nitrite production and consumption extending from the Subtropical Gyre to the Subarctic Front in the North Pacific Ocean. Our results indicate that the latitudinal distributions of nitrite across this basin are influenced by variations in phytoplankton-nitrifier interactions. In the well-lit oligotrophic surface, phytoplankton dominates rapid nitrite cycling via coupled release and re-assimilation; below the euphotic zone, diminished light stress on nitrite oxidizers results in rapid turnover and limits nitrite. By contrast, in subpolar regions where nitrate concentrations are elevated in the euphotic zone, nitrite is released during assimilative nitrate reduction and competition between phytoplankton and nitrifiers for ammonium is relaxed, facilitating ammonia oxidation. These processes, together with differential light sensitivities of ammonia and nitrite oxidizers, allow net accumulation of nitrite. Furthermore, we demonstrate a substantial contribution of urea oxidation in forming the primary nitrite maximum and balancing the two steps of marine nitrification. Our findings reveal physical- biological interactive controls on nitrite cycling and distributions in the ocean and help disentangle the complex effect of phytoplankton-microbe interactions on marine nitrogen biogeochemistry. [ABSTRACT FROM AUTHOR]

Upwelling of nutrient-rich deep waters make eastern boundary upwelling systems (EBUSs), such as the Humboldt Current system, hot spots of marine productivity. Associated settling of organic matter to depth and consecutive aerobic decomposition results in large subsurface water volumes being oxygen depleted. Under these circumstances, organic matter remineralisation can continue via denitrification, which represents a major loss pathway for bioavailable nitrogen. Additionally, anaerobic ammonium oxidation can remove significant amounts of nitrogen in these areas. Here we assess the interplay of suboxic water upwelling and nitrogen cycling in a manipulative offshore mesocosm experiment. Measured denitrification rates in incubations with water from the oxygen-depleted bottom layer of the mesocosms (via 15 N label incubations) mostly ranged between 5.5 and 20 nmol N 2 L -1 h -1 (interquartile range), reaching up to 80 nmol N 2 L -1 h -1. However, actual in situ rates in the mesocosms, estimated via Michaelis–Menten kinetic scaling, did most likely not exceed 0.2–4.2 nmol N 2 L -1 h -1 (interquartile range) due to substrate limitation. In the surrounding Pacific, measured denitrification rates were similar, although indications of substrate limitation were detected only once. In contrast, anammox (anaerobic ammonium oxidation) made only a minor contribution to the overall nitrogen loss when encountered in both the mesocosms and the Pacific Ocean. This was potentially related to organic matter C / N stoichiometry and/or process-specific oxygen and hydrogen sulfide sensitivities. Over the first 38 d of the experiment, total nitrogen loss calculated from in situ rates of denitrification and anammox was comparable to estimates from a full nitrogen budget in the mesocosms and ranged between ∼ 1 and 5.5 µ mol N L -1. This represents up to ∼ 20 % of the initially bioavailable inorganic and organic nitrogen standing stocks. Interestingly, this loss is comparable to the total amount of particulate organic nitrogen that was exported into the sediment traps at the bottom of the mesocosms at about 20 m depth. Altogether, this suggests that a significant portion, if not the majority of nitrogen that could be exported to depth, is already lost, i.e. converted to N 2 in a relatively shallow layer of the surface ocean, provided that there are oxygen-deficient conditions like those during coastal upwelling in our study. Published data for primary productivity and nitrogen loss in all EBUSs reinforce such conclusion. [ABSTRACT FROM AUTHOR]

Nitrogen (N) is used in many of life’s fundamental biomolecules, and it is also a participant in environmental redox chemistry. Biogeochemical processes control the amount and form of N available to organisms ("fixed” N). These interacting processes result in N acting as the proximate limiting nutrient in most surface environments. Here, we review the global biogeochemical cycle of N and its anthropogenic perturbation. We introduce important reservoirs and processes affecting N in the environment, focusing on the ocean, in which N cycling is more generalizable than in terrestrial systems, which are more heterogeneous. Particular attention is given to processes that create and destroy fixed N because these comprise the fixed N input/output budget, the most universal control on environmental N availability. We discuss preindustrial N budgets for terrestrial and marine systems and their modern-day alteration by N inputs from human activities. We summarize evidence indicating that the simultaneous roles of N as a required biomass constituent and an environmental redox intermediate lead to stabilizing feedbacks that tend to blunt the impact of N cycle perturbations at larger spatiotemporal scales, particularly in marine systems. As a result of these feedbacks, the anthropogenic "N problem” is distinct from the "carbon dioxide problem” in being more local and less global, more immediate and less persistent. [ABSTRACT FROM AUTHOR]

Understanding the interactions between microbial communities and their environment sufficiently to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. However, modeling microbial communities is problematic, because (i) communities are complex, (ii) most descriptions are qualitative, and (iii) quantitative understanding of the way communities interact with their surroundings remains incomplete. One approach to overcoming such complications is the integration of partial qualitative and quantitative descriptions into more complex networks. Here we outline the development of a probabilistic framework, based on Event Transition Graph (ETG) theory, to predict microbial community structure across observed chemical data. Using reverse engineering, we derive probabilities from the ETG that accurately represent observations from experiments and predict putative constraints on communities within dynamic environments. These predictions can feedback into the future development of field experiments by emphasizing the most important functional reactions, and associated microbial strains, required to characterize microbial ecosystems. [ABSTRACT FROM AUTHOR]

The redoxclines that form between the oxic and anoxic water layers in the central Baltic Sea are sites of intensive nitrogen cycling. To gain better understanding of nitrification, we measured the biogeochemical properties along with potential nitrification rates and analyzed the assemblages of ammonia-oxidizing bacteria and archaea using functional gene microarrays. To estimate nitrification in the entire water column, we constructed a regression model for the nitrification rates and applied it to the conditions prevailing in the area in 2008–2012. The highest ammonia oxidation rates were found in a thin layer at the top of the redoxcline and the rates quickly decreased below detection limit when oxygen was exhausted. This is probably because extensive suboxic layers, which are known to harbor pelagic nitrification, are formed only for short periods after inflows in the Baltic Sea. The nitrification rates were some of the highest measured in the water columns, but the thickness of the layer where conditions were favorable for nitrification, was very small and it remained fairly stable between years. However, the depth of the nitrification layer varied substantially between years, particularly in the eastern Gotland Basin (EGB) due to turbulence in the water column. The ammonia oxidizer communities clustered differently between the eastern and western Gotland Basin (WGB) and the composition of ammonia-oxidizing assemblages correlated with the environmental variables. The ammonia oxidizer community composition was more even in the EGB, which may be related to physical instability of the redoxcline that does not allow predominance of a single archetype, whereas in the WGB, where the position of the redoxcline is more constant, the ammonia-oxidizing community was less even. Overall the ammonia-oxidizing communities in the Baltic Sea redoxclines were very evenly distributed compared to other marine environments where microarrays have been applied previously. [ABSTRACT FROM AUTHOR]

Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated profiles of microbial communities and communities of micro-organisms containing specific nitrogen cycling genes that encode several enzymes (amoA, norB, nosZ) related to nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms involved in the production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that previously measured rates of nitrous oxide production and consumption are likely the result of changes in community structure, not simply changes in microbial activity. [ABSTRACT FROM AUTHOR]

The Eastern Tropical South Pacific is one of the three major oxygen deficient zones (ODZs) in the global ocean and is responsible for approximately one third of marine water column nitrogen loss. It is the best studied of the ODZs and, like the others, features a broad nitrite maximum across the low oxygen layer. How the microbial processes that produce and consume nitrite in anoxic waters interact to sustain this feature is unknown. Here we used 15N-tracer experiments to disentangle five of the biologically mediated processes that control the nitrite pool, including a high-resolution profile of nitrogen loss rates. Nitrate reduction to nitrite likely depended on organic matter fluxes, but the organic matter did not drive detectable rates of denitrification to N2. However, multiple lines of evidence show that denitrification is important in shaping the biogeochemistry of this ODZ. Significant rates of anaerobic nitrite oxidation at the ODZ boundaries were also measured. Iodate was a potential oxidant that could support part of this nitrite consumption pathway. We additionally observed N2 production from labeled cyanate and postulate that anammox bacteria have the ability to harness cyanate as another form of reduced nitrogen rather than relying solely on ammonification of complex organic matter. The balance of the five anaerobic rates measured-anammox, denitrification, nitrate reduction, nitrite oxidation, and dissimilatory nitrite reduction to ammonium-is sufficient to reproduce broadly the observed nitrite and nitrate profiles in a simple one-dimensional model but requires an additional source of reduced nitrogen to the deeper ODZ to avoid ammonium overconsumption. [ABSTRACT FROM AUTHOR]

Marine oxygen deficient zones (ODZs) have long been identified as sites of fixed nitrogen (N) loss. However, the mechanisms and rates of N loss have been debated, and traditional methods for measuring these rates are labor-intensive and may miss hot spots in spatially and temporally variable environments. Here we estimate rates of heterotrophic nitrate reduction, heterotrophic nitrite reduction (denitrification), nitrite oxidation, and anaerobic ammonium oxidation (anammox) at a coastal site in the eastern tropical South Pacific (ETSP) ODZ based on high-resolution concentration and natural abundance stable isotope measurements of nitrate (NO3−) and nitrite (NO2−). These measurements were used to estimate process rates using a two-step inverse modeling approach. The modeled rates were sensitive to assumed isotope effects for NO3− reduction and NO2− oxidation. Nevertheless, we addressed two questions surrounding the fates of NO2− in the ODZ: (1) Is NO2− being primarily reduced to N2 or oxidized to NO3− in the ODZ? and (2) what are the contributions of anammox and denitrification to NO2− removal? Depth-integrated rates from the model suggest that 72-88% of the NO2− produced in the ODZ was oxidized back to NO3−, while 12-28% of NO2− was reduced to N2. Furthermore, our model suggested that 36-74% of NO2− loss was due to anammox, with the remainder due to denitrification. These model results generally agreed with previously measured rates, though with a large range of uncertainty, and they provide a long-term integrated view that compliments incubation experiments to obtain a broader picture of N cycling in ODZs. [ABSTRACT FROM AUTHOR]

Connecting molecular information directly to microbial transformation rates remains a challenge, despite the availability of molecular methods to investigate microbial biogeochemistry. By combining information on gene abundance and expression for key genes with quantitative modeling of nitrogen fluxes, we can begin to understand the scales on which genetic signals vary and how they relate to key functions. We used quantitative PCR of DNA and cDNA, along with biogeochemical modeling to assess how the abundance and expression of microbes responsible for two steps in the nitrogen cycle changed over time in estuarine sediment mesocosms. Sediments and water were collected from coastal Massachusetts and maintained in replicated 20 L mesocosms for 45 days. Concentrations of all major inorganic nitrogen species were measured daily and used to derive rates of nitrification and denitrification from a Monte Carlo-based non-negative least-squares analysis of finite difference equations. The mesocosms followed a classic regeneration sequence in which ammonium released from the decomposition of organic matter was subsequently oxidized to nitrite and then further to nitrate, some portion of which was ultimately denitrified. Normalized abundances of ammonia oxidizing archaeal ammonia monoxoygenase (amoA) transcripts closely tracked rates of ammonia oxidation throughout the experiment. No such relationship, however, was evident between denitrification rates and the normalized abundance of nitrite reductase (nirS and nirK) transcripts. These findings underscore the complexity of directly linking the structure of the microbial community to rates of biogeochemical processes. [ABSTRACT FROM AUTHOR]

Nitrification rates, as well as the relationships between rates and ammonia oxidizer abundance (both archaeal and bacterial), were investigated in the Arabian Sea. Ammonia oxidation rates were measured directly using 15N-NH+4 stable isotope additions in gas-impermeable, trace metal clean trilaminate bags (500 mL) at in situ temperature. Tracer incubations were performed at three stations at depths above, below, and within the oxycline of the open-ocean oxygen minimum zone (OMZ). Ammonia oxidation rates were similar to previous open-ocean measurements, ranging from undetectable to 21.6 ± 0.1 nmol L-1 d-1. The highest rates at each station occurred at the primary nitrite maximum (above the OMZ), and rates were very low at depths greater than 900 m. The abundances of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were estimated using the amoA gene by quantitative polymerase chain reaction (qPCR). Both AOA and AOB amoA were detected above, within, and below the OMZ, although the AOA were always more abundant than the AOB, by a factor of 35-216. Nitrification rates were not directly correlated to AOA or AOB amoA abundance. These rates offer new insight into the role of nitrification in the mesopelagic zone. The abundance of AOA amoA genes at 1000 m suggests that ~50% of the microbial biomass could be autotrophic. Additionally, the integrated nitrification rate at depth implies that nitrification could consume most of the ammonium produced by the flux of organic carbon in the mesopelagic zone. [ABSTRACT FROM AUTHOR]

A missing link in the nitrogen cycle has recently been found: bacteria capable of oxidizing ammonium to nitrogen gas (N2). This new source of N2 has now been detected in both the water column and the sediments in marine environments. This discovery is important because it necessitates re-evaluation of (1) major fluxes in the global nitrogen budget and (2) regulation of the processes leading to fixed nitrogen loss. [Copyright &y& Elsevier]

An introduction is presented in which the editors discuss various reports within the issue on topics including nitrogen (N) fixation, the response of N fixers to Fe or P additions, and nitrification.

Abstract: The oxygen minimum zones (OMZs) of the world oceans are sites of enhanced anaerobic nitrogen transformations, such that the largest OMZ, the Arabian Sea, is responsible for 30–50% of the oceanic water column fixed N loss. Measurements of excess N2 and nitrate deficits have been interpreted to indicate a large net loss of fixed nitrogen through N2 production in waters with very low oxygen concentrations. Rates of N2 production both by denitrification and anaerobic ammonium oxidation (anammox) were investigated by measuring 15N–N2 production from , , and 46N2O in incubations at 3–4 depths at each of the three stations in the central region of the Arabian Sea OMZ. In addition to conventional measurements of anammox and denitrification rates from incubations in 12ml exetainers purged with He, we also investigated the effect of ammonium and organic carbon additions on N2 production rate. Denitrification was detected at every depth at every station; the maximum rate (25.3±9.1nmoll−1 d−1 from the 15NO2 tracer and 21.2±5.6nmoll−1 d−1 from the 46N2O tracer) occurred at the depth of the secondary nitrite maximum in the core of the OMZ. The 46N2O tracer was the most direct method to measure the denitrification rate. Rates of denitrification correlated strongly with water column nitrite concentration. Addition of organic carbon or ammonium did not consistently stimulate denitrification rates. Distribution of anammox was patchy; low rates of anammox production of 29N2 in incubations were detected at only four of eleven depths. The highest rate of anammox production (4.23±0.35nmoll−1 d−1) occurred near the upper boundary of the OMZ at one station. Overall, denitrification dominated N2 production at this time in the Arabian Sea OMZ. [Copyright &y& Elsevier]

Describes the DNA microarray method for the detection of functional gene diversity in the nitrogen cycle in the environment. Determination of the threshold values for specificity; Simplification of the complexities of microbial processes; Optimization of the hybridization conditions.