Greenhouse gas emissions from on-site sanitation systems: A systematic review and meta-analysis of emission rates, formation pathways and influencing factors

Onsite sanitation systems (OSS) are significant sources of greenhouse gases (GHG) including carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O). While a handful of studies have been conducted on GHG emissions from OSS, systematic evaluation of literature on this subject is limited. Our systematic review and meta-analysis provides state-of-the- art information on GHG emissions from OSS and identifies novel areas for investigation. The paper analyzes GHG emission rates from different OSS, the influence of various design, operational, and environmental factors on emission rates and proffers mitigation measures. Following the Preferred Reporting Items for Systematic reviews and Meta-analysis (PRISMA) guidelines, we identified 16 articles which quantified GHG emissions from OSS. Septic tanks emit substantial amounts of CO2 and CH4 ranging from 1.74 to 398.30 g CO2/cap/day and 0.06-110.13 g CH4/cap/day, respectively, but have low N2O emissions (0.01-0.06 g N₂O/cap/day). CH4 emissions from pit latrines range from 0.77 to 20.30 g CH4/cap/day N2O emissions range from 0.76 to 1.20 gN2O/cap/day. We observed statistically significant correlations (p < 0.05) between temperature, biochemical oxygen demand, chemical oxygen demand, dissolved oxygen, storage period, and GHG emissions from OSS. However, no significant correlation (p > 0.05) was observed between soil volumetric water content and CO2 emissions. CH4 emissions (expressed as CO2 equivalents) from OSS estimated following Intergovernmental Panel for Climate Change (IPCC) guidelines were found to be seven times lower (90.99 g CO2e/cap/day) than in-situ field emission measurements (704.7 g CO2e/cap/day), implying that relying solely on IPCC guidelines may lead to underestimation of GHG emission from OSS. Our findings underscore the importance of considering local contexts and environmental factors when estimating GHG emissions from OSS. Plausible mitigation measures for GHG emissions from OSS include converting waste to biogas in anaerobic systems (e.g. biogas), applying biochar, and implementing mitigation policies that equally address inequalities in sanitation service access. Future research on GHG from OSS should focus on in-situ measurements of GHGs from pit latrines and other common OSS in developing countries, understanding the fate and transport of dissolved organics like CH4 in OSS effluents and impacts of microbial communities in OSS on GHG emissions. Addressing these gaps will enable more holistic and effective management of GHG emissions from OSS.

Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential

Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.

IMPORTANCE

Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.

Reshaping the plastisphere upon deposition: Promote N2O production through affecting sediment microbial communities in aquaculture pond

Microplastics (MPs) could provide vector for microorganisms to form biofilm (plastisphere), but the shaping process of MPs biofilm and its effects on the structure and function of sedimentary microbial communities especially in aquaculture environments are not reported. For this, we incubated MPs biofilm in situ in an aquaculture pond and established a sediment microcosm with plastisphere. We found that the formation of MPs biofilm in surface water was basically stable after 30 d incubation, but the biofilm communities were reshaped after deposition for another 30 d, because they were more similar to plastisphere communities incubated directly within sediment but not surface water. Moreover, microbial communities of MPs-contaminated sediment were altered, which was mainly driven by the biofilm communities present on MPs, because they but not sediment communities in proximity to MPs had a more pronounced separation from the control sediment communities. In the presence of MPs, increased sediment nitrification, denitrification and N2O production rates were observed. The K00371 (NO2-⇋NO3-) pathway and elevated abundance of nxrB and narH genes were screened by metagenomic analysis. Based on structural equation model, two key bacteria (Alphaproteobacteria bacterium and Rhodobacteraceae bacterium) associated with N2O production were further identified. Overall, the settling of MPs could reshape the original biofilm and promote N2O production by selectively elevating sedimental microorganisms and functional genes in aquaculture pond.

Simultaneous suppression of As mobilization and N2O emission from NH4+/As-rich paddy soils by combined nitrate and birnessite amendment

The environmental impacts of As mobilization and nitrous oxide (N2O) emission in flooded paddy soils are serious issues for food safety and agricultural greenhouse gas emissions. Several As immobilization strategies utilizing microbially-mediated nitrate reducing-As(III) oxidation (NRAO) and birnessite (δ-MnO2)-induced oxidation/adsorption have proven effective for mitigating As bioavailability in flooded paddy soils. However, several inefficiency and unsustainability issues still exist in these remediation approaches. In this study, the effects of a combined treatment of nitrate and birnessite were assessed for the simultaneous suppression of As(III) mobilization and N2O emission from flooded paddy soils. Microcosm incubations confirmed that the combined treatment achieved an effective suppression of As(III) mobilization and N2O emission, with virtually no As(T) released and at least a 87% decrease in N2O emission compared to nitrate treatment alone after incubating for 8 days. When nitrate and birnessite are co-amended to flooded paddy soils, the activities of denitrifying enzymes within the denitrification electron transport pathway were suppressed by MnO2. As a result, the majority of applied nitrate participated in nitrate-dependent microbial Mn(II) oxidation. The regenerated biogenetic MnO2 was available to facilitate subsequent cycles of As(III) immobilization and concomitant N2O emission suppression, sustainable remediation strategy. Moreover, the combined nitrate-birnessite amendment promoted the enrichment of Pseudomonas, Achromobacter and Cupriavidu, which are known to participate in the oxidation of As(III)/Mn(II). Our findings document strong efficacy for the combined nitrate/birnessite treatment as a remediation strategy to simultaneously mitigate As-pollution and N2O emission, thereby improving food safety and reducing greenhouse gas emissions from flooded paddy soils enriched with NH4+ and As.

Microbial pathways of nitrous oxide emissions and mitigation approaches in drylands

Drylands refer to water scarcity and low nutrient levels, and their plant and biocrust distribution is highly diverse, making the microbial processes that shape dryland functionality particularly unique compared to other ecosystems. Drylands are constraint for sustainable agriculture and risk for food security, and expected to increase over time. Nitrous oxide (N2O), a potent greenhouse gas with ozone reduction potential, is significantly influenced by microbial communities in drylands. However, our understanding of the biological mechanisms and processes behind N2O emissions in these areas is limited, despite the fact that they highly account for total gaseous nitrogen (N) emissions on Earth. This review aims to illustrate the important biological pathways and microbial players that regulate N2O emissions in drylands, and explores how these pathways might be influenced by global changes for example N deposition, extreme weather events, and climate warming. Additionally, we propose a theoretical framework for manipulating the dryland microbial community to effectively reduce N2O emissions using evolving techniques that offer inordinate specificity and efficacy. By combining expertise from different disciplines, these exertions will facilitate the advancement of innovative and environmentally friendly microbiome-based solutions for future climate change vindication approaches.

Aerobic nitrous oxide emission in anoxic/aerobic and intermittent aeration sequencing batch reactors

This study characterized nitrogen removal and nitrous oxide (N2O) emissions from lab-scale anoxic/aerobic sequencing batch reactor (AOSBR) and intermittent aeration sequencing batch reactor (IASBR), respectively, for treating synthetic municipal wastewater. The N2O emission was evaluated in a simulated cycle, and batch conditions of aerobic nitrification, simultaneous nitrification and denitrification (SND), and aerobic denitrification. The results show that nitrogen removal was enhanced in IASBR compared to AOSBR, with 94.2% and 67.9% of total inorganic nitrogen removal efficiency in IASBR and AOSBR, respectively. In the simulated cycle, the emission factors (of oxidized ammonium) were 4.9% and 0.6% in AOSBR and IASBR, respectively. Under batch conditions, the N2O emission factors during SND were obviously higher than that during aerobic nitrification and denitrification. The N2O emission factors during SND ranging 0.68-11.68% in AOSBR and 1.25-5.13% in IASBR. Furthermore, N2O emission under batch conditions was affected by the aeration ratios. Moderate and high aeration ratios used in this study stimulated the N2O emission from SND. The N2O emission was enhanced with the nitrite accumulation during aerobic nitrification when the nitrite-oxidizing bacteria was inhibited by a chemical inhibitor. Aerobic denitrification via nitrite could be the main pathway of N2O generation from SND processes. The findings from our study can help further understand N2O emission mechanisms and guide the optimization of the current wastewater treatment process for minimizing N2O emission.

Transformation mechanisms of ammonium and nitrate in subsurface wastewater infiltration system: Implication for reducing greenhouse gas emissions

Subsurface wastewater infiltration system (SWIS) has been recognized as a cost-effective and environmentally friendly tool for wastewater treatment. However, there is a lack of knowledge on the transformation processes of nitrogen (N), hindering the improvement of the N removal efficiency in SWIS. Here, the migration and transformation mechanisms of ammonium (NH4+-N) and nitrate (NO3+-N) over 10 days were explored by 15N labeling technique. Over the study period, 49% of the added 15NH4+-N remained in the soil, 29% was removed via gaseous N emissions, and 14% was leaked with the effluent in the SWIS. In contrast, only 11% of the added 15NO3--N remained in the soil while 65% of the added 15NO3--N was removed via gaseous N emissions, and 12% with the effluent in the SWIS. The main pathway for N2O emission was denitrification (52-70%) followed by nitrification (15-28%) and co-denitrification (9-20%). Denitrification was also the predominant pathway for N loss as N2, accounting for 88-96% of the N2 emission. The dominant biological transformation processes were different at divergent soil depths, corresponding to nitrification zone and denitrification zone along the longitudinal continuum in SWIS, which was confirmed by the expression patterns of microbial gene abundance. Overall, our findings reveal the mechanism of N transformation in SWIS and provide a theoretical basis for establishing a pollutant management strategy and reducing greenhouse gas emissions from domestic wastewater treatment.

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

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 both for electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in darkness. 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.IMPORTANCEDenitrification is a form of microbial respiration wherein nitrate is converted via several nitrogen oxide intermediates into harmless dinitrogen gas. Partial denitrifying bacteria, which individually have some but not all denitrifying enzymes, can achieve complete denitrification as a community by cross-feeding nitrogen oxide intermediates. However, the last intermediate, nitrous oxide (N2O), is a potent greenhouse gas that often escapes, motivating efforts to understand and improve the efficiency of denitrification. Here, we found that at least some partial denitrifying N2O reducers can sense and respond to nitrogen oxide intermediates that they cannot otherwise use. The regulatory effects of nitrogen oxides on partial denitrifiers are thus an important consideration in understanding and applying denitrifying bacterial communities to combat greenhouse gas emissions.

Short term grazing increased growing-season N2O production and decreased its reduction potential by reducing the abundance and expression of nosZ clade II gene in a semi-arid steppe

Understanding nitrous oxide (N2O) production as well as reduction in response to grazing and mowing is essential for designing better management strategies to improve sustainability of grassland ecosystems. We evaluated how four years of grazing or mowing altered N2O production and reduction potential, gene abundance, and expression of microbial functional groups pertinent to N2O production in situ on a typical grassland in Inner Mongolia. In our study, we found that grazing dramatically raised soil ammonium (NH4+-N) and nitrate (NO3--N) concentrations, AOB gene abundance and potential of N2O production through nitrification (NN2O) and denitrification (DN2O) in summer, but lessened the expression of nosZ clade II gene in all seasons. Mowing had minor effect on soil inorganic nitrogen (N) concentrations. Mowing diminished the quantity of denitrification genes (narG and nosZ), expression of nosZ and nosZ clade II genes, and DN2O concentration. The expression and abundance of nosZ clade II gene were related to DN2. These results suggested that short-term grazing could enhance N2O production potential in peak growing season, while the reduction in abundance and expression of nosZ calde II gene might be an important contributor to the enhanced N2O production of semi-arid typical steppe grasslands.

Unveiling novel pathways and key contributors in the nitrogen cycle: Validation of enrichment and taxonomic characterization of oxygenic denitrifying microorganisms in environmental samples

Microorganisms play a crucial role in both the nitrogen cycle and greenhouse gas emissions. A recent discovery has unveiled a new denitrification pathway called oxygenic denitrification, entailing the enzymatic reduction of nitrite to nitric oxide (NO) by a putative nitric oxide dismutase (nod) enzyme. In this study, the presence of the nod gene was detected and subsequently enriched in anaerobic-activated sludge, farmland soil, and paddy soil samples. After 150 days, the enriched samples exhibited significant denitrification, and concomitant oxygen production. The removal efficiency of nitrite ranged from 64.6 % to 79.0 %, while the oxygen production rate was between 15.4 μL/min and 18.6 μL/min when exposed to a sole nitrogen source of 80 mg/L sodium nitrite. Additionally, batch experiments and kinetic analyses revealed the intricate pathways and underlying mechanisms governing the oxygenic denitrification reaction by using CARBOXY-PTIO, 18O-labelled water, and acetylene to unravel the intricacies of the reaction. The quantitative polymerase chain reaction (qPCR) results indicated a significant surge in the abundance of nod genes, escalating from 7.59 to 10.12-fold. Moreover, analysis of 16S ribosomal DNA (rDNA) amplicons revealed Proteobacteria as the dominant phylum and Thauera as the main genus, with the presumed affiliation. In this study, a new nitrogen conversion pathway, oxygenic denitrification, was discovered in environmental samples. This process provides the possibility for the control of nitrous oxide in the treatment of nitrogenous wastewater.

Quest for Nitrous Oxide-reducing Bacteria Present in an Anammox Biofilm Fed with Nitrous Oxide

N2O-reducing bacteria have been examined and harnessed to develop technologies that reduce the emission of N2O, a greenhouse gas produced by biological nitrogen removal. Recent investigations using omics and physiological activity approaches have revealed the ecophysiologies of these bacteria during nitrogen removal. Nevertheless, their involvement in‍ ‍anammox processes remain unclear. Therefore, the present study investigated the identity, genetic potential, and activity‍ ‍of N2O reducers in an anammox reactor. We hypothesized that N2O is limiting for N2O-reducing bacteria‍ ‍and an‍ ‍exogeneous N2O supply enriches as-yet-uncultured N2O-reducing bacteria. We conducted a 1200-day incubation of N2O-reducing bacteria in an anammox consortium using gas-permeable membrane biofilm reactors (MBfRs), which efficiently supply N2O in a bubbleless form directly to a biofilm grown on a gas-permeable membrane. A 15N tracer test indicated that the supply of N2O resulted in an enriched biomass with a higher N2O sink potential. Quantitative PCR and 16S rRNA amplicon sequencing revealed Clade II nosZ type-carrying N2O-reducing bacteria as protagonists of N2O sinks. Shotgun metagenomics showed the genetic potentials of the predominant Clade II nosZ-carrying bacteria, Anaerolineae and Ignavibacteria in MBfRs. Gemmatimonadota and non-anammox Planctomycetota increased their abundance in MBfRs despite their overall lower abundance. The implication of N2O as an inhibitory compound scavenging vitamin B12, which is essential for the synthesis of methionine, suggested its limited suppressive effect on the growth of B12-dependent bacteria, including N2O reducers. We identified Dehalococcoidia and Clostridia as predominant N2O sinks in an anammox consortium fed exogenous N2O because of the higher metabolic potential of vitamin B12-dependent biosynthesis.

Differential Nitrous oxide emission and microbiota succession in constructed wetlands induced by nitrogen forms

Nitrous oxide (N2O) emission during the sewage treatment process is a serious environmental issue that requires attention. However, the N2O emission in constructed wetlands (CWs) as affected by different nitrogen forms in influents remain largely unknown. This study investigated the N2O emission profiles driven by microorganisms in CWs when exposed to two typical nitrogen sources (NH4+-N or NO3--N) along with different carbon source supply (COD/N ratios: 3, 6, and 9). The results showed that CWs receiving NO3--N caused a slight increase in total nitrogen removal (by up to 11.8 %). This increase was accomplished by an enrichment of key bacteria groups, including denitrifiers, dissimilatory nitrate reducers, and assimilatory nitrate reducers, which enhanced the stability of microbial interaction. Additionally, it led to a greater abundance of denitrification genes (e.g., nirK, norB, norC, and nosZ) as inferred from the database. Consequently, this led to a gradual increase in N2O emission from 66.51 to 486.77 ug-N/(m2·h) as the COD/N ratio increased in CWs. Conversely, in CWs receiving NH4+-N, an increasing influent COD/N ratio had a negative impact on nitrogen biotransformation. This resulted in fluctuating trend of N2O emissions, which decreased initially, followed by an increase at later stage (with values of 122.87, 44.00, and 148.59 ug-N/(m2·h)). Furthermore, NH4+-N in the aquatic improved the nitrogen uptake by plants and promoted the production of more root exudates. As a result, it adjusted the nitrogen-transforming function, ultimately reducing N2O emissions in CWs. This study highlights the divergence in microbiota succession and nitrogen transformation in CWs induced by nitrogen form and COD/N ratio, contributing to a better understanding of the microbial mechanisms of N2O emission in CWs with NH4+-N or NO3--N at different COD/N ratios.

Microbial mechanism of biochar addition to reduce N2O emissions from soilless substrate systems

The soilless peat-based substrate partially solves the global soil problem in greenhouse vegetable production. However, it still produces serious N2O emissions due to the application of nutrient solutions. The pyrolysis biochar is regarded as an effective measure to reduce soil N2O emissions. However, the effect and mechanism of biochar on N2O emissions from the soilless substrate remain unknown. Therefore, this study set up six treatments by adjusting the ratio of biochar addition of peat-based substrate: 0% (0BC), 2% (2BC), 4% (4BC), 6% (6BC), 8% (8BC) and 10% (10BC) (v/v). The results showed that compared to the control treatment, N2O emissions reduced by 81%, 71%, 51%, 61%, and 75% in the 2BC, 4BC, 6BC, 8BC and 10BC treatments, respectively. In addition, lettuce yield increased by 10% and 7% in the 2BC and 4BC treatments and decreased by 0.5%, 4% and 6% in the 6BC, 8BC and 10BC treatments, respectively. Combining stable isotope technology, qPCR analysis and high-throughput sequencing, five microbial pathways of N2O production, including bacterial and archaea nitrification (BN and AN), denitrification performed by fungi, denitrifier bacteria and nitrifier bacteria (FD, DD and ND), were roughly distinguished. In addition, the extent of N2O reduction was obtained by δ18O vs.δ15NSP map. For all treatments, overall, the DD process (over 50%) was the main process of N2O production and reduction, while ND and AN processes were almost negligible (less 5%). In detail, the decrease of N2O emissions was caused by decreasing the contribution of FD in the 6BC, 8BC and 10BC treatments and reducing the contribution of BN in the 0BC and 2BC treatments. In addition, biochar addition increased the extent of N2O reduction to N2. In summary, the 2% biochar addition presented the greatest extent of N2O reduction to N2 (83%) and the lowest N2O emissions as well as the highest lettuce yields and nitrogen utilization efficiency. Therefore, 2% biochar is deemed the most optimal addition to the peat-based substrate.

Computational Exploration of Minimum Energy Reaction Pathway of N2O Formation from Intermediate I of P450nor Using an Active Center Model

P450nor is a heme-containing enzyme that catalyzes the conversion of nitric oxide (NO) to nitrous oxide (N2O). Its catalytic mechanism has attracted attention in chemistry, biology, and environmental engineering. The catalytic cycle of P450nor is proposed to consist of three major steps. The reaction mechanism for the last step, N2O generation, remains unknown. In this study, the reaction pathway of the N2O generation from the intermediate I was explored with the B3LYP calculations using an active center model after the examination of the validity of the model. In the validation, we compared the heme distortions between P450nor and other oxidoreductases, suggesting a small effect of protein environment on the N2O generation reaction in P450nor. We then evaluated the electrostatic environment effect of P450nor on the hydride affinity to the active site with quantum mechanics/molecular mechanics (QM/MM) calculations, confirming that the affinity was unchanged with or without the protein environment. The active center model for P450nor showed that the N2O generation process in the enzymatic reaction undergoes a reasonable barrier height without protein environment. Consequently, our findings strongly suggest that the N2O generation reaction from the intermediate I depends sorely on the intrinsic reactivity of the heme cofactor bound on cysteine residue.

The role of plant vasculature in tackling N2O emissions

Rising demand for protein-rich foods can impact N2O emissions from croplands. Recent research has pointed to the role of modified plant vasculature in grain protein increase. Here we highlight how discovering the mechanistic role of plant vasculature in protein improvement and nitrogen-use efficiency could reduce global N2O emissions.

Evaluation of nitrous oxide emission during ammonia retention from simulated industrial wastewater by microaerobic activated sludge process

Considering the reciprocating processes of nitrogen gas (N2) fixation to ammonia (NH4-N) and NH4-N removal to N2 through nitrification and denitrification during wastewater treatment, a microaerobic activated sludge process (MAS) is proposed in this study as a pretreatment to retain NH4-N from high-strength nitrogenous wastewater for further NH4-N recovery through membrane technology, that is, inhibit nitrification, with sufficient removal of total organic carbon (TOC). With DO and pH control, the 3-reactor bench-scale MAS systems successfully realized an NH4-N retention rate of over 80 %, with TOC removal rates of over 90 %. In addition, the emissions of carbon dioxide (CO2) and nitrous oxide (N2O) during MAS were evaluated. The total N2O emissions were 407 and 475 mg-N/day when pH was controlled at 6.2 (S1) and 6.8 (S2), respectively, with average emission factors to total nitrogen load over 2 % in both systems. Also, the global warming potential of N2O is one order of magnitude larger than that of CO2, indicating the significance of N2O in the MAS process. Therefore, the mechanisms of N2O emission from each reactor were investigated. The first reactor, where most of the TOC was adsorbed, emitted only 1.98 % (S1) and 2.43 % (S2) of the total N2O emissions through the denitrification of nitrite and nitrate (NOx) from the return sludge. The second reactor emitted 79.9 % (S1) and 69.0 % (S2) of the total N2O with the emission rates the same order of magnitude as the NOx production rates. Multiple pathways were considered to contribute to the high N2O emissions, and biotic NH2OH oxidation was one potential pathway at pH 6.2. Finally, the third reactor emitted 9.98 % (S1) and 16.8 % (S2) of the total N2O by nitrifier denitrification. Overall, this study showed that the large N2O emissions under nitrification-inhibiting conditions of the MAS process owed to the incomplete nitrification under acidic conditions and large abundances of denitrifiers. On the other hand, the lower N2O emissions at pH 6.2 evidenced the potential N2O mitigation under slightly more acidic conditions, underlining the necessity of further study on N2O mitigation when adapting to the trend of NH4-N recovery.

Suggested role of NosZ in preventing N2O inhibition of dissimilatory nitrite reduction to ammonium

IMPORTANCE

Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is a microbial energy-conserving process that reduces NO3 - and/or NO2 - to NH4 +. Interestingly, DNRA-catalyzing microorganisms possessing nrfA genes are occasionally found harboring nosZ genes encoding nitrous oxide reductases, i.e., the only group of enzymes capable of removing the potent greenhouse gas N2O. Here, through a series of physiological experiments examining DNRA metabolism in one of such microorganisms, Bacillus sp. DNRA2, we have discovered that N2O may delay the transition to DNRA upon an oxic-to-anoxic transition, unless timely removed by the nitrous oxide reductases. These observations suggest a novel explanation as to why some nrfA-possessing microorganisms have retained nosZ genes: to remove N2O that may otherwise interfere with the transition from O2 respiration to DNRA.

Unveiling the roles of biofilm in reducing N2O emission in a nitrifying integrated fixed-film activated sludge (IFAS) system

Biofilm process such as integrated fixed-film activated sludge (IFAS) system has been preliminarily found to produce less nitrous oxide (N2O) than suspended sludge system. However, the N2O emission behaviors and underlying N2O mitigation mechanism in such hybrid system remain unclear. This study therefore aims to fully unveil the roles of biofilm in reducing N2O emission in a nitrifying IFAS system with the aid of some advanced technologies such as N2O microsensor and site-preference analysis. It was found that ammonia oxidation occurred mostly in the sludge flocs (˃ 86%) and biofilm could reduce N2O emission by 43.77% in a typical operating cycle. Biofilm not only reduced nitrite accumulation in nitrification process, inhibiting N2O production via nitrifier denitrification pathway, but also served as a N2O sink, promoting the reduction of N2O via endogenous denitrification. As a result, N2O emissions from the IFAS system were 50%-83% lower than those from the solo sludge flocs. Further, more N2O emission was reduced in the presence of biofilm with decreasing the dissolved oxygen level in the range of 0.5-3.0 mg O2/L. Microbial community and key enzyme analyses revealed that biofilm had relatively high microbial diversity and unique enzyme composition, providing a reasonable explanation for the changed contributions of different N2O production pathways and reduced N2O emission.

Role of Nitric Oxide in Hydroxylamine Oxidation by Ammonia-Oxidizing Bacteria

An important role of nitric oxide (NO) as either a free intermediate in the NH3 oxidation pathway or a potential oxidant for NH3 or NH2OH has been proposed for ammonia-oxidizing bacteria (AOB) and archaea (AOA), respectively. However, tracing NO metabolism at low concentrations remains notoriously difficult. Here, we use electrochemical sensors and the mild NO scavenger 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) to trace apparent NO concentration and determine production rates at low micromolar concentrations in the model AOB strain Nitrosomonas europaea. In agreement with previous studies, we found that PTIO does not affect NH3 oxidation instantaneously in both Nitrosospira briensis and Nitrosomonas europaea, unlike inhibitors for ammonia oxidation such as allylthiourea and acetylene, although it effectively scavenged NO from the cell suspensions. Quantitative analysis showed that NO production by N. europaea amounted to 3.15% to 6.23% of NO2- production, whereas N. europaea grown under O2 limitation produced NO equivalent to up to 40% of NO2- production at high substrate concentrations. In addition, we found that PTIO addition to N. europaea grown under O2 limitation abolished N2O production. These results indicate different turnover rates of NO during NH3 oxidation under O2-replete and O2-limited growth conditions in AOB. The results suggest that NO may not be a free intermediate or remain tightly bound to iron centers of enzymes during hydroxylamine oxidation and that only NH3 saturation and adaptation to O2 limitation may lead to significant dissociation of NO from hydroxylamine dehydrogenase. IMPORTANCE Ammonia oxidation by chemolithoautotrophic ammonia-oxidizing bacteria (AOB) is thought to contribute significantly to global nitrous oxide (N2O) emissions and leaching of oxidized nitrogen, particularly through their activity in nitrogen (N)-fertilized agricultural production systems. Although substantial efforts have been made to characterize the N metabolism in AOB, recent findings suggest that nitric oxide (NO) may play an important mechanistic role as a free intermediate of hydroxylamine oxidation in AOB, further implying that besides hydroxylamine dehydrogenase (HAO), additional enzymes may be required to complete the ammonia oxidation pathway. However, the NO spin trap PTIO was found to not inhibit ammonia oxidation in AOB. This study provides a combination of physiological and spectroscopic evidence that PTIO indeed scavenges only free NO in AOB and that significant amounts of free NO are produced only during incomplete hydroxylamine oxidation or nitrifier denitrification under O2-limited growth conditions.

Reconnaissance of Oxygenic Denitrifiers in Agriculturally Impacted Soils

Row crop production in the agricultural Midwest pollutes waterways with nitrate, and exacerbates climate change through increased emissions of nitrous oxide and methane. Oxygenic denitrification processes in agricultural soils mitigate nitrate and nitrous oxide pollution by short-circuiting the canonical pathway to avoid nitrous oxide formation. Furthermore, many oxygenic denitrifiers employ a nitric oxide dismutase (nod) to create molecular oxygen that is used by methane monooxygenase to oxidize methane in otherwise anoxic soils. The direct investigation of nod genes that could facilitate oxygenic denitrification processes in agricultural sites is limited, with no prior studies investigating nod genes at tile drainage sites. Thus, we performed a reconnaissance of nod genes at variably saturated surface sites, and within a variably to fully saturated soil core in Iowa to expand the known distribution of oxygenic denitrifiers. We identified new nod gene sequences from agricultural soil and freshwater sediments in addition to identifying nitric oxide reductase (qNor) related sequences. Surface and variably saturated core samples displayed a nod to 16S rRNA gene relative abundance of 0.004% to 0.1% and fully saturated core samples had relative nod gene abundance of 1.2%. The relative abundance of the phylum Methylomirabilota increased from 0.6% and 1% in the variably saturated core samples to 3.8% and 5.3% in the fully saturated core samples. The more than 10-fold increase in relative nod abundance and almost 9-fold increase in relative Methylomirabilota abundance in fully saturated soils suggests that potential oxygenic denitrifiers play a greater nitrogen cycling role under these conditions. IMPORTANCE The direct investigation of nod genes in agricultural sites is limited, with no prior studies investigating nod genes at tile drains. An improved understanding of nod gene diversity and distribution is significant to the field of bioremediation and ecosystem services. The expansion of the nod gene database will advance oxygenic denitrification as a potential strategy for sustainable nitrate and nitrous oxide mitigation, specifically for agricultural sites.

Nitrogen removal by algal-bacterial consortium during mainstream wastewater treatment: Transformation mechanisms and potential N2O mitigation

This work investigated nitrogen transformation pathways of the algal-bacterial consortium as well as its potential in reducing nitrous oxide (N₂O) emission in enclosed, open and aerated reactors. The results confirmed the superior ammonium removal performance of the algal-bacterial consortium relative to the single algae (Chlorella vulgaris) or the activated sludge, achieving the highest efficiency at 100% and the highest rate of 7.34 mg N g MLSS^-1 h^-1 in the open reactor with glucose. Enhanced total nitrogen (TN) removal (to 74.6%) by the algal-bacterial consortium was achieved via mixotrophic algal assimilation and bacterial denitrification under oxygen-limited and glucose-sufficient conditions. Nitrogen distribution indicated that ammonia oxidation (∼41.8%) and algal assimilation (∼43.5%) were the main pathways to remove ammonium by the algal-bacterial consortium. TN removal by the algal-bacterial consortium was primarily achieved by algal assimilation (28.1-40.8%), followed by bacterial denitrification (2.9-26.5%). Furthermore, the algal-bacterial consortium contributed to N₂O mitigation compared with the activated sludge, reducing N₂O production by 35.5-55.0% via autotrophic pathways and by 81.0-93.6% via mixotrophic pathways. Nitrogen assimilation by algae was boosted with the addition of glucose and thus largely restrained N₂O production from nitrification and denitrification. The synergism between algae and bacteria was also conducive to an enhanced N₂O reduction by denitrification and reduced direct/indirect carbon emissions.

Quantitative discrimination of algae multi-impacts on N2O emissions in eutrophic lakes: Implications for N2O budgets and mitigation

It is generally accepted that eutrophic lakes significantly contribute to nitrous oxide (N₂O) emissions. However, how these emissions are affected by the formation, disappearance, and mechanisms of algal blooms in these lakes has not been systematically investigated. This study examined and determined the relative contribution of spatiotemporal N₂O production pathways in hypereutrophic Lake Taihu. Synchronously, the multi-impacts of algae on N₂O production and release potential were measured in the field and in microcosms using isotope ratios of oxygen (δ¹⁸O) and bulk nitrogen (δ¹⁵N) to N₂O and to intramolecular ¹⁵N site preference (SP). Results showed that N₂O production in Lake Taihu was derived from microbial effects (nitrification and incomplete denitrification) and water air exchanges. N₂O production was also affected by the N₂O reduction process. The mean dissolved N₂O concentrations in the water column during the pre-outbreak, outbreak, and decay stages of algae accumulation were almost the same (0.05 μmol·L^-1), which was 2-10 times higher than in lake areas algae was not accumulating. However, except for the central lake area, all surveyed areas (with and without accumulated algae) displayed strong release potential and acted as the emission source because of dissolved N₂O supersaturation in the water column. The mean N₂O release fluxes during the pre-outbreak, outbreak, and decay stages of algae accumulation areas were 17.95, 26.36, and 79.32 μmol·m^-2·d^-1, respectively, which were 2.0-7.5 times higher than the values in the non-algae accumulation areas. In addition, the decay and decomposition of algae released large amounts of nutrients and changed the physiochemical properties of the water column. Additionally, the increased algae biomass promoted N₂O release and improved the proportion of N₂O produced via denitrification process to being 9.8-20.4% microbial-derived N₂O. This proportion became higher when the N₂O consumption during denitrification was considered as evidenced by isotopic data. However, when the algae biomass was excessive in hypereutrophic state, the algae decomposition also consumed a large amount of oxygen, thus limiting the N₂O production due to complete denitrification as well as due to the limited substrate supply of nitrate by nitrification in hypoxic or anoxic conditions. Further, the excessive algae accumulation on the water surface reduced N₂O release fluxes via hindering the migration of the dissolved N₂O into the atmosphere. These findings provide a new perspective and understanding for accurately evaluating N₂O release fluxes driven by algae processes in eutrophic lakes.

Animal board invited review: Opportunities and challenges in using GWP* to report the impact of ruminant livestock on global temperature change

Ruminant livestock is a large contributor of CH4 emissions globally. Assessing how this CH4 and other greenhouse gases (GHG) from livestock contribute to anthropogenic climate change is key to understanding their role in achieving any temperature targets. The climate impacts of livestock, as well as other sectors or products/services, are generally expressed as CO2-equivalents using 100-year Global Warming Potentials (GWP100). However, the GWP100 cannot be used to translate emission pathways of short-lived climate pollutants (SLCPs) emissions to their temperature outcomes. A key limitation of handling long- and short-lived gases in the same manner is revealed in the context of any potential temperature stabilisation goals: to achieve this outcome, emissions of long-lived gases must decline to net-zero, but this is not the case for SLCPs. A recent alternative metric, GWP* (so-called 'GWP-star'), has been proposed to overcome these concerns. GWP* allows for simple appraisals of warming over time for emission series of different GHGs that may not be obvious if using pulse-emission metrics (i.e. GWP100). In this article, we explore some of the strengths and limitations of GWP* for reporting the contribution of ruminant livestock systems to global temperature change. A number of case studies are used to illustrate the potential use of the GWP* metric to, for example, understand the current contribution of different ruminant livestock production systems to global warming, appraise how different production systems or mitigations compare (having a temporal element), and seeing how possible emission pathways driven by changes in production, emissions intensity and gas composition show different impacts over time. We suggest that for some contexts, particularly if trying to directly infer contributions to additional warming, GWP* or similar approaches can provide important insight that would not be gained from conventional GWP100 reporting.

DksA, ppGpp, and RegAB Regulate Nitrate Respiration in Paracoccus denitrificans

The periplasmic (NAP) and membrane-associated (Nar) nitrate reductases of Paracoccus denitrificans are responsible for nitrate reduction under aerobic and anaerobic conditions, respectively. Expression of NAP is elevated in cells grown on a relatively reduced carbon and energy source (such as butyrate); it is believed that NAP contributes to redox homeostasis by coupling nitrate reduction to the disposal of excess reducing equivalents. Here, we show that deletion of either dksA1 (one of two dksA homologs in the P. denitrificans genome) or relA/spoT (encoding a bifunctional ppGpp synthetase and hydrolase) eliminates the butyrate-dependent increase in nap promoter and NAP enzyme activity. We conclude that ppGpp likely signals growth on a reduced substrate and, together with DksA1, mediates increased expression of the genes encoding NAP. Support for this model comes from the observation that nap promoter activity is increased in cultures exposed to a protein synthesis inhibitor that is known to trigger ppGpp synthesis in other organisms. We also show that, under anaerobic growth conditions, the redox-sensing RegAB two-component pair acts as a negative regulator of NAP expression and as a positive regulator of expression of the membrane-associated nitrate reductase Nar. The dksA1 and relA/spoT genes are conditionally synthetically lethal; the double mutant has a null phenotype for growth on butyrate and other reduced substrates while growing normally on succinate and citrate. We also show that the second dksA homolog (dksA2) and relA/spoT have roles in regulation of expression of the flavohemoglobin Hmp and in biofilm formation. IMPORTANCE Paracoccus denitrificans is a metabolically versatile Gram-negative bacterium that is used as a model for studies of respiratory metabolism. The organism can utilize nitrate as an electron acceptor for anaerobic respiration, reducing it to dinitrogen via nitrite, nitric oxide, and nitrous oxide. This pathway (known as denitrification) is important as a route for loss of fixed nitrogen from soil and as a source of the greenhouse gas nitrous oxide. Thus, it is important to understand those environmental and genetic factors that govern flux through the denitrification pathway. Here, we identify four proteins and a small molecule (ppGpp) which function as previously unknown regulators of expression of enzymes that reduce nitrate and oxidize nitric oxide.

Identification of Fungal and Bacterial Denitrification Inhibitors Targeting Copper Nitrite Reductase

The usage of nitrification inhibitors is one of the strategies that reduce or slow down the denitrification process to prevent nitrogen loss to the atmosphere in the form of N₂O. Directly targeting microbial denitrification could be one of the mitigation strategies; however, until now little efforts have been devoted toward the development of denitrification inhibitors. Here, we have identified small-molecule inhibitors of one of the proteins involved in the fungal denitrification pathway. Specifically, virtual screening was employed to identify the inhibitors of copper-containing nitrite reductase (FoNirK) of the filamentous fungus Fusarium oxysporum. Three series of chemical compounds were identified, out of which compounds belonging to two chemical scaffolds inhibited FoNirK enzymatic activity in low micromolar ranges. Several compounds also displayed moderate inhibition of fungal denitrification activity in vivo. Evaluation of in vitro activity against NirK from denitrifying bacterium Achromobacter xylosoxidans (AxNirK) and in vivo bacterial denitrification revealed a similar inhibitory profile.