Hydroxylamine released by nitrifying microorganisms is a precursor for HONO emission from drying soils

Emission fluxes of nitrous acid (HONO) from livestock and poultry wastes

Gaseous nitrous acid (HONO) is a critical contributor to daytime hydroxyl radical in the troposphere. Livestock farming has been recognized as an overlooked HONO source, but the lack of detailed flux measurements from livestock and poultry wastes would cause uncertainties in modeling its environmental impacts. Here, based on field flux measurements and laboratory experiments, we observed substantial HONO emissions from the composting of swine feces and chicken manure in the warm season, which might be mainly attributed to nitrification process in livestock and poultry wastes. The HONO emission from chicken manure was found to be much higher than that from swine feces, and the higher NH3 emission but lower N2O and NO emissions from chicken manure were also observed. Considering that the interaction among these nitrogen species during nitrification process, the obviously lower HONO emission from swine feces was likely to be explained by the lack of the total ammonia nitrogen and H+ donors in swine feces. Temperature is also a key factor that influences the HONO emission from livestock wastes. In addition, the total HONO emission from swine feces in China was estimated to be approximately 107.7 Gg-N/yr according to the national swine amounts, which is comparable to the national soil HONO emissions, underscoring its non-negligible contribution to regional air quality. Therefore, effective emission control of HONO from livestock and poultry wastes should be carried out to further improve air quality in China.

Nitrogen Availability and Changes in Precipitation Alter Microbially Mediated NO and N2O Emissions From a Pinyon-Juniper Dryland

Climate change is altering precipitation regimes that control nitrogen (N) cycling in terrestrial ecosystems. In ecosystems exposed to frequent drought, N can accumulate in soils as they dry, stimulating the emission of both nitric oxide (NO; an air pollutant at high concentrations) and nitrous oxide (N2O; a powerful greenhouse gas) when the dry soils wet up. Because changes in both N availability and soil moisture can alter the capacity of nitrifying organisms such as ammonia-oxidizing bacteria (AOB) and archaea (AOA) to process N and emit N gases, predicting whether shifts in precipitation may alter NO and N2O emissions requires understanding how both AOA and AOB may respond. Thus, we ask: How does altering summer and winter precipitation affect nitrifier-derived N trace gas emissions in a dryland ecosystem? To answer this question, we manipulated summer and winter precipitation and measured AOA- and AOB-derived N trace gas emissions, AOA and AOB abundance, and soil N concentrations. We found that excluding summer precipitation increased AOB-derived NO emissions, consistent with the increase in soil N availability, and that increasing summer precipitation amount promoted AOB activity. Excluding precipitation in the winter (the most extreme water limitation we imposed) did not alter nitrifier-derived NO emissions despite N accumulating in soils. Instead, nitrate that accumulated under drought correlated with high N2O emission via denitrification upon wetting dry soils. Increases in the timing and intensity of precipitation that are forecasted under climate change may, therefore, influence the emission of N gases according to the magnitude and season during which the changes occur.

A Novel Approach for Real-Time Determination of 15N-Enriched Hydroxylamine

Hydroxylamine (NH2OH) is a critical precursor of nitrous oxide (N2O) and key intermediate in the nitrogen cycle. However, the conversion of NH2OH is very fast, and the lack of real-time 15N analytical methods for NH2OH hinders the on-time capture of its biochemical signals in the N cycle. To bridge this gap, we developed a novel approach for real-time determination of 15N-enriched NH2OH. In this approach, an automated sample inlet unit was coupled to a membrane-inlet mass spectrometer, and NH2OH was converted to N2O by sodium hypochlorite for analysis. The interference of carbon dioxide was successfully removed by an ascarite trap, and the N2O signal showed good linearity over the targeted NH2OH concentrations. The limit of detection and limit of quantification of this approach were 0.38 and 1.28 μM, respectively, and 15N enrichment can be accurately detected when the 15N enrichment is higher than 5 atom %. This approach provides a first online analytical tool to capture real-time NH2OH transforming signals using the 15N tracing technique, which will advance mechanism studies of the N cycle.

Discovery of Candidatus Nitrosomaritimum as a New Genus of Ammonia-Oxidizing Archaea Widespread in Anoxic Saltmarsh Intertidal Aquifers

Ammonia-oxidizing archaea (AOA) are widely distributed in marine and terrestrial habitats, contributing significantly to global nitrogen and carbon cycles. However, their genomic diversity, ecological niches, and metabolic potentials in the anoxic intertidal aquifers remain poorly understood. Here, we discovered and named a novel AOA genus, Candidatus Nitrosomaritimum, from the intertidal aquifers of Yancheng Wetland, showing close metagenomic abundance to the previously acknowledged dominant Nitrosopumilus AOA. Further construction of ammonia monooxygenase-based phylogeny demonstrated the widespread distribution of Nitrosomaritimum AOA in global estuarine-coastal niches and marine sediment. Niche differentiation among sublineages of this new genus in anoxic intertidal aquifers is driven by salinity and dissolved oxygen gradients. Comparative genomics revealed that Candidatus Nitrosomaritimum has the genetic capacity to utilize urea and possesses high-affinity phosphate transporter systems (phnCDE) for surviving phosphorus-limited conditions. Additionally, it contains putative nosZ genes encoding nitrous-oxide (N2O) reductase for reducing N2O to nitrogen gas. Furthermore, we gained first genomic insights into the archaeal phylum Hydrothermarchaeota populations residing in intertidal aquifers and revealed their potential hydroxylamine-detoxification mutualism with AOA through utilizing the AOA-released extracellular hydroxylamine using hydroxylamine oxidoreductase. Together, this study unravels the overlooked role of priorly unknown but abundant AOA lineages of the newly discovered genus Candidatus Nitrosomaritimum in biological nitrogen transformation and their potential for nitrogen pollution mitigation in coastal environments.

Atmospheric HONO emissions in China: Unraveling the spatiotemporal patterns and their key influencing factors

Nitrous acid (HONO) can be photolyzed to produce hydroxyl radicals (OH) in the atmosphere. OH plays a critical role in the formation of secondary pollutants like ozone (O3) and secondary organic aerosols (SOA) via various oxidation reactions. Despite the abundance of recent HONO studies, research on national HONO emissions in China remains relatively limited. Therefore, this study employed a "wetting-drying" model and bottom-up approach to develop a high-resolution gridded inventory of HONO emissions for mainland China using multiple data. We used the Monte Carlo method to estimate the uncertainty in HONO emissions. In addition, the primary sources of HONO emissions were identified and their spatiotemporal distribution and main influencing factors were studied. The results indicated that the total HONO emissions in mainland China in 2016 were 0.77 Tg N (R50: 0.28-1.42 Tg N), with soil (0.42 Tg N) and fertilization (0.26 Tg N) as the primary sources, jointly contributing to over 87% of the total. Notably, the North China Plain (NCP) had the highest HONO emission density (3.51 kg N/ha/yr). Seasonal HONO emissions followed the order: summer (0.38 kg N/ha) > spring (0.19 kg N/ha) > autumn (0.17 kg N/ha) > winter (0.06 kg N/ha). Moreover, HONO emissions were strongly correlated with fertilization, cropland, temperature, and precipitation. This study provides vital scientific groundwork for the atmospheric nitrogen cycle and the formation of secondary pollutants.

Bacterial denitrification drives elevated N2O emissions in arid southern California drylands

Soils are the largest source of atmospheric nitrous oxide (N2O), a powerful greenhouse gas. Dry soils rarely harbor anoxic conditions to favor denitrification, the predominant N2O-producing process, yet, among the largest N2O emissions have been measured after wetting summer-dry desert soils, raising the question: Can denitrifiers endure extreme drought and produce N2O immediately after rainfall? Using isotopic and molecular approaches in a California desert, we found that denitrifiers produced N2O within 15 minutes of wetting dry soils (site preference = 12.8 ± 3.92 per mil, δ15Nbulk = 18.6 ± 11.1 per mil). Consistent with this finding, we detected nitrate-reducing transcripts in dry soils and found that inhibiting microbial activity decreased N2O emissions by 59%. Our results suggest that despite extreme environmental conditions-months without precipitation, soil temperatures of ≥40°C, and gravimetric soil water content of <1%-bacterial denitrifiers can account for most of the N2O emitted when dry soils are wetted.

Nitrite stimulates HONO and NOx but not N2O emissions in Chinese agricultural soils during nitrification

The long-lived greenhouse gas nitrous oxide (N2O) and short-lived reactive nitrogen (Nr) gases such as ammonia (NH3), nitrous acid (HONO), and nitrogen oxides (NOx) are produced and emitted from fertilized soils and play a critical role for climate warming and air quality. However, only few studies have quantified the production and emission potentials for long- and short-lived gaseous nitrogen (N) species simultaneously in agricultural soils. To link the gaseous N species to intermediate N compounds [ammonium (NH4+), hydroxylamine (NH2OH), and nitrite (NO2-)] and estimate their temperature change potential, ex-situ dry-out experiments were conducted with three Chinese agricultural soils. We found that HONO and NOx (NO + NO2) emissions mainly depend on NO2-, while NH3 and N2O emissions are stimulated by NH4+ and NH2OH, respectively. Addition of 3,4-dimethylpyrazole phosphate (DMPP) and acetylene significantly reduced HONO and NOx emissions, while NH3 emissions were significantly enhanced in an alkaline Fluvo-aquic soil. These results suggested that ammonia-oxidizing bacteria (AOB) and complete ammonia-oxidizing bacteria (comammox Nitrospira) dominate HONO and NOx emissions in the alkaline Fluvo-aquic soil, while ammonia-oxidizing archaea (AOA) are dominant in the acidic Mollisol. DMPP effectively mitigated the warming effect in the Fluvo-aquic soil and the Ultisol. In conclusion, our findings highlight NO2- significantly stimulates HONO and NOx emissions from dryland agricultural soils, dominated by nitrification. In addition, subtle differences of soil NH3, N2O, HONO, and NOx emissions indicated different N turnover processes, and should be considered in biogeochemical and atmospheric chemistry models.

Unveiling the underestimated direct emissions of nitrous acid (HONO)

Gaseous nitrous acid (HONO) is a critical source of hydroxyl radicals (OH) in the troposphere. While both direct and secondary sources contribute to atmospheric HONO, direct emissions have traditionally been considered minor contributors. In this study, we developed δ15N and δ18O isotopic fingerprints to identify six direct HONO emission sources and conducted a 1-y case study on the isotopic composition of atmospheric HONO at rural and urban sites. Interestingly, we identified that livestock farming is a previously overlooked direct source of HONO and determined its HONO to ammonia (NH3) emission ratio. Additionally, our results revealed that spatial and temporal variations in atmospheric HONO isotopic composition can be partially attributed to direct emissions. Through a detailed HONO budget analysis incorporating agricultural sources, we found that direct HONO emissions accounted for 39~45% of HONO production in rural areas across different seasons. The findings were further confirmed by chemistry transport model simulations, highlighting the significance of direct HONO emissions and their impact on air quality in the North China Plain. These findings provide compelling evidence that direct HONO emissions play a more substantial role in contributing to atmospheric HONO than previously believed. Moreover, the δ15N and δ18O isotopic fingerprints developed in this study may serve as a valuable tool for further research on the atmospheric chemistry of reactive nitrogen gases.

Effects of drought and recovery on soil volatile organic compound fluxes in an experimental rainforest

Drought can affect the capacity of soils to emit and consume biogenic volatile organic compounds (VOCs). Here we show the impact of prolonged drought followed by rewetting and recovery on soil VOC fluxes in an experimental rainforest. Under wet conditions the rainforest soil acts as a net VOC sink, in particular for isoprenoids, carbonyls and alcohols. The sink capacity progressively decreases during drought, and at soil moistures below ~19%, the soil becomes a source of several VOCs. Position specific 13C-pyruvate labeling experiments reveal that soil microbes are responsible for the emissions and that the VOC production is higher during drought. Soil rewetting induces a rapid and short abiotic emission peak of carbonyl compounds, and a slow and long biotic emission peak of sulfur-containing compounds. Results show that, the extended drought periods predicted for tropical rainforest regions will strongly affect soil VOC fluxes thereby impacting atmospheric chemistry and climate.

Large Contribution of Nitrous Acid to Soil-Emitted Reactive Oxidized Nitrogen and Its Effect on Air Quality

Soil emissions have long been recognized as an important source of nitric oxide (NO), which regulates atmospheric oxidative capacity and the production of air pollutants. Recent research has also indicated that nitrous acid (HONO) can be emitted in significant quantities from soil microbial activities. However, only a few studies have quantified emissions of HONO along with NO from a wide range of soil types. In this study, we measured emissions of HONO and NO from soil samples collected from 48 sites across China and found much higher emissions of HONO than of NO, especially for samples from northern China. We performed a meta-analysis of 52 field studies in China, which revealed that long-term fertilization increased the abundance of nitrite-producing genes much more than the abundance of NO-producing genes. This promotion effect was greater in northern China than in southern China. In simulations using a chemistry transport model with laboratory-derived parametrization, we found that HONO emissions had a greater effect than NO emissions on air quality. Moreover, we determined that with projected continuous reductions in anthropogenic emissions, the contribution from soils to maximum 1 h concentrations of hydroxyl radicals and ozone and daily average concentrations of particulate nitrate in the Northeast Plain will increase to 17%, 4.6%, and 14%, respectively. Our findings highlight the need to consider HONO in the assessment of the loss of reactive oxidized nitrogen from soils to the atmosphere and its effect on air quality.

Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot

The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.

HONO Measurement by Catalytic Conversion to NO on Nafion Surfaces

A selective catalytic converter has been developed to quantify nitrous acid (HONO), a photochemical precursor to NO and OH radicals that drives the formation of ozone and other pollutants in the troposphere. The converter is made from a sulfonated tetrafluoroethylene-based fluoropolymer-copolymer (Nafion) that was found to convert HONO to NO with unity yield under specific conditions. When coupled to a commercially available NO_x (=NO + NO₂) chemiluminescence (CL) analyzer, the system measures HONO with a limit of detection as low as 64 parts-per-trillion (ppt) (1 min average) in addition to NO_x. The converter is selective for HONO when tested against other common gas-phase reactive nitrogen species, although loss of O₃ on Nafion is a potential interference. The sensitivity and selectivity of this method allow for accurate measurement of atmospherically relevant concentrations of HONO. This was demonstrated by good agreement between HONO measurements made with the Nafion-CL method and those made with chemical ionization mass spectrometry in a simulation chamber and in indoor air. The observed reactivity of HONO on Nafion also has significant implications for the accuracy of CL NO_x analyzers that use Nafion to remove water from sampling lines.

Metabolism Interactions Promote the Overall Functioning of the Episymbiotic Chemosynthetic Community of Shinkaia crosnieri of Cold Seeps

Remarkably diverse bacteria have been observed as biofilm aggregates on the surface of deep-sea invertebrates that support the growth of hosts through chemosynthetic carbon fixation. Growing evidence also indicates that community-wide interactions, and especially cooperation among symbionts, contribute to overall community productivity. Here, metagenome-guided metatranscriptomic and metabolic analyses were conducted to investigate the taxonomic composition, functions, and potential interactions of symbionts dwelling on the seta of Shinkaia crosnieri lobsters in a methane cold seep. Methylococcales and Thiotrichales dominated the community, followed by the Campylobacteriales, Nitrosococcales, Flavobacteriales, and Chitinophagales Metabolic interactions may be common among the episymbionts since many separate taxon genomes encoded complementary genes within metabolic pathways. Specifically, Thiotrichales could contribute to detoxification of hydroxylamine that is a metabolic by-product of Methylococcales. Further, Nitrosococcales may rely on methanol leaked from Methylococcales cells that efficiently oxidize methane. Elemental sulfur may also serve as a community good that enhances sulfur utilization that benefits the overall community, as evidenced by confocal Raman microscopy. Stable intermediates may connect symbiont metabolic activities in cyclical oxic-hypoxic fluctuating environments, which then enhance overall community functioning. This hypothesis was partially confirmed via in situ experiments. These results highlight the importance of microbe-microbe interactions in symbiosis and deep-sea adaptation.

IMPORTANCE Symbioses between chemosynthetic bacteria and marine invertebrates are common in deep-sea chemosynthetic ecosystems and are considered critical foundations for deep-sea colonization. Episymbiotic microorganisms tend to form condensed biofilms that may facilitate metabolite sharing among biofilm populations. However, the prevalence of metabolic interactions among deep-sea episymbionts and their contributions to deep-sea adaptations are not well understood due to sampling and cultivation difficulties associated with deep-sea environments. Here, we investigated metabolic interactions among the episymbionts of Shinkaia crosnieri, a dominant chemosynthetic ecosystem lobster species in the Northwest Pacific Ocean. Meta-omics characterizations were conducted alongside in situ experiments to validate interaction hypotheses. Furthermore, imaging analysis was conducted, including electron microscopy, fluorescent in situ hybridization (FISH), and confocal Raman microscopy (CRM), to provide direct evidence of metabolic interactions. The results support the Black Queen Hypothesis, wherein leaked public goods are shared among cohabitating microorganisms to enhance the overall adaptability of the community via cooperation.

Climate warming, but not Spartina alterniflora invasion, enhances wetland soil HONO and NOx emissions

Climate warming and invasive plant growth (plant invasion) may aggravate air pollution by affecting soil nitrogen (N) cycling and the emissions of reactive N gases, such as nitrous acid (HONO) and nitrogen oxides (NO_x). However, little is known about the response of soil NO_y (HONO + NO_x) emissions and microbial functional genes to the interaction of climate warming and plant invasion. Here, we found that experimental warming (approximately 1.5 °C), but not Spartina alterniflora invasion, increased NO_y emissions (0-140 ng N m^-2 s^-1) of treated wetland soils by 4-10 fold. Warming also decreased soil archaeal and fungal richness and diversity, shifted their community structure (e.g., decreased the archaeal classes Thermoplasmata and Iainarchaeia, and increased the archaeal genus Candidatus Nitrosoarchaeum, and the fungal classes Saccharomycetes and Tritirachiomycetes), and decreased the overall abundance of soil N cycling genes. Structural equation modeling revealed that warming-associated changes in edaphic factors and the microbial N cycling potential are responsible for the observed increase in soil NO_y emissions. Collectively, the results showed that climate warming accelerates soil N cycling by stimulating large soil HONO and NO_x emissions, and influences air quality by contributing to atmospheric reactive N and ozone cycling.

Water-driven microbial nitrogen transformations in biological soil crusts causing atmospheric nitrous acid and nitric oxide emissions

Biological soil crusts (biocrusts) release the reactive nitrogen gases (N_r) nitrous acid (HONO) and nitric oxide (NO) into the atmosphere, but the underlying microbial process controls have not yet been resolved. In this study, we analyzed the activity of microbial consortia relevant in N_r emissions during desiccation using transcriptome and proteome profiling and fluorescence in situ hybridization. We observed that < 30 min after wetting, genes encoding for all relevant nitrogen (N) cycling processes were expressed. The most abundant transcriptionally active N-transforming microorganisms in the investigated biocrusts were affiliated with Rhodobacteraceae, Enterobacteriaceae, and Pseudomonadaceae within the Alpha- and Gammaproteobacteria. Upon desiccation, the nitrite (NO₂^-) content of the biocrusts increased significantly, which was not the case when microbial activity was inhibited. Our results confirm that NO₂^- is the key precursor for biocrust emissions of HONO and NO. This NO₂^- accumulation likely involves two processes related to the transition from oxygen-limited to oxic conditions in the course of desiccation: (i) a differential regulation of the expression of denitrification genes; and (ii) a physiological response of ammonia-oxidizing organisms to changing oxygen conditions. Thus, our findings suggest that the activity of N-cycling microorganisms determines the process rates and overall quantity of N_r emissions.

Role of chemical reactions in the nitrogenous trace gas emissions and nitrogen retention: A meta-analysis

Increasing evidence has been found that chemical reactions affect significantly the terrestrial nitrogen (N) cycle, which was previously assumed to be mainly dominated by biological processes. Due to the limitation of knowledge and analytical techniques, it is currently challenging to discern the contribution of biotic and abiotic processes to the terrestrial N cycle for geobiologists and biogeochemists alike. To better understand the role of abiotic reactions in the terrestrial N cycle, it is necessary to comprehend the chemical controls on nitrogenous trace gas emissions and N retention in soil under various environmental conditions. In this manuscript, we assess the role of abiotic reactions in nitrous oxide (N₂O) and nitric oxide (NO) emissions as well as N retention through a meta-analysis using all related peer-reviewed publications before August 2020. Results show that abiotic reactions contributed 29.3-37.7% and 44.0-57.0% to the total N₂O emission and N retention, representing 3.7-4.7 and 4.0-6.0 Tg year^-1 of global terrestrial N₂O emission and N retention, respectively. Much higher NO production was observed in sterilized soils than that in unsterilized treatments indicating the major contribution of chemical reactions to NO emission and rapid microbial reduction of NO to N₂O and N₂. Chemical hydroxylamine oxidation accounts for the largest abiotic contribution to N₂O emission, while chemical nitrite reduction and fixation represent for the largest contribution to abiotic NO production and soil N retention, respectively. Factors influencing the abiotic processes include pH, total organic carbon (TOC), total nitrogen (TN), the ratio of carbon to nitrogen (C/N), and transition metals. These results broadened our knowledge about the mechanisms involved in chemical N reactions and provided a simplified estimation about their contribution to nitrogenous trace gas emission and N retention, which is meaningful to further study interactions of biologically and chemically mediated reactions in biogeochemical N cycle.

Agricultural Fertilization Aggravates Air Pollution by Stimulating Soil Nitrous Acid Emissions at High Soil Moisture

Nitrogen lost from fertilized soil is a potentially large source of atmospheric nitrous acid (HONO), a major precursor of the hydroxyl radical. Yet, the impacts of fertilizer types and other influencing factors on HONO emissions are unknown. As a result, the current state-of-the-art models lack an appropriate parameterization scheme to quantify the HONO impact on air quality after fertilization. Here, we report laboratory measurements of high HONO emissions from soils at a 75-95% water-holding capacity after applying three common fertilizers, which contrasts with previous lower predictions at high soil moisture. Urea use leads to the largest release of HONO compared to the other two commonly used fertilizers (ammonium bicarbonate and ammonium nitrate). The significant promotion effect of fertilization lasted up to 1 week. Implementation of the lab-derived parametrization in a chemistry transport model (CMAQ) significantly improved postfertilization HONO predictions at a rural site in the agriculture-intensive North China Plain and increased the regionally averaged daytime OH, O₃, and daily fine particulate nitrate concentrations by 41, 8, and 47%, respectively. The results of our study underscore the necessity to include this large postfertilization HONO source in modeling air quality and atmospheric chemistry. Fertilizer structure adjustments may reduce HONO emissions and improve the air quality in polluted regions with intense agriculture.

N2O and NOy production by the comammox bacterium Nitrospira inopinata in comparison with canonical ammonia oxidizers

Nitrous oxide (N₂O) and NO_y (nitrous acid (HONO) + nitric oxide (NO) + nitrogen dioxide (NO₂)) are released as byproducts or obligate intermediates during aerobic ammonia oxidation, and further influence global warming and atmospheric chemistry. The ammonia oxidation process is catalyzed by groups of globally distributed ammonia-oxidizing microorganisms, which are playing a major role in atmospheric N₂O and NO_y emissions_. Yet, little is known about HONO and NO₂ production by the recently discovered, widely distributed complete ammonia oxidizers (comammox), able to individually perform the oxidation of ammonia to nitrate via nitrite. Here, we examined the N₂O and NO_y production patterns by comammox bacterium Nitrospira inopinata during aerobic ammonia oxidation, in comparison to its canonical ammonia-converting counterparts, representatives of the ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings, i) show low yield NO_y production by the comammox bacterium compared to AOB; ii) highlight the role of the NO reductase in the biological formation of N₂O based on results from NH₂OH inhibition assays and its stimulation during archaeal and bacterial ammonia oxidations; iii) postulate that the lack of hydroxylamine (NH₂OH) and NO transformation enzymatic activities may lead to a buildup of NH₂OH/NO which can abiotically react to N₂O ; iv) collectively confirm restrained N₂O and NO_y emission by comammox bacteria, an unneglectable consortium of microbes in global atmospheric emission of reactive nitrogen gases.

Characteristics of HONO and its impact on O3 formation in the Seoul Metropolitan Area during the Korea-US Air Quality Study

Photolysis of nitrous acid (HONO) is recognized as an early-morning source of OH radicals in the urban air. During the Korea-US air quality (KORUS-AQ) campaign, HONO was measured using quantum cascade - tunable infrared laser differential absorption spectrometer (QC-TILDAS) at Olympic Park in Seoul from 17 May, 2016 to 14 June, 2016. The HONO concentration was in the range of 0.07-3.46 ppbv, with an average of 0.93 ppbv. Moreover, it remained high from 00:00-05:00 LST. During this time, the mean concentration was higher during the high-O3 episodes (1.82 ppbv) than the non-episodes (1.20 ppbv). In the morning, the OH radicals that were produced from HONO photolysis were 50% higher (0.95 pptv) during the high-O3 episodes than the non-episodes. Diurnal variations in HOx and O3 concentrations were simulated by the F0AM model, which revealed a difference of ~20 ppbv in the daily maximum O3 concentrations between the high-O3 episodes and non-episodes. Furthermore, the HONO concentration increased with an increase in relative humidity (RH) up to 80%; the highest HONO was associated with the top 10% NO2 in each RH group, confirming that NO2 is one of the main precursors of HONO. At night, the conversion ratio of NO2 to HONO was estimated to be 0.88×10-2 h-1; this ratio was found to increase with an increase in RH. The Aitken mode particles (30-120 nm), which act as catalyst surfaces, exhibited a similar tendency with a conversion ratio that increased along with RH, indicating the coupling of surfaces with HONO conversion. Using an artificial neural network (ANN) model, HONO concentrations were successfully simulated with measured variables (r2 = 0.66 as an average of five models). Among these variables, NOx, aerosol surface area, and RH were found to be the main factors affecting the ambient HONO concentrations. The results reveal that RH facilitates the conversion of NO2 to HONO by constraining the availability of aerosol surfaces. This study demonstrates the coupling of HONO with the HOx-O3 cycle in the Seoul Metropolitan Area (SMA) and provides practical evidence of the heterogeneous formation of HONO by employing the ANN model.

An automated dynamic chamber system for exchange flux measurement of reactive nitrogen oxides (HONO and NOX) in farmland ecosystems of the Huaihe River Basin, China

An automated dynamic chamber system was first developed to simultaneously measure the HONO flux and NOx flux. The new dynamic chamber system was applied to field observation, and the HONO and NO_X exchange flux of farmland in the Huaihe River Basin was obtained for the first time. The performance of the dynamic chamber system was verified in the field. In the field observation, the diurnal variations of the HONO fluxes and NO fluxes before and after a rainfall event exhibited two different trends. Before the rainfall and in the latter stage after the rainfall, the maxima of the HONO fluxes and NO fluxes occurred in the morning, then decreased gradually. However, during the early stage after the rainfall, the HONO fluxes and NO fluxes gradually increased in the morning and reached their maximum values in the afternoon. During the measurement period, the maximum HONO flux was 7.69 ng N m^-2 s^-1 and the maximum NO flux was 34.52 ng N m^-2 s^-1. There was no significant correlation between HONO flux and temperature before the rainfall and in the latter stage after the rainfall period, although the correlation coefficient (R) between HONO flux and temperature reached 0.78 in the early stage after the rainfall period, and the R between NO flux and HONO flux reached more than 0.6 before and after rainfall periods. The HONO flux of fresh soil samples were the same order of magnitude as that of field observations. The field results indicate that soil emissions are an important source of atmospheric HONO during the crop growth stage. Negative NO₂ fluxes were found in most observation periods, and there were significant negative linear correlations between NO₂ fluxes and atmospheric NO₂ concentrations. The R between ambient NO₂ concentration and NO₂ flux was 0.79, and the compensation point of NO₂ was 5 ppbv.

Thaumarchaea Genome Sequences from a High Arctic Active Layer

The role of archaeal ammonia oxidizers often exceeds that of bacterial ammonia oxidizers in marine and terrestrial environments but has been understudied in permafrost, where thawing has the potential to release ammonia. Here, three thaumarchaea genomes were assembled and annotated from metagenomic data sets from carbon-poor Canadian High Arctic active-layer cryosols.

The role of archaeal ammonia oxidizers often exceeds that of bacterial ammonia oxidizers in marine and terrestrial environments but has been understudied in permafrost, where thawing has the potential to release ammonia. Here, three thaumarchaea genomes were assembled and annotated from metagenomic data sets from carbon-poor Canadian High Arctic active-layer cryosols.

Impacts of six potential HONO sources on HOx budgets and SOA formation during a wintertime heavy haze period in the North China Plain

The Weather Research and Forecasting/Chemistry (WRF-Chem) model updated with six potential HONO sources (i.e., traffic, soil, biomass burning and indoor emissions, and heterogeneous reactions on aerosol and ground surfaces) was used to quantify the impact of the six potential HONO sources on the production and loss rates of OH and HO₂ radicals and the concentrations of secondary organic aerosol (SOA) in the Beijing-Tianjin-Heibei (BTH) region of China during a winter heavy haze period of Nov. 29-Dec. 3, 2017. The updated WRF-Chem model well simulated the observed HONO concentrations at the Wangdu site, especially in the daytime, and well reproduced the observed diurnal variations of regional-mean O₃ in the BTH region. The traffic emission source was an important HONO source during nighttime but not significant during daytime, heterogeneous reactions on ground/aerosol surfaces were important during nighttime and daytime. We found that the six potential HONO sources led to a significant enhancement in the dominant production and loss rates of HO_x on the wintertime heavy haze and nonhaze days (particularly on the heavy haze day), an enhancement of 5-25 μg m^-3 (75-200%) in the ground SOA in the studied heavy haze event, and an enhancement of 2-15 μg m^-3 in the meridional-mean SOA on the heavy haze day, demonstrating that the six potential HONO sources accelerate the HO_x cycles and aggravate haze events. HONO was the key precursor of primary OH in the BTH region in the studied wintertime period, and the photolysis of HONO produced a daytime mean OH production rate of 2.59 ppb h^-1 on the heavy haze day, much higher than that of 0.58 ppb h^-1 on the nonhaze day. Anthropogenic SOA dominated in the BTH region in the studied wintertime period, and its main precursors were xylenes (42%), BIGENE (31%) and toluene (21%).

Development and application of a twin open-top chambers method to measure soil HONO emission in the North China Plain

HONO (nitrous acid) is a crucial precursor for tropospheric OH radicals, and its sources are not well understood. In the past decade, soil was proven to be a potential source for HONO. However, more field measurements of soil HONO emission flux are needed to explore the mechanism and its impact on regional air quality. Here, we developed a system based on twin open-top chambers (OTCs) and wet chemical methods to measure HONO emission flux from agricultural soil in the North China Plain (NCP). The performance of the OTC system was tested under laboratory and field measurement conditions. The results showed that the system could reflect the strength (>90%) and variation of gas emission with an average residence time of 4-5 min. The greenhouse effect and chemical reaction interference in the chamber was proven to have no significant influence on the HONO flux measurement. Field measurement revealed that agricultural soil before fertilization was an important source of HONO. The emission flux showed radiation-dependent or temperature-dependent variation, with a peak of 3.21 ng m^-2 s^-1 at noontime that could account for approximately 67 pptv h^-1 of the missing HONO source under an assumed mixing layer height of 300 m. Fertilization substantially accelerated HONO emission, which was rationally attributed to biological processes including nitrification. Considering the high fertilization rate in the NCP and other similar regions in China, HONO emission from agricultural soil likely has enormous impact on regional photochemistry and air quality, suggesting that more research should be conducted on this aspect.

Soil HONO emissions at high moisture content are driven by microbial nitrate reduction to nitrite: tackling the HONO puzzle

Nitrous acid (HONO) is a precursor of the hydroxyl radical (OH), a key oxidant in the degradation of most air pollutants. Field measurements indicate a large unknown source of HONO during the day time. Release of nitrous acid (HONO) from soil has been suggested as a major source of atmospheric HONO. We hypothesize that nitrite produced by biological nitrate reduction in oxygen-limited microzones in wet soils is a source of such HONO. Indeed, we found that various contrasting soil samples emitted HONO at high water-holding capacity (75-140%), demonstrating this to be a widespread phenomenon. Supplemental nitrate stimulated HONO emissions, whereas ethanol (70% v/v) treatment to minimize microbial activities reduced HONO emissions by 80%, suggesting that nitrate-dependent biotic processes are the sources of HONO. High-throughput Illumina sequencing of 16S rRNA as well as functional gene transcripts associated with nitrate and nitrite reduction indicated that HONO emissions from soil samples were associated with nitrate reduction activities of diverse Proteobacteria. Incubation of pure cultures of bacterial nitrate reducers and gene-expression analyses, as well as the analyses of mutant strains deficient in nitrite reductases, showed positive correlations of HONO emissions with the capability of microbes to reduce nitrate to nitrite. Thus, we suggest biological nitrate reduction in oxygen-limited microzones as a hitherto unknown source of atmospheric HONO, affecting biogeochemical nitrogen cycling, atmospheric chemistry, and global modeling.

Microbial mechanisms and ecosystem flux estimation for aerobic NOy emissions from deciduous forest soils

Reactive nitrogen oxides (NO_y; NO_y = NO + NO₂ + HONO) decrease air quality and impact radiative forcing, yet the factors responsible for their emission from nonpoint sources (i.e., soils) remain poorly understood. We investigated the factors that control the production of aerobic NO_y in forest soils using molecular techniques, process-based assays, and inhibitor experiments. We subsequently used these data to identify hotspots for gas emissions across forests of the eastern United States. Here, we show that nitrogen oxide soil emissions are mediated by microbial community structure (e.g., ammonium oxidizer abundances), soil chemical characteristics (pH and C:N), and nitrogen (N) transformation rates (net nitrification). We find that, while nitrification rates are controlled primarily by chemoautotrophic ammonia-oxidizing archaea (AOA), the production of NO_y is mediated in large part by chemoautotrophic ammonia-oxidizing bacteria (AOB). Variation in nitrification rates and nitrogen oxide emissions tracked variation in forest communities, as stands dominated by arbuscular mycorrhizal (AM) trees had greater N transformation rates and NO_y fluxes than stands dominated by ectomycorrhizal (ECM) trees. Given mapped distributions of AM and ECM trees from 78,000 forest inventory plots, we estimate that broadleaf forests of the Midwest and the eastern United States as well as the Mississippi River corridor may be considered hotspots of biogenic NO_y emissions. Together, our results greatly improve our understanding of NO_y fluxes from forests, which should lead to improved predictions about the atmospheric consequences of tree species shifts owing to land management and climate change.