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We quantified the removal of fixed nitrogen as N₂ production by anammox and N₂ and N₂O production by denitrification over a distance of 1900 km along the coasts of Chile and Peru, using short-term incubations with 15N-labeled substrates. The eastern South Pacific contains an oxygen minimum zone (OMZ) characterized by an anoxic, nitrate- and nitrite-rich layer of ∼ 200-m thickness below 30–90 m of oxic water. Anammox and denitrification were almost exclusively recorded when the in situ O₂ concentration was below detection, indicating that the induction of these processes is highly oxygen sensitive. Anammox was detected in 70% of the samples from anoxic depths. Denitrification was detected in fewer samples, but maximum rates were an order of magnitude higher than those of anammox. In our incubations denitrification was responsible for 72% of the total N₂ production and 77% of the total removal of fixed nitrogen including N₂O production. However, at the individual depths it could be one or the other process that was responsible for all of the nitrogen removal. Anammox activity was highest just below the oxic–anoxic interface and declined exponentially with depth, whereas no depth dependence was discerned for denitrification. Denitrification resulted in net production of N₂O in some of the samples and consumption of added 15N₂O in others. Together with the accumulation of NO 2 − this indicates that denitrification must be seen as a sequence of individually regulated reactions, each of which may start and stop depending on the electron donor input, while anammox is much less variable. The highly patchy distribution of denitrification contributes to explain the apparent imbalances between ammonium sources and sinks suggested by previous 15N-based studies in OMZs.

A major percentage of fixed nitrogen (N) loss in the oceans occurs within nitrite-rich oxygen minimum zones (OMZs) via denitrification and anammox. It remains unclear to what extent ammonium and nitrite oxidation co-occur, either supplying or competing for substrates involved in nitrogen loss in the OMZ core. Assessment of the oxygen (O₂) sensitivity of these processes down to the O₂ concentrations present in the OMZ core (<10 nmol·L−1) is therefore essential for understanding and modeling nitrogen loss in OMZs. We determined rates of ammonium and nitrite oxidation in the seasonal OMZ off Concepcion, Chile at manipulated O₂ levels between 5 nmol·L−1 and 20 μmol·L−1. Rates of both processes were detectable in the low nanomolar range (5–33 nmol·L−1 O₂), but demonstrated a strong dependence on O₂ concentrations with apparent half-saturation constants (Km s) of 333 ± 130 nmol·L−1 O₂ for ammonium oxidation and 778 ± 168 nmol·L−1 O₂ for nitrite oxidation assuming one-component Michaelis–Menten kinetics. Nitrite oxidation rates, however, were better described with a two-component Michaelis–Menten model, indicating a high-affinity component with a Km of just a few nanomolar. As the communities of ammonium and nitrite oxidizers were similar to other OMZs, these kinetics should apply across OMZ systems. The high O₂ affinities imply that ammonium and nitrite oxidation can occur within the OMZ core whenever O₂ is supplied, for example, by episodic intrusions. These processes therefore compete with anammox and denitrification for ammonium and nitrite, thereby exerting an important control over nitrogen loss.

Nitrogen cycling is normally thought to dominate the biogeochemistry and microbial ecology of oxygen-minimum zones in marine environments. Through a combination of molecular techniques and process rate measurements, we showed that both sulfate reduction and sulfide oxidation contribute to energy flux and elemental cycling in oxygen-free waters off the coast of northern Chile. These processes may have been overlooked because in nature, the sulfide produced by sulfate reduction immediately oxidizes back to sulfate. This cryptic sulfur cycle is linked to anammox and other nitrogen cycling processes, suggesting that it may influence biogeochemical cycling in the global ocean.

A major percentage (20 to 40%) of global marine fixed-nitrogen loss occurs in oxygen minimum zones (OMZs). Concentrations of O 2 and the sensitivity of the anaerobic N 2 -producing processes of anammox and denitrification determine where this loss occurs. We studied experimentally how O 2 at nanomolar levels affects anammox and denitrification rates and the transcription of nitrogen cycle genes in the anoxic OMZ off Chile. Rates of anammox and denitrification were reversibly suppressed, most likely at the enzyme level. Fifty percent inhibition of N 2 and N 2 O production by denitrification was achieved at 205 and 297 nM O 2 , respectively, whereas anammox was 50% inhibited at 886 nM O 2 . Coupled metatranscriptomic analysis revealed that transcripts encoding nitrous oxide reductase ( nosZ ), nitrite reductase ( nirS ), and nitric oxide reductase ( norB ) decreased in relative abundance above 200 nM O 2 . This O 2 concentration did not suppress the transcription of other dissimilatory nitrogen cycle genes, including nitrate reductase ( narG ), hydrazine oxidoreductase ( hzo ), and nitrite reductase ( nirK ). However, taxonomic characterization of transcripts suggested inhibition of narG transcription in gammaproteobacteria, whereas the transcription of anammox narG , whose gene product is likely used to oxidatively replenish electrons for carbon fixation, was not inhibited. The taxonomic composition of transcripts differed among denitrification enzymes, suggesting that distinct groups of microorganisms mediate different steps of denitrification. Sulfide addition (1 µM) did not affect anammox or O 2 inhibition kinetics but strongly stimulated N 2 O production by denitrification. These results identify new O 2 thresholds for delimiting marine nitrogen loss and highlight the utility of integrating biogeochemical and metatranscriptomic analyses. IMPORTANCE The removal of fixed nitrogen via anammox and denitrification associated with low O 2 concentrations in oceanic oxygen minimum zones (OMZ) is a major sink in oceanic N budgets, yet the sensitivity and dynamics of these processes with respect to O 2 are poorly known. The present study elucidated how nanomolar O 2 concentrations affected nitrogen removal rates and expression of key nitrogen cycle genes in water from the eastern South Pacific OMZ, applying state-of-the-art 15 N techniques and metatranscriptomics. Rates of both denitrification and anammox responded rapidly and reversibly to changes in O 2 , but denitrification was more O 2 sensitive than anammox. The transcription of key nitrogen cycle genes did not respond as clearly to O 2 , although expression of some of these genes decreased. Quantifying O 2 sensitivity of these processes is essential for predicting through which pathways and in which environments, from wastewater treatment to the open oceans, nitrogen removal may occur. The removal of fixed nitrogen via anammox and denitrification associated with low O 2 concentrations in oceanic oxygen minimum zones (OMZ) is a major sink in oceanic N budgets, yet the sensitivity and dynamics of these processes with respect to O 2 are poorly known. The present study elucidated how nanomolar O 2 concentrations affected nitrogen removal rates and expression of key nitrogen cycle genes in water from the eastern South Pacific OMZ, applying state-of-the-art 15 N techniques and metatranscriptomics. Rates of both denitrification and anammox responded rapidly and reversibly to changes in O 2 , but denitrification was more O 2 sensitive than anammox. The transcription of key nitrogen cycle genes did not respond as clearly to O 2 , although expression of some of these genes decreased. Quantifying O 2 sensitivity of these processes is essential for predicting through which pathways and in which environments, from wastewater treatment to the open oceans, nitrogen removal may occur.

A 38-year record of bottom-water dissolved oxygen concentrations in coastal marine ecosystems around Denmark (1965-2003) and a longer, partially reconstructed record of total nitrogen (TN) inputs (1900-2003) were assembled with the purpose of describing long-term patterns in hypoxia and anoxia. In addition, interannual variations in bottom-water oxygen concentrations were analyzed in relation to various explanatory variables (bottom temperature, wind speed, advective transport, TN loading). Reconstructed TN loads peaked in the 1980s, with a gradual decline to the present, commensurate with a legislated nutrient reduction strategy. Mean bottom-water oxygen concentrations during summer have significantly declined in coastal marine ecosystems, decreasing substantially during the 1980s and were extremely variable thereafter. Despite decreasing TN loads, the worst hypoxic event ever recorded in open waters occurred in 2002. For estuaries and coastal areas, bottom-water oxygen concentrations were best described by TN input from land and wind speed in July-September, explaining 52% of the interannual variation in concentrations. For open sea areas, bottom-water oxygen concentrations were also modulated by TN input from land; however, additional significant variables included advective transport of water and Skagerrak surface-water temperature and explained 49% of interannual variations in concentrations. Reductions in the number of benthic species and alpha diversity were significantly related to the duration of the 2002 hypoxic event. Gradual decreases in diversity measures (number of species and alpha diversity) over the first 2-4 weeks show that the benthic community undergoes significant changes before the duration of hypoxia is severe enough to cause the community to collapse. Enhanced sediment-water fluxes of NH4⁺₄ and PO₄3 occur with hypoxia, increasing nutrient concentrations in the water column and stimulating additional phytoplankton production. Repeated hypoxic events have changed the character of benthic communities and how organic matter is processed in sediments. Our data suggest that repeated hypoxic events lead to an increase in susceptibility of Danish waters to eutrophication and further hypoxia.

We investigated the pathways of N2production in the oxygen-deficient water column of the eastern tropical South Pacific off Iquique, Chile, at$20\\textdegree S$, through short anoxic incubations with$^{15}N-labelled$nitrogen compounds. The location was characterized by steep chemical gradients, with oxygen decreasing to below detection at ~50-m depth, while nitrite reached$6 \\mu mol L^{-1}$and ammonium was less than$50 nmol L^{-1}$Ammonium was oxidized to N2with no lag phase during the incubations, and when only NH4 +was$^{15}N-labeled$,15N appeared in the form of$^{14}N^{15}N$, whereas$^{15}N^{15}N$was not detected. Likewise, nitrite was reduced to N2at rates similar to the rates of ammonium oxidation, and when only NO2 -was$^{15}N-labeled$,15N appeared mainly as$^{14}N^{15}N$, whereas$^{15}N^{15}N$appeared in only one incubation. These observations indicate that ammonium was oxidized and nitrite was reduced through the anammox reaction, whereas denitriflcation was generally not detected and, therefore, was a minor sink for nitrite. Anammox rates were highest, up to$0.7 nmol N_2 L^{-1} h^{-1}$, just below the oxycline, whereas rates were undetectable,$<0.2 nmol N_2 L^{-1} h^{-1}$, deeper in the oxygen-deficient zone. Instead of complete denitriflcation to N2, oxidation of organic matter during the incubations may have been coupled to reduction of nitrate to nitrite. This process was evident from strong increases in nitrite concentrations toward the end of the incubations. The results point to anammox as an active process in the major open-ocean oxygen-deficient zones, which are generally recognized as important sites of denitrification. Still, denitrification remains the simplest explanation for most of the nitrogen deficiency in these zones.

In oxygen-depleted zones of the open ocean, and in anoxic basins and fjords, denitrification (the bacterial reduction of nitrate to give N 2 ) is recognized as the only significant process converting fixed nitrogen to gaseous N 2 . Primary production in the oceans is often limited by the availability of fixed nitrogen such as ammonium or nitrate 1 , and nitrogen-removal processes consequently affect both ecosystem function and global biogeochemical cycles. It was recently discovered that the anaerobic oxidation of ammonium with nitrite—the ‘anammox’ reaction, performed by bacteria—was responsible for a significant fraction of N 2 production in some marine sediments 2 . Here we show that this reaction is also important in the anoxic waters of Golfo Dulce, a 200-m-deep coastal bay in Costa Rica, where it accounts for 19–35% of the total N 2 formation in the water column. The water-column chemistry in Golfo Dulce is very similar to that in oxygen-depleted zones of the oceans—in which one-half to one-third of the global nitrogen removal is believed to occur 3 , 4 . We therefore expect the anammox reaction to be a globally significant sink for oceanic nitrogen.

Accurate quantification of pelagic primary production is essential for quantifying the marine carbon turnover and the energy supply to the food web. Knowing the electron requirement (Κ) for carbon (C) fixation (ΚC) and oxygen (O2) production (ΚO2), variable fluorescence has the potential to quantify primary production in microalgae, and hereby increasing spatial and temporal resolution of measurements compared to traditional methods. Here we quantify ΚC and ΚO2 through measures of Pulse Amplitude Modulated (PAM) fluorometry, C fixation and O2 production in an Arctic fjord (Godthåbsfjorden, W Greenland). Through short- (2h) and long-term (24h) experiments, rates of electron transfer (ETRPSII), C fixation and/or O2 production were quantified and compared. Absolute rates of ETR were derived by accounting for Photosystem II light absorption and spectral light composition. Two-hour incubations revealed a linear relationship between ETRPSII and gross 14C fixation (R2 = 0.81) during light-limited photosynthesis, giving a ΚC of 7.6 ± 0.6 (mean ± S.E.) mol é (mol C)-1. Diel net rates also demonstrated a linear relationship between ETRPSII and C fixation giving a ΚC of 11.2 ± 1.3 mol é (mol C)-1 (R2 = 0.86). For net O2 production the electron requirement was lower than for net C fixation giving 6.5 ± 0.9 mol é (mol O2)-1 (R2 = 0.94). This, however, still is an electron requirement 1.6 times higher than the theoretical minimum for O2 production [i.e. 4 mol é (mol O2)-1]. The discrepancy is explained by respiratory activity and non-photochemical electron requirements and the variability is discussed. In conclusion, the bio-optical method and derived electron requirement support conversion of ETR to units of C or O2, paving the road for improved spatial and temporal resolution of primary production estimates.

We measured rates of N2 production through anaerobic NH4+ oxidation with NO2- (anammox) and denitrification in permanently cold (from -1.7°C to 4°C) sediments off the east and west coasts of Greenland. The investigated sites (36- to 100-m water depth) covered sediments in which carbon contents ranged from 0.3 to 3.2 dry weight %, O2 uptake rates ranged from 3.4 to 8.3 mmol m-2 d-1, O2 penetration depths ranged from 0.25 to 1.70 cm, and bottom-water NO3- concentrations ranged from 0.3 to 15.3 μmol L-1 Total N2 production was 34-344 μmol $\\text{N}\\ \\text{m}^{-2}\\ \\text{d}^{-1}$, of which anammox accounted for 1-92 μmol $\\text{N}\\ \\text{m}^{-2}\\ \\text{d}^{-1}$ (1-35% of total) and denitrification for 33-265 μmol $\\text{N}\\ \\text{m}^{-2}\\ \\text{d}^{-1}$ At one of the high-Arctic sites, anammox activity had an optimum temperature $(T_{\\text{opt}})$ of 12°C, while that of bacterial denitrification was 24°C. According to the classical temperature scheme for metabolic growth, the anammox response was psychrophilic, while denitrification was psychrotrophic. Although $T_{\\text{opt}}$ was considerably higher than in situ temperatures, rates of denitrification and anammox were still high at -1.3°C, reaching 17% and 40%, respectively, of those found at $T_{\\text{opt}}$. The activation energies, Ea, of anammox and denitrification were 51.0 and 60.6 kJ mol-1, respectively, and the corresponding Q10 values were 2.2 and 2.4. Rates of anammox were linearly correlated with bottom-water NO3- concentrations $(r^{2}=0.96,\\ p<0.0001,\\ n=11)$ at the investigated sites. We suggest that the slow-growing anammox bacteria are favored in sediments with high and stable NO3- conditions. This may be a general pattern in deeper waters at other latitudes as well.

Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following experimental perturbation. Unambiguously identifying differential transcription between control and experimental treatments requires constraining effects that are simply due to sampling and bottle enclosure. These effects remain largely uncharacterized for \"challenging\" microbial samples, such as those from anoxic regions that require special handling to maintain in situ conditions. Here, we demonstrate substantial changes in microbial transcription induced by sample collection and incubation in experimental bioreactors. Microbial communities were sampled from the water column of a marine oxygen minimum zone by a pump system that introduced minimal oxygen contamination and subsequently incubated in bioreactors under near in situ oxygen and temperature conditions. Relative to the source water, experimental samples became dominated by transcripts suggestive of cell stress, including chaperone, protease, and RNA degradation genes from diverse taxa, with strong representation from SAR11-like alphaproteobacteria. In tandem, transcripts matching facultative anaerobic gammaproteobacteria of the Alteromonadales (e.g., Colwellia) increased 4-13 fold up to 43% of coding transcripts, and encoded a diverse gene set suggestive of protein synthesis and cell growth. We interpret these patterns as taxon-specific responses to combined environmental changes in the bioreactors, including shifts in substrate or oxygen availability, and minor temperature and pressure changes during sampling with the pump system. Whether such changes confound analysis of transcriptional patterns may vary based on the design of the experiment, the taxonomic composition of the source community, and on the metabolic linkages between community members. These data highlight the impressive capacity for transcriptional changes within complex microbial communities, underscoring the need for caution when inferring in situ metabolism based on transcript abundances in experimental incubations.