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Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3− to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment.

 

Abstract Nitrous oxide (N 2 O) is important to the global radiative budget of the atmosphere and contributes to the depletion of stratospheric ozone. Globally the ocean represents a large net flux of N 2 O to the atmosphere but the direction of this flux varies regionally. Our understanding of N 2 O production and consumption processes in the ocean remains incomplete. Traditional understanding tells us that anaerobic denitrification, the reduction of NO 3 − to N 2 with N 2 O as an intermediate step, is the sole biological means of reducing N 2 O, a process known to occur in anoxic environments only. Here we present experimental evidence of N 2 O removal under fully oxygenated conditions, coupled with observations of bacterial communities with novel, atypical gene sequences for N 2 O reduction. The focus of this work was on the high latitude Atlantic Ocean where we show bacterial consumption sufficient to account for oceanic N 2 O depletion and the occurrence of regional sinks for atmospheric N 2 O. 

Abstract The ocean is a net source of N 2 O, a potent greenhouse gas and ozone-depleting agent. However, the removal of N 2 O via microbial N 2 O consumption is poorly constrained and rate measurements have been restricted to anoxic waters. Here we expand N 2 O consumption measurements from anoxic zones to the sharp oxygen gradient above them, and experimentally determine kinetic parameters in both oxic and anoxic seawater for the first time. We find that the substrate affinity, O 2 tolerance, and community composition of N 2 O-consuming microbes in oxic waters differ from those in the underlying anoxic layers. Kinetic parameters determined here are used to model in situ N 2 O production and consumption rates. Estimated in situ rates differ from measured rates, confirming the necessity to consider kinetics when predicting N 2 O cycling. Microbes from the oxic layer consume N 2 O under anoxic conditions at a much faster rate than microbes from anoxic zones. These experimental results are in keeping with model results which indicate that N 2 O consumption likely takes place above the oxygen deficient zone (ODZ). Thus, the dynamic layer with steep O 2 and N 2 O gradients right above the ODZ is a previously ignored potential gatekeeper of N 2 O and should be accounted for in the marine N 2 O budget. 

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.

 

Estuaries emit a large but highly uncertain amount of Nitrous oxide (N₂O) into the atmosphere. To better understand N₂O cycling processes in estuaries, we provide the first direct observations of N₂O consumption in the seasonally anoxic Chesapeake Bay, the largest estuary in the United States. N₂O consumption rates in anoxic waters reached up to 3.3 nmol L⁻¹ d⁻¹but were generally undetectable in oxygenated waters. However, N₂O consumption rates were substantially enhanced when the oxygen concentration was experimentally decreased in initially oxygenated samples, indicating the potential of N₂O consumption in oxygenated environments, for example, surface waters. These potential N₂O consumption rates followed Michaelis‐Menten kinetics as a function of increasing N₂O substrate concentration. N₂O‐consuming microbes that predominantly contained the clade II nitrous oxide reductase gene were detected throughout the water column. These new observations of environmental controls on N₂O consumption will benefit the modeling of N₂O cycling and help to constrain the estuarine N₂O flux.

 

Examination of dinitrogen (N₂) fixation in the Eastern Tropical South Pacific oxygen deficient zone has raised questions about the range of diazotrophs in the deep sea and their quantitative importance as a source of new nitrogen globally. However, technical considerations in the deployment of stable isotopes in quantifying N₂fixation rates have complicated interpretation of this research. Here, we report the findings of a comprehensive survey of N₂fixation within, above and below the Eastern Tropical South Pacific oxygen deficient zone. N₂fixation rates were measured using a robust¹⁵N tracer method (bubble removal) that accounts for the slow dissolution of N₂gas and calculated using a conservative approach. N₂fixation was only detected in a subset of samples (8 of 125 replicated measurements) collected within suboxic waters (< 20 μmol O₂kg⁻¹) or at the oxycline. Most of these detectable rates were measured at nearshore stations, or where surface productivity was high. These findings support the hypothesis that low oxygen/high organic carbon conditions favor non‐cyanobacterial diazotrophs. Nevertheless, this study indicates that N₂fixation is neither widespread nor quantitatively important throughout this region.

 

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. 

Oxygen minimum zones (OMZs) are marine regions where O2 is undetectable at intermediate depths. Within OMZs, the oxygen-depleted zone (ODZ) induces anaerobic microbial processes that lead to fixed nitrogen loss via denitrification and anammox. Surprisingly, nitrite oxidation is also detected in ODZs, although all known marine nitrite oxidizers (mainly Nitrospina) are aerobes. We used metagenomic binning to construct metagenome-assembled genomes (MAGs) of nitrite oxidizers from OMZs. These MAGs represent two novel Nitrospina-like species, both of which differed from all known Nitrospina species, including cultured species and published MAGs. Relative abundances of different Nitrospina genotypes in OMZ and non-OMZ seawaters were estimated by mapping metagenomic reads to newly constructed MAGs and published high-quality genomes of members from the Nitrospinae phylum. The two novel species were present in all major OMZs and were more abundant inside ODZs, which is consistent with the detection of higher nitrite oxidation rates in ODZs than in oxic seawaters and suggests novel adaptations to anoxic environments. The detection of a large number of unclassified nitrite oxidoreductase genes in the dataset implies that the phylogenetic diversity of nitrite oxidizers is greater than previously thought.