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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 Nitrogen (N) bioavailability affects phytoplankton growth and primary production in the aquatic environment. N bioavailability is partly determined by biological N cycling processes that either transform N species or remove fixed N. Reliable estimates of their kinetic parameters can help understand the distribution of N cycling processes. However, available estimates of kinetic parameters are often derived from microbial isolates and may not be representative of the natural environment. Observations are particularly lacking in estuarine and coastal waters. We conducted isotope tracer addition incubations to evaluate substrate affinities of nitrification, denitrification and anammox in the Chesapeake Bay water column. The half‐saturation constant for ammonia oxidation ranged from 0.38 to 0.75 μM ammonium, substantially higher than observed in the open oceans. Half‐saturation constants for denitrification—0.92–1.86 μM nitrite or 1.15 μM nitrate—were within the lower end or less than those reported for other aquatic environments and for denitrifier isolates. Interestingly, water column denitrification potential was comparable to that of sedimentary denitrification, highlighting the contribution of the water column to N removal during anoxia. Mostly undetectable anammox rates prevented us from deriving the half‐saturation constants, suggesting a low affinity of anammox. Using these substrate kinetics, we were able to predict in situ N cycling rates and explain the vertical distribution of N nutrient concentrations. Our newly derived substrate kinetics parameters can be useful for improving model representation of N nutrient dynamics in estuarine and coastal waters, which is critical for assessing the ecosystem productivity and function.