Primary production in over half of the world's oceans is limited by fixed nitrogen availability. The main loss term from the fixed nitrogen inventory is the production of dinitrogen gas (N(2)) by heterotrophic denitrification or the more recently discovered autotrophic process, anaerobic ammonia oxidation (anammox). Oceanic oxygen minimum zones (OMZ) are responsible for about 35% of oceanic N(2) production and up to half of that occurs in the Arabian Sea. Although denitrification was long thought to be the only loss term, it has recently been argued that anammox alone is responsible for fixed nitrogen loss in the OMZs. Here we measure denitrification and anammox rates and quantify the abundance of denitrifying and anammox bacteria in the OMZ regions of the Eastern Tropical South Pacific and the Arabian Sea. We find that denitrification rather than anammox dominates the N(2) loss term in the Arabian Sea, the largest and most intense OMZ in the world ocean. In seven of eight experiments in the Arabian Sea denitrification is responsible for 87-99% of the total N(2) production. The dominance of denitrification is reproducible using two independent isotope incubation methods. In contrast, anammox is dominant in the Eastern Tropical South Pacific OMZ, as detected using one of the isotope incubation methods, as previously reported. The abundance of denitrifying bacteria always exceeded that of anammox bacteria by up to 7- and 19-fold in the Eastern Tropical South Pacific and Arabian Sea, respectively. Geographic and temporal variability in carbon supply may be responsible for the different contributions of denitrification and anammox in these two OMZs. The large contribution of denitrification to N(2) loss in the Arabian Sea indicates the global significance of denitrification to the oceanic nitrogen budget.

Toxicogenomics has provided innovative approaches to chemical screening, risk assessment, and predictive toxicology. If applied to ecotoxicology, genomics tools could greatly enhance the ability to understand the modes of toxicity in environmentally relevant organisms. Daphnia magna, a small aquatic crustacean, is considered a "keystone" species in ecological food webs and is an indicator species for toxicant exposure. Our objective was to demonstrate the potential utility of gene expression profiling in ecotoxicology by identifying novel biomarkers and uncovering potential modes of action in D. magna. Using a custom D. magna cDNA microarray, we identified distinct expression profiles in response to sublethal copper, cadmium, and zinc exposures and discovered specific biomarkers of exposure including two probable metallothioneins, and a ferritin mRNA with a functional IRE. The gene expression patterns support known mechanisms of metal toxicity and reveal novel modes of action including zinc inhibition of chitinase activity. By integrating gene expression profiling into an environmentally important organism, this study provides experimental support for the utility of ecotoxicogenomics.

Biologically available nitrogen (N) limits phytoplankton growth over much of the ocean. The rate at which N is removed from the contemporary ocean by denitrifying bacteria is highly uncertain 1-3 . Some studies suggest that N losses exceed inputs 2,4-6 ; others argue for a balanced budget 3,7,8 . Here, we use a global ocean circulation model to simulate the distribution of N 2 gas produced by denitrifying bacteria in the three main suboxic zones in the open ocean. By fitting the model to measured N 2 gas concentrations, we infer a globally integrated rate of water-column denitrification of 66 ± 6 Tg N yr −1 . Taking into account isotopic constraints on the fraction of denitrification occurring in the water column versus marine sediments, we estimate that the global rate of N loss from marine sediments and the oceanic water column combined amounts to around 230 ± 60 Tg N yr −1 . Given present estimates of N input rates, our findings imply a net loss of around 20 ± 70 Tg of N from the global ocean each year, indistinguishable from a balanced budget. A balanced N budget, in turn, implies that the marine N cycle is governed by strong regulatory feedbacks.The loss of N in the ocean occurs as bacteria reduce N to N 2 gas through a combination of heterotrophic denitrification and anaerobic ammonium oxidation (hereafter collectively termed denitrification). Suboxic conditions in which O 2 is scarce enough to favour these processes are found in three principal locations in the water column: the Arabian Sea, the eastern tropical South Pacific (ETSP) and the eastern tropical North Pacific (ETNP; Fig. 1). Denitrification rates in these areas estimated from nitrate deficits and water-mass age tracers yield a global rate of watercolumn denitrification in the range of 60-90 Tg N yr −1 (refs 9-14), but recently rates as large as 150 Tg N yr −1 have been proposed 2 . Denitrification also occurs in suboxic pore waters of sediments throughout the ocean, but the rates are spatially heterogeneous and have been measured at only a handful of sites 15 , precluding a direct global estimate. However, the global rate of sedimentary N loss (primarily denitrification, but also a small burial of organic N) is constrained by the isotopic ratio of mean ocean nitrate to be one to four times as large as the rate of denitrification in the suboxic water column 6,16,17 . Estimates of the total rate of N loss in the ocean therefore inherit and amplify the uncertainty in the rate of denitrification in suboxic waters, yielding a combined rate of about 270 Tg N yr −1 (ref.3) to more than 400 Tg N yr −1 (refs 2,6). These rates far exceed the estimated global rate of N fixation, which is in the range of 100-160 Tg N yr −1 (refs 7,18). The apparent deficit is partially offset by riverine and atmospheric inputs of about 40-125 Tg N yr −1 (refs 3,15). Still, if the upper end of the denitrification-rate estimates are correct, the ocean must be rapidly losing fixed N.

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Assessment of the global budget of the greenhouse gas nitrous oxide (N2O) is limited by poor knowledge of the oceanicN2O flux to the atmosphere, of which the magnitude, spatial distribution, and temporal variability remain highly uncertain. Here, we reconstruct climatologicalN2O emissions from the ocean by training a supervised learning algorithm with over 158,000N2O measurements from the surface ocean—the largest synthesis to date. The reconstruction captures observed latitudinal gradients and coastal hot spots ofN2O flux and reveals a vigorous global seasonal cycle. We estimate an annual meanN2O flux of 4.2 ± 1.0 Tg N⋅y−1, 64% of which occurs in the tropics, and 20% in coastal upwelling systems that occupy less than 3% of the ocean area. ThisN2O flux ranges from a low of 3.3 ± 1.3 Tg N⋅y−1in the boreal spring to a high of 5.5 ± 2.0 Tg N⋅y−1in the boreal summer. Much of the seasonal variations in globalN2O emissions can be traced to seasonal upwelling in the tropical ocean and winter mixing in the Southern Ocean. The dominant contribution to seasonality by productive, low-oxygen tropical upwelling systems (>75%) suggests a sensitivity of the globalN2O flux to El Niño–Southern Oscillation and anthropogenic stratification of the low latitude ocean. This ocean flux estimate is consistent with the range adopted by the Intergovernmental Panel on Climate Change, but reduces its uncertainty by more than fivefold, enabling more precise determination of other terms in the atmosphericN2O budget.

Biological nitrogen fixation (BNF) was investigated above and within the oxygen-depleted waters of the oxygen-minimum zone of the Eastern Tropical North Pacific Ocean. BNF rates were estimated using an isotope tracer method that overcame the uncertainty of the conventional bubble method by directly measuring the tracer enrichment during the incubations. Highest rates of BNF (~4 nM day) occurred in coastal surface waters and lowest detectable rates (~0.2 nM day) were found in the anoxic region of offshore stations. BNF was not detectable in most samples from oxygen-depleted waters. The composition of the N-fixing assemblage was investigated by sequencing of nifH genes. The diazotrophic assemblage in surface waters contained mainly Proteobacterial sequences (Cluster I nifH), while both Proteobacterial sequences and sequences with high identities to those of anaerobic microbes characterized as Clusters III and IV type nifH sequences were found in the anoxic waters. Our results indicate modest input of N through BNF in oxygen-depleted zones mainly due to the activity of proteobacterial diazotrophs.

Dinitrogen (N 2 ) fixation is an important source of biologically reactive nitrogen (N) to the global ocean. The magnitude of this flux, however, remains uncertain, in part because N 2 fixation rates have been estimated following divergent protocols and because associated levels of uncertainty are seldom reported-confounding comparison and extrapolation of rate measurements. A growing number of reports of relatively low but potentially significant rates of N 2 fixation in regions such as oxygen minimum zones, the mesopelagic water column of the tropical and subtropical oceans, and polar waters further highlights the need for standardized methodological protocols for measurements of N 2 fixation rates and for calculations of detection limits and propagated error terms. To this end, we examine current protocols of the 15 N 2 tracer method used for estimating diazotrophic rates, present results of experiments testing the validity of specific practices, and describe established metrics for reporting detection limits. We put forth a set of recommendations for best practices to estimate N 2 fixation rates using 15 N 2 tracer, with the goal of fostering transparency in reporting sources of uncertainty in estimates, and to render N 2 fixation rate estimates intercomparable among studies.

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