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1. Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired

   LaSarre, B; Morlen, R; Neumann, GC; Harwood, CS; McKinlay, JB (September 2023, bioRxiv)

   Denitrification is a form of anaerobic respiration wherein nitrate (NO3-) is sequentially reduced via nitrite (NO2-), nitric oxide, and nitrous oxide (N2O) to dinitrogen gas (N2) by four reductase enzymes. Partial denitrifying bacteria possess only one, or some, of these four reductases and use them as independent respiratory modules. However, it is unclear if partial denitrifiers sense and respond to denitrification intermediates outside of their reductase repertoire. Here we tested the denitrifying capabilities of two purple nonsulfur bacteria, Rhodopseudomonas palustris CGA0092 and Rhodobacter capsulatus SB1003. Each had denitrifying capabilities that matched their genome annotation; CGA0092 reduced NO2- to N2 and SB1003 reduced N2O to N2. For each bacterium, N2O reduction could be used for both electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in the dark. However, N2O reduction required supplementation with a denitrification intermediate, including those for which there was no associated denitrification enzyme. For CGA0092, NO3- served as a stable, non-catalyzable molecule that was sufficient to activate N2O reduction. Using a β-galactosidase reporter we found that NO3- acted, at least in part, by stimulating N2O reductase gene expression. In SB1003, NO2-, but not NO3-, activated N2O reduction but NO2- was slowly removed, likely by a promiscuous enzyme activity. Our findings reveal that partial denitrifiers can still be subject to regulation by denitrification intermediates that they cannot use. 

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2. Nitrous oxide processing in carbonate karst aquifers

   https://doi.org/https://doi.org/10.1016/j.jhydrol.2020.125936  

   Flint, Madison K; Martin, Jonathan B.; Summerall, Tatiana I.; Barry-Sosa, Adrian; Christner, Brent C. (March 2021, Journal of hydrology)

   null (Ed.)

   The increased environmental abundance of anthropogenic reactive nitrogen species (Nr = ammonium [NH4+], nitrite [NO2−] and nitrate [NO3−]) may increase atmospheric nitrous oxide (N2O) concentrations, and thus global warming and stratospheric ozone depletion. Nitrogen cycling and N2O production, reduction, and emissions could be amplified in carbonate karst aquifers because of their extensive global range, susceptibility to nitrogen contamination, and groundwater-surface water mixing that varies redox conditions of the aquifer. The magnitude of N2O cycling in karst aquifers is poorly known, however, and thus we sampled thirteen springs discharging from the karstic Upper Floridan Aquifer (UFA) to evaluate N2O cycling. The springs can be separated into three groups based on variations in subsurface residence times, differences in surface–groundwater interactions, and variable dissolved organic carbon (DOC) and dissolved oxygen (DO) concentrations. These springs are oxic to sub-oxic and have NO3− concentrations that range from < 0.1 to 4.2 mg N-NO3−/L and DOC concentrations that range from < 0.1 to 50 mg C/L. Maximum spring water N2O concentrations are 3.85 μg N-N2O/L or ~ 12 times greater than water equilibrated with atmospheric N2O. The highest N2O concentrations correspond with the lowest NO3− concentrations. Where recharge water has residence times of a few days, partial denitrification to N2O occurs, while complete denitrification to N2 is more prominent in springs with longer subsurface residence times. Springs with short residence times have groundwater emission factors greater than the global average of 0.0060, reflecting N2O production, whereas springs with residence times of months to years have groundwater emission factors less than the global average. These findings imply that N2O cycling in karst aquifers depends on DOC and DO concentrations in recharged surface water and subsequent time available for N processing in the subsurface. 

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3. Nitrous oxide processing in carbonate karst aquifers

   https://doi.org/doi.org/10.1016/j.jhydrol.2020.125936  

   Flint, M.k. (January 2021, Journal of hydrology)

   null (Ed.)

   The increased environmental abundance of anthropogenic reactive nitrogen species (Nr = ammonium [NH4+], nitrite [NO2􀀀 ] and nitrate [NO3􀀀 ]) may increase atmospheric nitrous oxide (N2O) concentrations, and thus global warming and stratospheric ozone depletion. Nitrogen cycling and N2O production, reduction, and emissions could be amplified in carbonate karst aquifers because of their extensive global range, susceptibility to nitrogen contamination, and groundwater-surface water mixing that varies redox conditions of the aquifer. The magnitude of N2O cycling in karst aquifers is poorly known, however, and thus we sampled thirteen springs discharging from the karstic Upper Floridan Aquifer (UFA) to evaluate N2O cycling. The springs can be separated into three groups based on variations in subsurface residence times, differences in surface–groundwater interactions, and variable dissolved organic carbon (DOC) and dissolved oxygen (DO) concentrations. These springs are oxic to sub-oxic and have NO3􀀀 concentrations that range from < 0.1 to 4.2 mg N-NO3􀀀 /L and DOC concentrations that range from < 0.1 to 50 mg C/L. Maximum spring water N2O concentrations are 3.85 μg N-N2O/L or ~ 12 times greater than water equilibrated with atmospheric N2O. The highest N2O concentrations correspond with the lowest NO3􀀀 concentrations. Where recharge water has residence times of a few days, partial denitrification to N2O occurs, while complete denitrification to N2 is more prominent in springs with longer subsurface residence times. Springs with short residence times have groundwater emission factors greater than the global average of 0.0060, reflecting N2O production, whereas springs with residence times of months to years have groundwater emission factors less than the global average. These findings imply that N2O cycling in karst aquifers depends on DOC and DO concentrations in recharged surface water and subsequent time available for N processing in the subsurface. 

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4. Impacts of Climate Change and Agricultural Practices on Nitrogen Processes, Genes, and Soil Nitrous Oxide Emissions: A Quantitative Review of Meta-Analyses

   https://doi.org/10.3390/agriculture14020240  

   Hui, Dafeng; Ray, Avedananda; Kasrija, Lovish; Christian, Jaekedah (February 2024, Agriculture)

   Microbial-driven processes, including nitrification and denitrification closely related to soil nitrous oxide (N2O) production, are orchestrated by a network of enzymes and genes such as amoA genes from ammonia-oxidizing bacteria (AOB) and archaea (AOA), narG (nitrate reductase), nirS and nirK (nitrite reductase), and nosZ (N2O reductase). However, how climatic factors and agricultural practices could influence these genes and processes and, consequently, soil N2O emissions remain unclear. In this comprehensive review, we quantitatively assessed the effects of these factors on nitrogen processes and soil N2O emissions using mega-analysis (i.e., meta-meta-analysis). The results showed that global warming increased soil nitrification and denitrification rates, leading to an overall increase in soil N2O emissions by 159.7%. Elevated CO2 stimulated both nirK and nirS with a substantial increase in soil N2O emission by 40.6%. Nitrogen fertilization amplified NH4+-N and NO3−-N contents, promoting AOB, nirS, and nirK, and caused a 153.2% increase in soil N2O emission. The application of biochar enhanced AOA, nirS, and nosZ, ultimately reducing soil N2O emission by 15.8%. Exposure to microplastics mostly stimulated the denitrification process and increased soil N2O emissions by 140.4%. These findings provide valuable insights into the mechanistic underpinnings of nitrogen processes and the microbial regulation of soil N2O emissions. 

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5. Dissolved oxygen concentrations influence microbial community structure and key players in an oxygen minimum zone

   https://doi.org/10.1128/msphere.00751-25  

   Dombroski, Kaitlin R; Campbell, Lauren G; Morris, Robert M; Mason, Olivia U (August 2026, mSphere)

   Lahmers, Kevin K (Ed.)

   ABSTRACT Oxygen minimum zones (OMZs) are expanding in the global ocean. Declining oxygen can alter microbial processes that regulate carbon, nitrogen, and sulfur cycling, including pathways with the potential to produce nitrous oxide (N₂O), a potent greenhouse gas. Yet, we lack a full understanding of how microbial communities respond to declining oxygen in some globally important OMZs. This is particularly true for the understudied northern Benguela Upwelling System (nBUS), an important source of marine N₂O. Here, we analyzed the influence of oxygen concentrations on microbial communities in the nBUS OMZ using 16S rRNA gene sequence data. Microbial diversity did not decline linearly with oxygen and was highest under dysoxic (0.2–2.0 mL/L) conditions and lowest under suboxic (0.0–0.2 mL/L) conditions. This pattern was primarily due to changes in community evenness, which decreased in suboxic samples as the relative abundance ofThioglobaceae(SUP05) increased.Thioglobaceaerelative abundance was significantly inversely correlated with oxygen, andThioglobaceaewere abundant in the nBUS OMZ. Analysis of 216 publicly available medium- to high-qualityThioglobaceaegenomes from cultured and uncultured microbes sampled in the nBUS and other OMZs revealed the metabolic potential of this clade for carbon fixation and consumption, sulfur oxidation, and denitrification. Importantly, fewThioglobaceaepossess the genetic potential to carry out complete denitrification as most lack the gene that converts N₂O to dinitrogen gas. As OMZs expand in size and severity, decreasing microbial diversity and a concomitant increase in the relative abundance ofThioglobaceaecould contribute to enhanced N₂O production through incomplete denitrification.IMPORTANCEMarine microbes mediate biogeochemical cycles, which are influenced by oxygen concentrations, including microbial pathways that can lead to nitrous oxide (N₂O) production. The oxygen minimum zone (OMZ) in the northern Benguela Upwelling System (nBUS) is a biogeochemical hotspot and an important source of nitrous oxide. Yet, microbial community responses remain poorly characterized in this understudied OMZ. Analysis of microbial communities in this OMZ, combined with comparative genomic analysis ofThioglobaceaefrom the global ocean, revealed that members of this group have the capacity to fix carbon, potentially supporting growth through sulfur oxidation coupled to denitrification. However, fewThioglobaceaehave the genetic potential to carry out complete denitrification, with the final nitrous oxide reduction step often missing. Incomplete denitrification is an important source of N₂O in OMZs. Collectively, this study linked oxygen-associated community shifts in this OMZ to incomplete denitrification in a microbial group that increased in relative abundance as oxygen declined. 

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