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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.

 

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.

 

The ocean is estimated to contribute up to ~20% of global fluxes of atmospheric nitrous oxide (N₂O), an important greenhouse gas and ozone depletion agent. Marine oxygen minimum zones contribute disproportionately to this flux. To further understand the partition of nitrification and denitrification and their environmental controls on marine N₂O fluxes, we report new relationships between oxygen concentration and rates of N₂O production from nitrification and denitrification directly measured with¹⁵N tracers in the Eastern Tropical Pacific. Highest N₂O production rates occurred near the oxic‐anoxic interface, where there is strong potential for N₂O efflux to the atmosphere. The dominant N₂O source in oxygen minimum zones was nitrate reduction, the rates of which were 1 to 2 orders of magnitude higher than those of ammonium oxidation. The presence of oxygen significantly inhibited the production of N₂O from both nitrification and denitrification. These experimental data provide new constraints to a multicomponent global ocean biogeochemical model, which yielded annual oceanic N₂O efflux of 1.7–4.4 Tg‐N (median 2.8 Tg‐N, 1 Tg = 10¹² g), with denitrification contributing 20% to the oceanic flux. Thus, denitrification should be viewed as a net N₂O production pathway in the marine environment.

 

Abstract Oxygen minimum zones (OMZs) are unique marine regions where broad redox gradients stimulate biogeochemical cycles. Despite the important and unique role of OMZ microbes in these cycles, they are less characterized than microbes from the oxic ocean. Here we recovered 39 high- and medium-quality metagenome-assembled genomes (MAGs) from the Eastern Tropical South Pacific OMZ. More than half of these MAGs were not represented at the species level among 2631 MAGs from global marine datasets. OMZ MAGs were dominated by denitrifiers catalyzing nitrogen loss and especially MAGs with partial denitrification metabolism. A novel bacterial genome with nitrate-reducing potential could only be assigned to the phylum level. A Marine-Group II archaeon was found to be a versatile denitrifier, with the potential capability to respire multiple nitrogen compounds including N 2 O. The newly discovered denitrifying MAGs will improve our understanding of microbial adaptation strategies and the evolution of denitrification in the tree of life. 

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.