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Nitrite reduction is an essential step in the oceanic Nitrogen cycle. Nitrite reductase genes, mainlynirSandnirK, are found in dozens of phyla, are often associated with denitrifiers, ammonia- and nitrite-oxidizing bacteria (AOB and NOB) as well as ammonia-oxidizing archaea (AOA).nirKis found throughout the ocean, including in oxygenated surface water as well as in oxygen minimum zones (OMZs). The diverse and complex evolutionary history of thenirKgenes makes it challenging to study the population structure and distribution ofnirKcontaining organisms in the environment. The organisms containingnirKplay key roles in the global nitrogen cycle, including the loss of fixed N, and have the potential to influence nitrous oxide (N₂O) emissions via multiple pathways. This study surveyed the phylogeny and environmental distribution of over 12,000nirKgenes, focusing on those originating from marine and aquatic sources. Sequences were clustered into OTUs based on DNA sequence identity and their phylogeny and environmental sources were examined. The distribution of the sequences showed habitat separation within taxonomic groups, i.e., the majority of the OTUs were associated with only one environmental source. BacterialnirKis more diverse phylogenetically and has a wider distribution across environmental sources than archaealnirK. Most of the bacterial sequences were obtained from marine sediments, but there was variation in the dominant environmental source across phyla and classes. Archaeal sequences demonstrated niche separation between phyla as sequences from the more phylogenetically diverse phylum, Euryarchaeota, were all isolated from hypersaline environments while Nitrososphaerota sequences came from a wider range of environmental sources. This study expands the known diversity ofnirKgenes and provides a clearer picture of hownirKorganisms are distributed across diverse environments. 

Many estuaries experience eutrophication, deoxygenation and warming, with potential impacts on greenhouse gas emissions. However, the response of N₂O production to these changes is poorly constrained. Here we applied nitrogen isotope tracer incubations to measure N₂O production under experimentally manipulated changes in oxygen and temperature in the Chesapeake Bay—the largest estuary in the United States. N₂O production more than doubled from nitrification and increased exponentially from denitrification when O₂was decreased from >20 to <5 micromolar. Raising temperature from 15° to 35°C increased N₂O production 2- to 10-fold. Developing a biogeochemical model by incorporating these responses, N₂O emissions from the Chesapeake Bay were estimated to decrease from 157 to 140 Mg N year⁻¹from 1986 to 2016 and further to 124 Mg N year⁻¹in 2050. Although deoxygenation and warming stimulate N₂O production, the modeled decrease in N₂O emissions, attributed to decreased nutrient inputs, indicates the importance of nutrient management in curbing greenhouse gas emissions, potentially mitigating climate change. 

Nitrous oxide (N₂O) is a potent greenhouse gas and a major cause of ozone depletion. One-third of atmospheric N₂O originates in aquatic environments. Reduction of N₂O to dinitrogen gas (N₂) requires the nitrous oxide reductase enzyme, which is encoded by the genenosZ. Organisms that containnosZare the only known biological sinks of N₂O and are found in diverse genera and a wide range of environments. The two clades ofnosZ(Clade I and II) contain great diversity, making it challenging to study the population structure and distribution ofnosZcontaining organisms in the environment. A database of over 11,000nosZsequences was compiled from NCBI (representing diverse aquatic environments) and unpublished sequences and metagenomes (primarily from oxygen minimum zones, OMZs, where N₂O levels are often elevated). Sequences were clustered into archetypes based on DNA and amino acid sequence identity and their clade, phylogeny, and environmental source were determined. Further analysis of the source and environmental distribution of the sequences showed strong habitat separation between clades and phylogeny. Although there are more Clade InosZgenes in the compilation, Clade II is more diverse phylogenetically and has a wider distribution across environmental sources. On the other hand, Clade InosZgenes are predominately found within marine sediment and are primarily from the phylum Pseudonomonadota. The majority of the sequences analyzed from marine OMZs represented distinct phylotypes between different OMZs showing that thenosZgene displays regional and environmental separation. This study expands the known diversity ofnosZgenes and provides a clearer picture of how the clades and phylogeny ofnosZorganisms are distributed across diverse environments. 

Abstract. Nitrous oxide (N2O), a potent greenhouse gas and ozone-destroying agent, is produced during nitrogen transformations in both natural and human-constructed environments. Wastewater treatment plants (WWTPs) produce and emit N2O into the atmosphere during the nitrogen removal process. However, the impact of WWTPs on N2O emissions in downstream aquatic systems remains poorly constrained. By measuring N2O concentrations at a monthly resolution over a year in the Potomac River Estuary, a tributary of Chesapeake Bay in the eastern United States, we found a strong seasonal variation in N2O concentrations and fluxes: N2O concentrations were larger in fall and winter but the flux was larger in summer and fall. Observations at multiple stations across the Potomac River Estuary revealed hotspots of N2O emissions downstream of WWTPs. N2O concentrations were higher at stations downstream of WWTPs compared to other stations (median: 21.2 nM vs 16.2 nM) despite the similar concentration of dissolved inorganic nitrogen, suggesting the direct discharge of N2O from WWTPs into the aquatic system or a higher N2O production yield in waters influenced by WWTPs. Since wastewater production has increased substantially with the growing population and is projected to continue to rise, accurately accounting for N2O emissions downstream of the WWTPs would better constrain the global N2O emissions. Efficient N2O removal, in addition to dissolved nitrogen removal, should be an essential part of water quality control in WWTPs. 

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 Standard methods for calculating microbial growth rates (μ) through the use of proxies, such as in situ fluorescence, cell cycle, or cell counts, are critical for determining the magnitude of the role bacteria play in marine carbon (C) and nitrogen (N) cycles. Taxon-specific growth rates in mixed assemblages would be useful for attributing biogeochemical processes to individual species and understanding niche differentiation among related clades, such as found in Synechococcus and Prochlorococcus . We tested three novel DNA sequencing-based methods (iRep, bPTR, and GRiD) for evaluating the growth of light-synchronized Synechococcus cultures under different light intensities and temperatures. In vivo fluorescence and cell cycle analysis were used to obtain standard estimates of growth rate for comparison with those of the sequence-based methods (SBM). None of the SBM values were correlated with growth rates calculated by standard techniques despite the fact that all three SBM were correlated with the percentage of cells in S phase (DNA replication) over the diel cycle. Inaccuracy in determining the time of maximum DNA replication is unlikely to account entirely for the absence of a relationship between SBM and growth rate, but the fact that most microbes in the surface ocean exhibit some degree of diel cyclicity is a caution for application of these methods. SBM correlate with DNA replication but cannot be interpreted quantitatively in terms of growth rate. IMPORTANCE Small but abundant, cyanobacterial strains such as the photosynthetic Synechococcus spp. are important because they contribute significantly to primary productivity in the ocean. These bacteria generate oxygen and provide biologically available carbon, which is essential for organisms at higher trophic levels. The small size and diversity of natural microbial assemblages mean that taxon-specific activities (e.g., growth rate) are difficult to obtain in the field. It has been suggested that sequence-based methods (SBM) may be able to solve this problem. We find, however, that SBM can detect DNA replication and are correlated with phases of the cell cycle but cannot be interpreted in terms of absolute growth rate for Synechococcus cultures growing under a day-night cycle, like that experienced in the ocean. 

Abstract. Oxygen minimum zones (OMZs), due to their large volumes of perennially deoxygenated waters, are critical regions for understanding how the interplay between anaerobic and aerobic nitrogen (N) cycling microbial pathways affects the marine N budget. Here, we present a suite of measurements of the most significant OMZ N cycling rates, which all involve nitrite (NO2-) as a product, reactant, or intermediate, in the eastern tropical North Pacific (ETNP) OMZ. These measurements and comparisons to data from previously published OMZ cruisespresent additional evidence that NO3- reduction is the predominant OMZ N flux, followed by NO2- oxidation back to NO3-. The combined rates of both of these N recycling processes were observed to be much greater (up to nearly 200 times) thanthe combined rates of the N loss processes of anammox and denitrification, especially in waters near the anoxic–oxic interface. We also showthat NO2- oxidation can occur when O2 is maintained near 1 nM by a continuous-purge system, NO2-oxidation and O2 measurements that further strengthen the case for truly anaerobic NO2- oxidation. We also evaluate thepossibility that NO2- dismutation provides the oxidative power for anaerobic NO2- oxidation. The partitioning ofN loss between anammox and denitrification differed widely from stoichiometric predictions of at most 29 % anammox; in fact,N loss rates at many depths were entirely due to anammox. Our new NO3- reduction, NO2- oxidation, dismutation, andN loss data shed light on many open questions in OMZ N cycling research, especially the possibility of truly anaerobicNO2- oxidation. 

Abstract The removal of carbon dioxide from the atmosphere by the marine biological pump is a key regulator of Earth’s climate; however, the ocean also serves as a large source of nitrous oxide, a potent greenhouse gas and ozone-depleting substance. Although biological carbon sequestration and nitrous oxide production have been individually studied in the ocean, their combined impacts on net greenhouse forcing remain uncertain. Here we show that the magnitude of nitrous oxide production in the epipelagic zone of the subtropical ocean covaries with remineralization processes and thus acts antagonistically to weaken the radiative benefit of carbon removal by the marine biological pump. Carbon and nitrogen isotope tracer incubation experiments and nitrogen isotope natural abundance data indicate enhanced biological activity promotes nitrogen recycling, leading to substantial nitrous oxide production via both oxidative and reductive pathways. These shallow-water nitrous oxide sources account for nearly half of the air–sea flux and counteract 6–27% (median 9%) of the greenhouse warming mitigation achieved by carbon export via the biological pump. 

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.