The pH dependency of N-converting enzymatic processes, pathways and microbes: effect on net N2O production

Organic fertilization reduces nitrous oxide emission by altering nitrogen cycling microbial guilds favouring complete denitrification at soil aggregate scale

Agricultural management practices can induce changes in soil aggregation structure that alter the microbial nitrous oxide (N2O) production and reduction processes occurring at the microscale, leading to large-scale consequences for N2O emissions. However, the mechanistic understanding of how organic fertilization affects these context-dependent small-scale N2O emissions and associated key nitrogen (N) cycling microbial communities is lacking. Here, denitrification gas (N2O, N2) and potential denitrification capacity N2O/(N2O + N2) were assessed by automated gas chromatography in different soil aggregates (>2 mm, 2-0.25 and <0.25 mm), while associated microbial communities were assessed by sequencing and qPCR of N2O-producing (nirK and nirS) and reducing (nosZ clade I and II) genes. The results indicated that organic fertilization reduced N2O emissions by enhancing the conversion of N2O to N2 in all aggregate sizes. Moreover, potential N2O production and reduction hotspots occurred in smaller soil aggregates, with the degree depending on organic fertilizer type and application rate. Further, significantly higher abundance and diversity of nosZ clades relative to nirK and nirS revealed complete denitrification promoted through selection of denitrifying communities at microscales favouring N2O reduction. Communities associated with high and low emission treatments form modules with specific sequence types which may be diagnostic of emission levels. Taken together, these findings suggest that organic fertilizers reduced N2O emissions through influencing soil factors and patterns of niche partitioning between N2O-producing and reducing communities within soil aggregates, and selection for communities that overall are more likely to consume than emit N2O. These findings are helpful in strengthening the ability to predict N2O emissions from agricultural soils under organic fertilization as well as contributing to the development of net-zero carbon strategies for sustainable agriculture.

Sustained bacterial N2O reduction at acidic pH

Nitrous oxide (N2O) is a climate-active gas with emissions predicted to increase due to agricultural intensification. Microbial reduction of N2O to dinitrogen (N2) is the major consumption process but microbial N2O reduction under acidic conditions is considered negligible, albeit strongly acidic soils harbor nosZ genes encoding N2O reductase. Here, we study a co-culture derived from acidic tropical forest soil that reduces N2O at pH 4.5. The co-culture exhibits bimodal growth with a Serratia sp. fermenting pyruvate followed by hydrogenotrophic N2O reduction by a Desulfosporosinus sp. Integrated omics and physiological characterization revealed interspecies nutritional interactions, with the pyruvate fermenting Serratia sp. supplying amino acids as essential growth factors to the N2O-reducing Desulfosporosinus sp. Thus, we demonstrate growth-linked N2O reduction between pH 4.5 and 6, highlighting microbial N2O reduction potential in acidic soils.

Enhancing the relative abundance of comammox nitrospira in ammonia oxidizer community decreases N2O emission in nitrification exponentially

Comammox Nitrospira and canonical ammonia-oxidizing bacteria (cAOB) generally coexist in activated sludge. In present study, the effect of comammox Nitrospira on N2O production during nitrification of activated sludge was investigated. Comammox Nitrospira and cAOB were separately enriched in two nitrifying reactors, with respective relative abundance of approximately 98% in ammonia oxidizer community. The N2O emission factor (EF) of nitrification in comammox Nitrospira dominated reactor was 0.35%, consistently lower than that (2.2%) in cAOB dominated reactor. When increasing the relative abundance of comammox Nitrospira in ammonia oxidizer community, the N2O EF of nitrification decreased exponentially, which suggested that comammox Nitrospira not only decreased N2O production directly but also might have reduced N2O yield by cAOB. When cAOB dominated the ammonia oxidizer community of sludge, decreasing pH to 6.3, lowering DO to less than 0.5 mg/L, and increasing nitrite concentration enhanced N2O EF dramatically. When comammox Nitrospira became the dominant ammonia oxidizer, however, the N2O EF correlated to nitrite insignificantly and a low DO of 0.2 mg/L and weakly acidic pH (6.3) decreased N2O EF by approximately 70% and 60%, respectively. These results imply that enhancing the relative abundance of comammox Nitrospira in sludge is an effective way to reducing N2O emissions and can also offset the promoting effects of acidic pH, low DO, and high nitrite concentration on N2O production during nitrification.

Partial substitution of manure increases N2O emissions in the alkaline soil but not acidic soils

The fertilization regimes of combining manure with synthetic fertilizer are benefits for crop yields and soil fertility in cropping systems as compared to sole synthetic fertilization, but the responses of nitrous oxide (N2O) emissions to these practices are inconsistent in the literatures. We hypothesized that it is caused by different proportions of nitrogen (N) applied as manure and various soil properties. Here, we conducted a microcosm experiment, and measured the N2O emissions from control (no N) and five manure substitution treatments (supplied 100 mg N kg-1 using the combination of urea with manure) with a range of proportions of N applied as manure (0, 25%, 50%, 75%, and 100%) in three different soil types (fluvo-aquic soil, black soil, and latosol) under aerobic condition. The stimulated effect on N2O emissions was more pronounced after manure application in an alkaline soil with high nitrification rate, due to relatively rapid soil DOC depletion and N mineralization of manure. N2O emissions from partial substitution of urea with manure were significantly higher than manure-only addition under high soil pH due to abundant labile C from manure. However, there was no difference between manure substitution treatments under acid soils. Nitrification inhibitor substantially decreased N2O emissions with increasing soil pH, but it was less effective in mitigating N2O emissions with larger proportion of manure. This is likely due to the slow nitrification under low soil pH, and denitrification derived N2O increased with increasing manure application rate. Collectively, our study shows that the application of manure substitution to alkaline soils requires careful consideration, which might have rapid nitrification potential and hence trigger significant N2O emissions. The knowledge gained in this work will help the decision-makers in optimizing a sound N fertilization regime interacted with soil properties for sustainable crop production and N2O mitigation.

Microbial Sources and Sinks of Nitrous Oxide during Organic Waste Composting

Composting is widely used for organic waste management and is also a major source of nitrous oxide (N2O) emission. New insight into microbial sources and sinks is essential for process regulation to reduce N2O emission from composting. This study used genome-resolved metagenomics to decipher the genomic structures and physiological behaviors of individual bacteria for N2O sources and sinks during composting. Results showed that several nosZ-lacking denitrifiers in feedstocks drove N2O emission at the beginning of the composting. Such emission became negligible at the thermophilic stage, as high temperatures inhibited all denitrifiers for N2O production except for those containing nirK. The nosZ-lacking denitrifiers were notably enriched to increase N2O production at the cooling stage. Nevertheless, organic biodegradation limited energy availability for chemotaxis and flagellar assembly to restrain nirKS-containing denitrifiers for nitrate reduction toward N2O sources but insignificantly interrupt norBC- and nosZ-containing bacteria (particularly nosZ-containing nondenitrifiers) for N2O sinks by capturing N2O and nitric oxide (NO) for energy production, thereby reducing N2O emission at the mature stage. Furthermore, nosZII-type bacteria included all nosZ-containing nondenitrifiers and dominated N2O sinks. Thus, targeted strategies can be developed to restrict the physiological behaviors of nirKS-containing denitrifiers and expand the taxonomic distribution of nosZ for effective N2O mitigation in composting.

Urea amendment decouples nitrification in hydrocarbon contaminated Antarctic soil

Hydrocarbon contaminated soils resulting from human activities pose a risk to the natural environment, including in the Arctic and Antarctic. Engineered biopiles constructed at Casey Station, Antarctica, have proven to be an effective strategy for remediating hydrocarbon contaminated soils, with active ex-situ remediation resulting in significant reductions in hydrocarbons, even in the extreme Antarctic climate. However, the use of urea-based fertilisers, whilst providing a nitrogen source for bioremediation, has also altered the natural soil chemistry leading to increases in pH, ammonium and nitrite. Monitoring of the urea amended biopiles identified rising levels of nitrite to be of particular interest, which misaligns with the long term goal of reducing contaminant levels and returning soil communities to a 'healthy' state. Here, we combine amplicon sequencing, microfluidic qPCR on field samples and laboratory soil microcosms to assess the impact of persistent nitrite accumulation (up to 60 months) on nitrifier abundances observed within the Antarctic biopiles. Differential inhibition of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) Nitrobacter and Nitrospira in the cold, urea treated, alkaline soils (pH 8.1) was associated with extensive nitrite accumulation (76 ± 57 mg N/kg at 60 months). When the ratio of Nitrospira:AOB dropped below ∼1:1, Nitrobacter was completely inhibited or absent from the biopiles, and nitrite accumulated. Laboratory soil microcosms (incubated at 7 °C and 15 °C for 9 weeks) reproduced the pattern of nitrite accumulation in urea fertilized soil at the lower temperature, consistent with our longer-term observations from the Antarctic biopiles, and with other temperature-controlled microcosm studies. Diammonium phosphate amended soil did not exhibit nitrite accumulation, and could be a suitable alternative biostimulant to avoid excessive nitrite build-up.

Digestate induces significantly higher N2O emission compared to urea under different soil properties and moisture

Digestate is considered as an option for recycling resources and a part of the substitution for chemical fertilizers to reduce environmental impacts. However, its application may lead to significant nitrous oxide (N2O) emissions because of its high concentration of ammonium and degradable carbon. The research objectives are to evaluate how N2O emissions respond to digestate as compared to urea application and whether this depends on soil properties and moisture. Either digestate or urea (100 mg N kg-1) was applied with and without a nitrification inhibitor of 3,4-dimethylpyrazole phosphate (DMPP) to three soil types (fluvo-aquic soil, black soil, and latosol) under three different soil moisture conditions (45, 65, and 85% water-filled pore space (WFPS)) through microcosm incubations. Results showed that digestate- and urea-induced N2O emissions increased exponentially with soil moisture in the three studied soils, and the magnitude of the increase was much greater in the alkaline fluvo-aquic soil, coinciding with high net nitrification rate and transient nitrite accumulation. Compared with urea-amended soils, digestate led to significantly higher peaks in N2O and carbon dioxide (CO2) emissions, which might be due to stimulated rapid oxygen consumption and mineralized N supply. Digestate-induced N2O emissions were all more than one time higher than those induced by urea at the three moisture levels in the three studied soils, except at 85% WFPS in the fluvo-aquic soil. DMPP was more effective at mitigating N2O emissions (inhibitory efficacy: 73%-99%) in wetter digestate-fertilized soils. Overall, our study shows the contrasting effect of digestate to urea on N2O emissions under different soil properties and moisture levels. This is of particular value for determining the optimum of applying digestate under varying soil moisture conditions to minimize stimulated N2O emissions in specific soil properties.

pH selects for distinct N2O-reducing microbiomes in tropical soil microcosms

Nitrous oxide (N2O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N2O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N2O reduction has remained elusive. Acidic (pH < 5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02 mM) and high (2 mM) N2O assessed N2O reduction at pH 4.5 and 7.3. All microcosms consumed N2O, with lag times of up to 7 months observed in microcosms with 2 mM N2O. Comparative metagenome analysis revealed that Rhodocyclaceae dominated in circumneutral microcosms under both N2O feeding regimes. At pH 4.5, Peptococcaceae dominated in high-N2O, and Hyphomicrobiaceae in low-N2O microcosms. Seventeen high-quality metagenome-assembled genomes (MAGs) recovered from the N2O-reducing microcosms harbored nos operons, with all eight MAGs derived from acidic microcosms carrying the Clade II type nosZ and lacking nitrite reductase genes (nirS/K). Five of the eight MAGs recovered from pH 4.5 microcosms represent novel taxa indicating an unexplored N2O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that nosZ genes commonly occur, suggesting broad distribution of N2O reduction potential in acidic soils.

Decoupling the simultaneous effects of NO2-, pH and free nitrous acid on N2O and NO production from enriched nitrifying activated sludge

In the pursuit of energy and carbon neutrality, nitrogen removal technologies have been developed featuring nitrite (NO2-) accumulation. However, high NO2- accumulations are often associated with stimulated greenhouse gas (i.e., nitrous oxide, N2O) emissions. Furthermore, the coexistence of free nitrous acid (FNA) formed by NO2- and proton (pH) makes the consequence of NO2- accumulation on N2O emissions complicated. The concurrent three factors, NO2-, pH and FNA may play different roles on N2O and nitric oxide (NO) emissions simultaneously, which has not been systematically studied. This study aims to decouple the effects of NO2- (0-200 mg N/L), pH (6.5-8) and FNA (0-0.15 mg N/L) on the N2O and NO production rates and the production pathways by ammonia oxidizing bacteria (AOB), with the use of a series of precisely executed batch tests and isotope site-preference analysis. Results suggested the dominant factors affecting the N2O production rate were NO2- and FNA concentrations, while pH alone played a relatively insignificant role. The most influential factor shifted from NO2- to FNA as FNA concentrations increased from 0 to 0.15 mg N/L. At concentrations below 0.0045 mg HNO2-N/L, nitrite rather than FNA played a significant role stimulating N2O production at elevated nitrite concentrations. The inhibition effect of FNA emerged with further increase of FNA between 0.0045-0.015 mg HNO2-N/L, weakening the promoting effect of increased nitrite. While at concentrations above 0.015 mg HNO2-N/L, FNA inhibited N2O production especially from nitrifier denitrification pathway with the level of inhibition linearly correlated with the FNA concentration. pH and the nitrite concentration regulated the production pathways, with elevated pH promoting the nitrifier nitrification pathway, while elevated NO2- concentrations promoting the nitrifier denitrification pathway. In contrast to N2O, NO emission was less susceptible to FNA at concentrations up to 0.015 mg N/L but was stimulated by increasing NO2- concentrations. This study, for the first time, distinguished the effects of pH, NO2- and FNA on N2O and NO production, thereby providing support to the design and operation of novel nitrogen removal systems with NO2- accumulation.

Nitrification in acidic and alkaline environments

Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.

Ligneous amendments increase soil organic carbon content in fine-textured boreal soils and modulate N2O emissions

Organic soil amendments are used to improve soil quality and mitigate climate change. However, their effects on soil structure, nutrient and water retention as well as greenhouse gas (GHG) emissions are still poorly understood. The purpose of this study was to determine the residual effects of a single field application of four ligneous soil amendments on soil structure and GHG emissions. We conducted a laboratory incubation experiment using soil samples collected from an ongoing soil-amendment field experiment at Qvidja Farm in south-west Finland, two years after a single application of four ligneous biomasses. Specifically, two biochars (willow and spruce) produced via slow pyrolysis, and two mixed pulp sludges from paper industry side-streams were applied at a rate of 9-22 Mg ha-1 mixed in the top 0.1 m soil layer. An unamended fertilized soil was used as a control. The laboratory incubation lasted for 33 days, during which the samples were kept at room temperature (21°C) and at 20%, 40%, 70% or 100% water holding capacity. Carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4) fluxes were measured periodically after 1, 5, 12, 20 and 33 days of incubation. The application of ligneous soil amendments increased the pH of the sampled soils by 0.4-0.8 units, whereas the effects on soil organic carbon content and soil structure varied between treatments. The GHG exchange was dominated by CO2 emissions, which were mainly unaffected by the soil amendment treatments. The contribution of soil CH4 exchange was negligible (nearly no emissions) compared to soil CO2 and N2O emissions. The soil N2O emissions exhibited a positive exponential relationship with soil moisture. Overall, the soil amendments reduced N2O emissions on average by 13%, 64%, 28%, and 37%, at the four soil moisture levels, respectively. Furthermore, the variation in N2O emissions between the amendments correlated positively with their liming effect. More specifically, the potential for the pulp sludge treatments to modulate N2O emissions was evident only in response to high water contents. This tendency to modulate N2O emissions was attributed to their capacity to increase soil pH and influence soil processes by persisting in the soil long after their application.

Study on diversity, nitrogen-fixing capacity, and heavy metal tolerance of culturable Pongamia pinnata rhizobia in the vanadium-titanium magnetite tailings

Introduction

The diversity, nitrogen-fixing capacity and heavy metal tolerance of culturable rhizobia in symbiotic relationship with Pongamia pinnata surviving in vanadium (V) - titanium (Ti) magnetite (VTM) tailings is still unknown, and the rhizobia isolates from the extreme barren VTM tailings contaminated with a variety of metals would provide available rhizobia resources for bioremediation.

Methods

P. pinnata plants were cultivated in pots containing the VTM tailings until root nodules formed, and then culturable rhizobia were isolated from root nodules. The diversity, nitrogen-fixing capacity and heavy metal tolerance of rhizobia were performed.

Results

Among 57 rhizobia isolated from these nodules, only twenty strains showed different levels of tolerance to copper (Cu), nickel (Ni), manganese (Mn) and zinc (Zn), especially strains PP1 and PP76 showing high tolerance against these four heavy metals. Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens and one as Rhizobium pisi. Some rhizobia isolates showed a high nitrogen-fixing capacity and promoted P. pinnata growth by increasing nitrogen content by 10%-145% in aboveground plant part and 13%-79% in the root. R. pachyrhizi PP1 showed the strongest capacity of nitrogen fixation, plant growth promotion and resistance to heavy metals, which provided effective rhizobia strains for bioremediation of VTM tailings or other contaminated soils. This study demonstrated that there are at least three genera of culturable rhizobia in symbiosis with P. pinnata in VTM tailings.

Discussion

Abundant culturable rhizobia with the capacity of nitrogen fixation, plant growth promotion and resistance to heavy metals survived in VTM tailings, indicating more valuable functional microbes could be isolated from extreme soil environments such as VTM tailings.

Aerobic biodegradation of quinoline under denitrifying conditions in membrane-aerated biofilm reactor

Aerobic denitrification is being investigated as a novel biological nitrogen removal process, yet the knowledge on aerobic denitrification is limited to pure culture isolations and its occurrence in bioreactors remains unclear. This study investigated the feasibility and capacity of applying aerobic denitrification in membrane aerated biofilm reactor (MABR) for biological treatment of quinoline-laden wastewater. Stable and efficient removals of quinoline (91.5 ± 5.2%) and nitrate (NO₃^-) (86.5 ± 9.3%) were obtained under different operational conditions. Enhanced formation and function of extracellular polymeric substances (EPS) were observed at increasing quinoline loadings. MABR biofilm was highly enriched with aerobic quinoline-degrading bacteria, with a predominance of Rhodococcus (26.9 ± 3.7%) and secondary abundance of Pseudomonas (1.7 ± 1.2%) and Comamonas (0.94 ± 0.9%). Metagenomic analysis indicated that Rhodococcus contributed significantly to both aromatic degradation (24.5 ± 21.3%) and NO₃^- reduction (4.5 ± 3.9%), indicating its key role in aerobic denitrifying quinoline biodegradation. At increasing quinoline loadings, abundances of aerobic quinoline degradation gene oxoO and denitrifying genes of napA, nirS and nirK increased; there was a significant positive correlation of oxoO with nirS and nirK (p < 0.05). Aerobic quinoline degradation was likely initiated by hydroxylation, encoded by oxoO, followed by stepwise oxidations through 5,6-dihydroxy-1H-2-oxoquinoline or 8-hydroxycoumarin pathway. The results advance our understanding of quinoline degradation during biological nitrogen removal, and highlight the potential implementation of aerobic denitrification driven quinoline biodegradation in MABR for simultaneous removal of nitrogen and recalcitrant organic carbon from coking, coal gasification and pharmaceutical wastewaters.

Effect of low temperature on contributions of ammonia oxidizing archaea and bacteria to nitrous oxide in constructed wetlands

Constructed wetlands (CWs) have been widely used for ecological remediation of micro-polluted source water. Nitrous oxide (N₂O) from CWs has caused great concern as a greenhouse gas. However, the contribution of ammonia oxidation driven by ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) to N₂O emission, especially at low temperature, was unknown. This study aimed to quantify the contributions of AOA and AOB to N₂O through lab-scale subsurface CWs. The N₂O emission flux of CW at 8 °C was 1.23 mg m^-2·h^-1, significantly lower than that at 25 °C (1.92 mg m^-2·h^-1). The contribution of ammonia oxidation to N₂O at 8 °C (33.04%) was significantly higher than that at 25 °C (24.17%). The N₂O production from AOA increased from 1.91 ng N·g^-1 at 25 °C to 4.11 ng N·g^-1 soil at 8 °C and its contribution increased from 23.38% to 30.18% (P < 0.05). Low temperature impaired functional gene groups and inhibited the activity of AOB, resulting in its declined contribution. Based on the transcriptional analysis, AOA was less affected by low temperature, thus stably contributing to N₂O. Moreover, community diversity and relationships of AOA were enhanced at 8 °C, while AOB declined. The results confirmed the significant contribution of AOA and demonstrated molecular mechanisms (higher activity and community stability) of the increased contribution of AOA to N₂O at low temperature.

pH-dependent microbial niches succession and antibiotic resistance genes distribution in an oxygen-based membrane biofilm reactor treating greywater

System pH is found to crucially affect biofilm growth and microorganisms' activity in the biofilm-based wastewater treatment system. This study investigated the pH-dependent pollutants removal, microbial niches succession and antibiotic resistance genes (ARGs) accumulation in an oxygen-based membrane biofilm reactor treating greywater. Results indicated that neutral conditions achieved the highest biofilm concentration and living cells, which enabled the highest pollutants removal rates; multifarious functional groups in biofilm enabled pollutants adsorption, which favored its continuous bio-removal. Microbial communities under acidic condition (pH = 5.0) were significantly different with that under other conditions (p < 0.05). The neutral and alkaline niches (pH = 7.0 and 9.0) were predominant by organics biodegradation and nitrogen reduction bacteria (e.g. Sphingobacteriales, Pseudomonas, Flavobacterium and Phenylobacterium), but which were significantly dropped under acidic conditions, leading to the declined reactor performance. ARGs in biofilm (predominant by korB, intI-1, sul1 and sul2) were much higher than that in the cell-free liquid and the target ARGs accumulation (korB, intI-1, bla_CTX-M, qnrS) had nearly linear positive relationships (R² > 0.95, P < 0.01) with biofilm-attached linear alkylbenzene sulfonate (LAS). LAS stimulate ARGs proliferation in functional microorganisms (korB, sul-1 and intI-1 were significantly associated with related microbial genus) and biofilm played a key role in ARGs dissemination. The relatively low ARGs in both biofilm and effluent under neutral conditions suggested that pH controlling can be an effective strategy to inhibit ARGs dissemination and proliferation in the system.

Denitrification for acidic wastewater treatment: Long-term performance, microbial communities, and nitrous oxide emissions

Acidic nitrogenous wastewater often requires alkali pretreatment before biological treatment, which results in increased system complexity and operating costs. The demonstration of denitrification under acidic conditions would provide a theoretical basis for the direct treatment of such wastewater. In this study, the denitrification performance, microbial community, and nitrous oxide (N₂O) emissions under acidic conditions were investigated using a sequencing batch reactor. When the influent pH decreased from 5.5 to 4.5, the sequencing batch reactor removed 99.8 ± 0.2% of the nitrate and 92.5 ± 1.6% (n = 171) of the chemical oxygen demand, and the production efficiency of N₂O increased significantly to 11.45%. This was 2.6-fold higher than that observed at pH 5.5. The long-term denitrification treatment of acidic wastewater (pH 4.5) led to the formation of granular sludge, and Thauera, Allorhizobium-Neorhizobium-Parararhizobium-Rhizobium, and Diaphorobacter became the dominant microbes with a collective abundance of 81.3%. More importantly, only 0.25% of the nitrate was denitrified as N₂O, and the batch test revealed that the emissions of N₂O decreased with the increase in sludge size. These results indicate that denitrifying granular sludge formed under acidic conditions and denitrifying bacteria capable of N₂O reduction proliferated, which both resulted in a significant reduction in the release of N₂O.

Ammonia and greenhouse emissions from cow's excreta are affected by feeding system, stage of lactation and sampling time

Decomposition of dairy cows' excreta on housing floor leads to ammonia and greenhouse gases production, yet factors affecting total emissions have not been fully disclosed. This work aimed to assess the impact of lactation stage, feeding system and sampling time on gaseous emission potential of cow's faeces and urine in laboratory chambers systems. Individual faeces and urine were collected from two groups of four cows, at peak and post peak lactation, from three commercial farms with distinct feeding systems: total mixed ration (TMR), total mixed ration plus concentrate at robot (TMR + robot), and total mixed ration plus concentrate in automatic feeders (TMR + AF). Samples were collected before a.m. (T8h), at middle day (T12h), and before p.m. (T17h) milking. In a laboratory chambers system, faeces and urine were mixed in a ratio of 1.7:1, and ammonia and greenhouse gases emissions were monitored during 48-h. Cumulative N-N₂O emissions were the highest in TMR + robot system, post peak cows and sampling time T17h. An interaction between stage of lactation and sampling time was detected for N-NH₃ and N-N₂O (g/kg organic soluble N) emissions. Post peak cows also produced the highest cumulative N-NH₃ emissions. Overall results contribute for the identification of specific on-farm strategies to reduce gaseous emissions from cows' excreta.

Interactive effects of aquatic nitrogen and plant biomass on nitrous oxide emission from constructed wetlands

Understanding of mechanisms in nitrous oxide (N₂O) emission from constructed wetland (CW) is particularly important for the establishment of related strategies to reduce greenhouse gas (GHG) production during its wastewater treatment. However, plant biomass accumulation, microbial communities and nitrogen transformation genes distribution and their effects on N₂O emission from CW as affected by different nitrogen forms in aquatic environment have not been reported. This study investigated the interactive effects of aquatic nitrogen and plant biomass on N₂O emission from subsurface CW with NH₄⁺-N (CW-A) or NO₃^--N (CW-B) wastewater. The experimental results show that NH₄⁺-N and NO₃^--N removal efficiencies from CW mesocosms were 49.4% and 87.6%, which indirectly lead to N₂O emission fluxes of CW-A and CW-B maintained at 213 ± 67 and 462 ± 71 μg-N/(m²·h), respectively. Correlation analysis of nitrogen conversion dynamic indicated that NO₂^--N accumulation closely related to N₂O emission from CW. Aquatic NH₄⁺-N could up-regulate plant biomass accumulation by intensifying citric acid cycle, glycine-serine-threonine metabolism etc., resulting in more nitrogen uptake and lower N₂O emission/total nitrogen (TN) removal ratio of CW-A compared to CW-B. Although the abundance of denitrifying bacteria and N₂O reductase nosZ in CW-B were significantly higher than that of CW-A, after fed with mixed NH₄⁺-N and NO₃^--N influent, N₂O fluxes and N₂O emission/TN removal ratio in CW-A were extremely close to that of CW-B, suggesting that nitrogen form rather than nitrogen transformation microbial communities and N₂O reductase nosZ determines N₂O emission from CW. Hence, the selection of nitrate-loving plants will play an important role in inhibiting N₂O emission from CW.

Using isotope pool dilution to understand how organic carbon additions affect N2 O consumption in diverse soils

Nitrous oxide (N2 O) is a formidable greenhouse gas with a warming potential ~300× greater than CO2 . However, its emissions to the atmosphere have gone largely unchecked because the microbial and environmental controls governing N2 O emissions have proven difficult to manage. The microbial process N2 O consumption is the only know biotic pathway to remove N2 O from soil pores and therefore reduce N2 O emissions. Consequently, manipulating soils to increase N2 O consumption by organic carbon (OC) additions has steadily gained interest. However, the response of N2 O emissions to different OC additions are inconsistent, and it is unclear if lower N2 O emissions are due to increased consumption, decreased production, or both. Simplified and systematic studies are needed to evaluate the efficacy of different OC additions on N2 O consumption. We aimed to manipulate N2 O consumption by amending soils with OC compounds (succinate, acetate, propionate) more directly available to denitrifiers. We hypothesized that N2 O consumption is OC-limited and predicted these denitrifier-targeted additions would lead to enhanced N2 O consumption and increased nosZ gene abundance. We incubated diverse soils in the laboratory and performed a 15 N2 O isotope pool dilution assay to disentangle microbial N2 O emissions from consumption using laser-based spectroscopy. We found that amending soils with OC increased gross N2 O consumption in six of eight soils tested. Furthermore, three of eight soils showed Increased N2 O Consumption and Decreased N2 O Emissions (ICDE), a phenomenon we introduce in this study as an N2 O management ideal. All three ICDE soils had low soil OC content, suggesting ICDE is a response to relaxed C-limitation wherein C additions promote soil anoxia, consequently stimulating the reduction of N2 O via denitrification. We suggest, generally, OC additions to low OC soils will reduce N2 O emissions via ICDE. Future studies should prioritize methodical assessment of different, specific, OC-additions to determine which additions show ICDE in different soils.

Light-introduced partial nitrification in an algal-bacterial granular sludge bioreactor: Performance evolution and microbial community shift

This objective of study was to evaluate the influence of light on the achievement of partial nitrification algal-bacterial granular bioreactor and its related nitrite accumulation mechanism. After 150-days operation, partial nitrification algal-bacterial granulation bioreactor was achieved under the 200 μmol/(m²·s) illuminance condition. The effluent NH₄⁺-N, NO₂^--N, NO₃^--N concentrations were average at 1.1, 61.7 and 8.0 mg/L (n = 21), respectively. The average sphericity of algal-bacterial aerobic granular sludge (AB-AGS) increased from 82.7% to 91.1%, accompanied by the significantly increased diameter. Additionally, extracellular protein increased by 1.5 times and 0.5 times higher in LB-EPS and TB-EPS of AB-AGS, respectively. According to typical cycles, N₂O emission amount reactor accounted for 2.4% of the removed nitrogen. Under the combined inhibition of light and free ammonia (FA), Nitrosomonas-related AOB (0.2% to 2.1%) were the predominant functional bacteria, whereas Nitrospira-related NOB (0.07% to below 0.01%) was fully inhibited.

Assessment and optimization of the oxygen based membrane biofilm reactor as a novel technology for source-diverted greywater treatment

The oxygen based membrane biofilm (O₂-MBfR) has been proved to be a novel technology in treating greywater (GW) and response surface methodology (RSM) was used to model the removal of chemical oxygen demand (COD) and total nitrogen (TN) with operation parameters COD/TN ratio, system pH and lumen air pressure (LAP). Results indicated that the all target single factors affect GW treatment efficiency, and the regression model with central composite design (CCD) showed good agreement with the experimental results with high R² and R2 adj values (all >0.97) for all the target responses. Statistical evaluation revealed that system pH was the most significant parameter affecting COD and TN removal, followed by COD/TN ratio and LAP. The interaction between COD/TN ratio and system pH also played an important role on the GW treatment. The optimized maximum removal of COD (96.48%) and TN (133 g N/m²-day) were achieved with the COD/TN ratio 17.76 g COD/g TN, system pH 7.10 and LAP 1.00 psi. Thus, RSM combined with CCD could be used for predicting the organics and nitrogen removal during GW treatment in the O₂-MBfR.

NosZ gene cloning, reduction performance and structure of Pseudomonas citronellolis WXP-4 nitrous oxide reductase

Nitrous oxide reductase (N₂OR) is the only known enzyme that can reduce the powerful greenhouse gas nitrous oxide (N₂O) to harmless nitrogen at the final step of bacterial denitrification. To alleviate the N₂O emission, emerging approaches aim at microbiome biotechnology. In this study, the genome sequence of facultative anaerobic bacteria Pseudomonas citronellolis WXP-4, which efficiently degrades N₂O, was obtained by de novo sequencing for the first time, and then, four key reductase structure coding genes related to complete denitrification were identified. The single structural encoding gene nosZ with a length of 1914 bp from strain WXP-4 was cloned in Escherichia coli BL21(DE3), and the N₂OR protein (76 kDa) was relatively highly efficiently expressed under the optimal inducing conditions of 1.0 mM IPTG, 5 h, and 30 °C. Denitrification experiment results confirmed that recombinant E. coli had strong denitrification ability and reduced 10 mg L⁻¹ of N₂O to N₂ within 15 h under the optimal conditions of pH 7.0 and 40 °C, its corresponding N₂O reduction rate was almost 2.3 times that of Alcaligenes denitrificans strain TB, but only 80% of that of wild strain WXP-4, meaning that nos gene cluster auxiliary gene deletion decreased the activity of N₂OR. The 3D structure of N₂OR predicted on the basis of sequence homology found that electron transfer center CuA had only five amino acid ligands, and the S2 of the catalytically active center CuZ only bound one Cu_I atom. The unique 3D structure was different from previous reports and may be closely related to the strong N₂O reduction ability of strain WXP-4 and recombinant E. coli. The findings show a potential application of recombinant E. coli in alleviating the greenhouse effect and provide a new perspective for researching the relationship between structure and function of N₂OR.

Nitrous oxide reductase (N₂OR) is the only known enzyme that can reduce the powerful greenhouse gas nitrous oxide (N₂O) to harmless nitrogen at the final step of bacterial denitrification. The recombinant E. coli and wild strain WXP-4 demonstrate strong N₂O reduction ability.

Enzymatic Methods for Salivary Biomarkers Detection: Overview and Current Challenges

Early detection is a key factor in patient fate. Currently, multiple biomolecules have been recognized as biomarkers. Nevertheless, their identification is only the starting line on the way to their implementation in disease diagnosis. Although blood is the biofluid par excellence for the quantification of biomarkers, its extraction is uncomfortable and painful for many patients. In this sense, there is a gap in which saliva emerges as a non-invasive and valuable source of information, as it contains many of the biomarkers found in blood. Recent technological advances have made it possible to detect and quantify biomarkers in saliva samples. However, there are opportunity areas in terms of cost and complexity, which could be solved using simpler methodologies such as those based on enzymes. Many reviews have focused on presenting the state-of-the-art in identifying biomarkers in saliva samples. However, just a few of them provide critical analysis of technical elements for biomarker quantification in enzymatic methods for large-scale clinical applications. Thus, this review proposes enzymatic assays as a cost-effective alternative to overcome the limitations of current methods for the quantification of biomarkers in saliva, highlighting the technical and operational considerations necessary for sampling, method development, optimization, and validation.

Sulfur-driven autotrophic denitrification of nitric oxide for efficient nitrous oxide recovery

Nitrous oxide (N₂ O) was previously deemed as a potent greenhouse gas but is actually an untapped energy source, which can accumulate during the microbial denitrification of nitric oxide (NO). Compared with the organic electron donor required in heterotrophic denitrification, elemental sulfur (S⁰ ) is a promising electron donor alternative due to its cheap cost and low biomass yield in sulfur-driven autotrophic denitrification. However, no effort has been made to test N₂ O recovery from sulfur-driven denitrification of NO so far. Therefore, in this study, batch and continuous experiments were carried out to investigate the NO removal performance and N₂ O recovery potential via sulfur-driven NO-based denitrification under various Fe(II)EDTA-NO concentrations. Efficient energy recovery was achieved, as up to 35.5%-40.9% of NO was converted to N₂ O under various NO concentrations. N₂ O recovery from Fe(II)EDTA-NO could be enhanced by the low bioavailability of sulfur and the acid environment caused by sulfur oxidation. The NO reductase (NOR) and N₂ O reductase (N₂ OR) were inhibited distinctively at relatively low NO levels, leading to efficient N₂ O accumulation, but were suppressed irreversibly at NO level beyond 15 mM in continuous experiments. Such results indicated that the regulation of NO at a relatively low level would benefit the system stability and NO removal capacity during long-term system operation. The continuous operation of the sulfur-driven Fe(II)EDTA-NO-based denitrification reduced the overall microbial diversity but enriched several key microbial community. Thauera, Thermomonas, and Arenimonas that are able to carry out sulfur-driven autotrophic denitrification became the dominant organisms with their relative abundance increased from 25.8% to 68.3%, collectively.

Physiology of the Nitrite-Oxidizing Bacterium Candidatus Nitrotoga sp. CP45 Enriched From a Colorado River

Nitrogen cycling microbes, including nitrite-oxidizing bacteria (NOB), perform critical ecosystem functions that help mitigate anthropogenic stresses and maintain ecosystem health. Activity of these beneficial nitrogen cycling microbes is dictated in part by the microorganisms’ response to physicochemical conditions, such as temperature, pH, and nutrient availability. NOB from the newly described Candidatus Nitrotoga genus have been detected in a wide range of habitats across the globe, yet only a few organisms within the genus have been physiologically characterized. For freshwater systems where NOB are critical for supporting aquatic life, Ca. Nitrotoga have been previously detected but little is known about the physiological potential of these organisms or their response to changing environmental conditions. Here, we determined functional response to environmental change for a representative freshwater species of Ca. Nitrotoga (Ca. Nitrotoga sp. CP45, enriched from a Colorado river). The physiological findings demonstrated that CP45 maintained nitrite oxidation at pH levels of 5–8, at temperatures from 4 to 28°C, and when incubated in the dark. Light exposure and elevated temperature (30°C) completely halted nitrite oxidation. Ca. Nitrotoga sp. CP45 maintained nitrite oxidation upon exposure to four different antibiotics, and potential rates of nitrite oxidation by river sediment communities were also resilient to antibiotic stress. We explored the Ca. Nitrotoga sp. CP45 genome to make predictions about adaptations to enable survival under specific conditions. Overall, these results contribute to our understanding of the versatility of a representative freshwater Ca. Nitrotoga sp. Identifying the specific environmental conditions that maximize NOB metabolic rates may ultimately direct future management decisions aimed at restoring impacted systems.

In-situ expressions of comammox Nitrospira along the Yangtze River

The recent discovery of comammox Nitrospira as complete nitrifiers has significantly enriched our understanding on the nitrogen cycle, yet little is known about their metabolic transcripts in natural aquatic ecosystems. Using the genome-centric metatranscriptomics, we provided the first in-situ expression patterns of comammox Nitrospira along the Yangtze River. Our study confirmed widespread expressions of comammox Nitrospira, with the highest transcription accounting for 33.3% and 63.8% of amoA and nxrAB genes expressed in ammonia-oxidizing prokaryotes (AOPs) and Nitrospira sublineages I/II, respectively. Moreover, comammox two clades differed in nitrification, with clade A acting as the dominator to ammonia oxidation in comammox, and clade B contributing more transcripts to nitrite oxidation than to ammonia oxidation. Compared to canonical Nitrospira, comammox community had lower expressions of ammonia/nitrite transporters and nitrogen assimilatory genes, but far higher expressions in urea transport and hydrolysis, facilitating to derivation of ammonia and energy mainly through intracellular ureolytic metabolism. This suggests no need for "reciprocal-feeding" between canonical Nitrospira and AOPs in a natural river. Aerobic mixotrophy of comammox bacteria was suggested by expressions of genes coding for respiratory complexes I-V, oxidative/reductive TCA cycle, oxygen stress defenses, and transport/catabolism of simple carbohydrates and low-biosynthetic-cost amino acids. Intriguingly, significant positive correlations among expressions of ammonia monooxygenases, hydroxylamine dehydrogenase and copper-dependent nitrite reductase indicated that comammox Nitrospira had the potential of converting nitrite to nitric oxide accompanied by ammonia oxidation under low-C/N and aerobic conditions, while gene expressions in this pathway were significantly and positively associated with pH. Overall, this study illustrated novel transcriptional characteristics of comammox Nitrospira, and highlighted the necessity of reassessing their contributions to biogeochemical carbon and nitrogen cycling with perspective of in-situ meta-omics as well as culture experiments.

Prioritize effluent quality, operational costs or global warming? - Using predictive control of wastewater aeration for flexible management of objectives in WRRFs

This study presents a general model predictive control (MPC) algorithm for optimizing wastewater aeration in Water Resource Recovery Facilities (WRRF) under different management objectives. The flexibility of the MPC is demonstrated by controlling a WRRF under four management objectives, aiming at minimizing: (A) effluent concentrations, (B) electricity consumption, (C) total operations costs (sum electricity costs and discharge effluent tax) or (D) global warming potential (direct and indirect nitrous oxide emissions, and indirect from electricity production) . The MPC is tested with data from the alternating WRRF in Nørre Snede (Denmark) and from the Danish electricity grid. Results showed how the four control objectives resulted in important differences in aeration patterns and in the concentration dynamics over a day. Controls B and C showed similarities when looking at total costs, while similarities in global warming potential for controls A and D suggest that improving effluent quality also reduced greenhouse gasses emissions. The MPC flexibility in handling different objectives is shown by using a combined objective function, optimizing both cost and greenhouse emissions. This shows the trade-off between the two objectives, enabling the calculation of marginal costs and thus allowing WRRF operators to carefully evaluate prioritization of management objectives. The long-term MPC performance is evaluated over 51 days covering seasonal and inter-weekly variations. On a daily basis, control A was 9-30% cheaper on average compared to controls A, D and to the current rule-based control. Similarly, control D resulted on average in 35-43% lower greenhouse gasses daily emission compared to the other controls. Difference between control performance increased for days with greater inter-diurnal variations in electricity price or greenhouse emissions from electricity production, i.e. when MPC has greater possibilities for exploiting input variations. The flexibility of the proposed MPC can easily accommodate for additional control objectives, allowing WRRF operators to quickly adapt the plant operation to new management objectives and to face new performance requirements.

The effect of long-term biochar amendment on N2O emissions: Experiments with N15-O18 isotopes combined with specific inhibition approaches

Numerous studies reporting a transient decrease in soil nitrous oxide (N₂O) emissions after biochar amendment have mainly used short-term experiments. Thus, long-term field trials are needed to clarify the actual impact of biochar on N₂O emissions and the underlying mechanisms. To address this, both a ¹⁵N¹⁸O labeling technique and gene analyses were applied to investigate how N₂O production pathways and microbial mediation were affected by long term biochar amendment in field. Then, 1-octyne and 2-phenyl l-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) were used in combination with potassium chlorate to evaluate the relative contribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to potential ammonia oxidation (PAO) and the associated N₂O production. Acidic and alkaline greenhouse vegetable soils that had each received two separate treatments were collected (control, no biochar amendment; biochar, biochar amended in the field after 2 or 7 years). The results showed that biochar decreased N₂O emissions by 48% in acidic soils and by 22% in alkaline soils compared to those in control. These results were explained by decreases in nitrifier denitrification- (by 74%) and heterotrophic denitrification-derived N₂O production (by 58%), as further evidenced by a decrease in NO₂^- (by 87%) and the (nirK+nirS+fungal nirK):(nosZ-I + nosZ-II) ratio (by 5%) in both greenhouse vegetable soils. However, biochar increased nitrifier nitrification-derived N₂O in both soils because of increases in pH and PAO, which were attributed to an increased abundance of AOB rather than AOA. The contribution of AOB to PAO (or N₂O) exceeded 69% (or 68%) of the total in acidic soil and 88% (or 85%) of the total in alkaline soil after biochar amendment. Our findings demonstrated that the mitigation of N₂O by biochar is linked to specific N₂O production pathways.

Nitrous oxide emission in a laboratory anoxic-oxic process at different influent pHs: Generation pathways and the composition and function of bacterial community

This study focused on the nitrous oxide (N₂O) generation from the biological nitrogen removal process under different pH levels. To explore a pH optimum, the online N₂O emission and the bacterial composition and function in the anoxic-oxic process were investigated. The mean gaseous N₂O emission accounted for 0.329%, 0.103%, 0.085%, and 0.793% of the influent total nitrogen at pH of 5, 6, 8, and 9, respectively. Incomplete oxidation in oxic tanks was the primary source of N₂O, while N₂O in the anoxic tank was mainly generated by nitrifier denitrification. No direct correlations were observed between N₂O emission and potential nitrifiers and denitrifiers. The impacts of pH on N₂O generation were more likely related to the response of bacterial enzymes and nitrogen compounds, rather than the feedback of bacterial community structure itself. Above all, an influent pH range of 6-8 is recommended for nitrogen removal and N₂O mitigation in anoxic-oxic process.

Optimization of the Aeration Strategies in a Deammonification Sequencing Batch Reactor for Efficient Nitrogen Removal and Mitigation of N2O Production

In deammonification systems, nitrite-oxidizing bacteria (NOB) suppression and nitrous oxide (N₂O) mitigation are two important operational objectives. To carry out this multivariable analysis of response, a comprehensive model for the N cycle was developed and evaluated against experimental data from a laboratory-scale deammonification granular sludge sequencing batch reactor. Different aeration strategies were tested, and the manipulated variables comprised the dissolved oxygen (DO) set point in the aerated phase, aeration on/off frequency (F), and the ratio (R) between the non-aerated and aerated phase durations. Experimental results showed that a high ammonium utilization rate (AUR) in relation to the low nitrate production rate (NPR) (NPR/AUR = 0.07-0.08) and limited N₂O emissions (E_N2O < 2%) could be achieved at the DO set point = 0.7 mg O₂/L, R ratio = 2, and F frequency = 6-7 h^-1. Under specific operational conditions (biomass concentration, NH₄⁺-N loading rate, and temperature), simulation results confirmed the feasible aeration strategies for the trade-offs between the NOB suppression and N₂O emission. The intermittent aeration regimes led to frequent shifts in the predominating N₂O production pathways, that is, hydroxylamine (NH₂OH) oxidation (aerated phase) versus autotrophic denitrification (non-aerated phase). The inclusion of the extracellular polymeric substance mechanism in the model explained the observed activity of heterotrophs, especially Anaerolineae, and granule formation.

Co-association of Two nir Denitrifiers Under the Influence of Emergent Macrophytes

Diverse microorganisms perform similar metabolic process in biogeochemical cycles, whereas they are found of highly genomic differentiation. Biotic interactions should be considered in any community survey of these functional groups, as they contribute to community assembly and ultimately alter ecosystem properties. Current knowledge has mainly been achieved based on functional community characterized by a single gene using co-occurrence network analysis. Biotic interactions between functionally equivalent microorganisms, however, have received much less attention. Herein, we propose the nirK- and nirS-type denitrifier communities represented by these two nitrite reductase (nir)-encoding genes, as model communities to investigate the potential interactions of two nir denitrifiers. We evaluated co-occurrence patterns and co-association network structures of nir denitrifier community from an emergent macrophyte-dominated riparian zone of highly active denitrification in Lake Taihu, China. We found a more segregated pattern in combined nir communities than in individual communities. Network analyses revealed a modularized structure of associating nir denitrifiers. An increased proportion of negative associations among combined communities relative to those of individual communities indicated potential interspecific competition between nirK and nirS denitrifiers. pH and NH₄⁺-N were the most important factors driving co-occurrence and mutual exclusion between nirK and nirS denitrifiers. We also showed the topological importance of nirK denitrifiers acting as module hubs for constructing entire association networks. We revealed previously unexplored co-association relationships between nirK and nirS denitrifiers, which were previously neglected in network analyses of individual communities. Using nir denitrifier community as a model, these findings would be helpful for us to understand the biotic interactions and mechanisms underlying how functional groups co-exist in performing biogeochemical cycles.

Distribution and Diversity of Comammox Nitrospira in Coastal Wetlands of China

Complete ammonia oxidizers (comammox), able to individually oxidize ammonia to nitrate, are considered to play a significant role in the global nitrogen cycle. However, the distribution of comammox Nitrospira in estuarine tidal flat wetland and the environmental drivers affecting their abundance and diversity remain unknown. Here, we present a large-scale investigation on the geographical distribution of comammox Nitrospira along the estuarine tidal flat wetlands of China, where comammox Nitrospira were successfully detected in 9 of the 16 sampling sites. The abundance of comammox Nitrospira ranged from 4.15 × 10⁵ to 6.67 × 10⁶ copies/g, 2.21- to 5.44-folds lower than canonical ammonia oxidizers: ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Phylogenetic analysis based on the alpha subunit of the ammonia monooxygenase encoding gene (amoA) revealed that comammox Nitrospira Clade A, mainly originating from upstream river inputs, accounts for more than 80% of the detected comammox Nitrospira, whereas comammox Nitrospira clade B were rarely detected. Comammox Nitrospira abundance and dominant comammox Nitrospira OTUs varied within the estuarine samples, showing a geographical pattern. Salinity and pH were the most important environmental drivers affecting the distribution of comammox Nitrospira in estuarine tidal flat wetlands. The abundance of comammox Nitrospira was further negatively correlated with high ammonia and nitrite concentrations. Altogether, this study revealed the existence, abundance and distribution of comammox Nitrospira and the driving environmental factors in estuarine ecosystems, thus providing insights into the ecological niches of this recently discovered nitrifying consortium and their contributions to nitrification in global estuarine environments.

The effect of pH on Marinobacter hydrocarbonoclasticus denitrification pathway and nitrous oxide reductase

Increasing atmospheric concentration of N₂O has been a concern, as it is a potent greenhouse gas and promotes ozone layer destruction. In the N-cycle, release of N₂O is boosted upon a drop of pH in the environment. Here, Marinobacter hydrocarbonoclasticus was grown in batch mode in the presence of nitrate, to study the effect of pH in the denitrification pathway by gene expression profiling, quantification of nitrate and nitrite, and evaluating the ability of whole cells to reduce NO and N₂O. At pH 6.5, accumulation of nitrite in the medium occurs and the cells were unable to reduce N₂O. In addition, the biochemical properties of N₂O reductase isolated from cells grown at pH 6.5, 7.5 and 8.5 were compared for the first time. The amount of this enzyme at acidic pH was lower than that at pH 7.5 and 8.5, pinpointing to a post-transcriptional regulation, though pH did not affect gene expression of N₂O reductase accessory genes. N₂O reductase isolated from cells grown at pH 6.5 has its catalytic center mainly as CuZ(4Cu1S), while that from cells grown at pH 7.5 or 8.5 has it as CuZ(4Cu2S). This study evidences that an in vivo secondary level of regulation is required to maintain N₂O reductase in an active state.

A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea

The continuous increase of nitrous oxide (N₂O) in the atmosphere has become a global concern because of its property as a potent greenhouse gas. Given the important role of ammonia-oxidizing archaea (AOA) in ammonia oxidation and their involvement in N₂O production, a clear understanding of the knowledge on archaeal N₂O production is necessary for global N₂O mitigation. Compared to bacterial N₂O production by ammonia-oxidizing bacteria (AOB), AOA-driven N₂O production pathways are less-well elucidated. In this Critical Review, we synthesized the currently proposed AOA-driven N₂O production pathways in combination with enzymology distinction, analyzed the role of AOA species involved in N₂O production pathways, discussed the relative contribution of AOA to N₂O production in both natural and anthropogenic environments, summarized the factors affecting archaeal N₂O yield, and compared the distinctions among approaches used to differentiate ammonia oxidizer-associated N₂O production. We, then, put forward perspectives for archaeal N₂O production and future challenges to further improve our understanding of the production pathways, putative enzymes involved and potential approaches for identification in order to potentially achieve effective N₂O mitigations.

Cultivation of methanotrophic bacteria in a novel bubble-free membrane bioreactor for microbial protein production

Microbial protein is proposed as an alternative protein source with low environmental impact. Methane oxidizing bacteria are already produced at commercial scale from natural gas. However, their productivity is limited because of the creation of explosive atmospheres in the fermenters during production. This work demonstrates the applicability of bioreactors with a membrane-based gas supply via diffusion. Methanotrophic bacteria were successfully cultivated, with growth yields from 0.26 to 0.43 g-VSS g-CH₄^-1, slightly below those observed in analogous fermenters relying on bubbling. However, ammonia yields ranged from 5.2 to 6.9 g-VSS g-NH₃^-1, indicating higher nitrogen assimilation than in conventional fermenters. Indeed, protein content increased during the operational period reaching up to 51% of dry weight. The amino acid profile included the majority of the essential amino acids, demonstrating suitability as feed ingredient. Never during the operational period was an explosive atmosphere established in the reactor. Thus, bubble-free membrane bioreactors are a promising technology for microbial protein production relying on explosive gas mixtures.

Gross N2O Production Process, Not Consumption, Determines the Temperature Sensitivity of Net N2O Emission in Arable Soil Subject to Different Long-Term Fertilization Practices

Chronic amendment of agricultural soil with synthetic nitrogen fertilization and/or livestock manure has been demonstrated to enhance the feedback intensity of net N₂O emission to temperature variation (i.e., temperature sensitivity, TS). Yet few studies have explored the relevance of changes in underlying gross N₂O production and consumption processes toward explaining this phenomenon, in particular for the latter. Furthermore, the microbe-based mechanisms associated with the variation of N₂O consumption process remain largely unexplored. To address this knowledge gap, a temperature- (15, 25, and 35°C) and moisture-controlled (50% water holding capacity) microcosm incubation experiment was established using an arable soil subject to long-term addition of synthetic fertilizer (NPK), a mixture of synthetic fertilizer with livestock manure (MNPK), or with no fertilizer treatment (CT). Over the incubation time period, the C₂H₂ inhibition method was adopted to monitor reaction rates of gross N₂O production and consumption; the population sizes and community structures of nosZI- and nosZII-N₂O reducers were analyzed using quantitative PCR (Q-PCR) and terminal restriction fragment length polymorphism (T-RFLP). The results indicated that only NPK significantly increased the TS of net N₂O emission, and gross N₂O consumption process consistently occurred under all treatment combinations (temperature and fertilization) at each sampling time point. The responses of gross N₂O production and consumption processes to temperature elevation exhibited fertilization- and sampling time-dependent pattern, and the higher net N₂O production TS in the NPK treatment was underlain by its higher TS of gross production process and insensitivity of gross consumption process to temperature. The size and structure of nosZII-N₂O reducers, as well as the community structure of nosZI-N₂O reducers, were positively correlated with variation of gross N₂O production and consumption rates across all fertilization regimes. NosZII-N₂O reducer abundance was less responsive to temperature change, and its community structure less susceptible to fertilization, as compared with nosZI-N₂O reducers. Overall, our results demonstrate that the TS of the gross N₂O production process, not gross consumption, is the key step regulating the TS of net N₂O production, and both nosZI- and nosZII-N₂O clades are likely active N₂O reducers in the tested soil.

Ubiquity, diversity, and activity of comammox Nitrospira in agricultural soils

The recent discovery of complete ammonia oxidation (comammox) process in a single organism challenged the division of labor between two functional groups in the classical two-step nitrification model. However, the distribution and activity of comammox bacteria in various environments remain largely unknown. This study presented a large-scale investigation of the geographical distribution, phylogenetic diversity, and activity of comammox Nitrospira in typical agricultural soils. Among the 23 samples harvested across China, comammox Nitrospira clade A was ubiquitously detected at 4.14 × 10⁴-1.65 × 10⁷amoA gene copies/g dry soil, with 90% belonging to the subclade A2. The abundance of comammox Nitrospira clade B was two orders of magnitude lower than clade A. In all samples, comammox Nitrospira were 1-2 orders of magnitude less abundant than canonical nitrifiers, and soils with slightly high pH and C/N tended to enrich more comammox Nitrospira. Unlike canonical nitrifiers, comammox Nitrospira had sustained amoA gene transcription regardless of external ammonia supply, indicating their competitive advantage over other nitrifiers under low-ammonia conditions. When fed with 1 mM ammonium for 15 days, comammox Nitrospira in tested soils were enriched 2.36 times higher than those enriched by the same amount of nitrite, indicating their preference to utilizing ammonia as the substrate. DNA-SIP further confirmed the in situ nitrification activity of comammox Nitrospira. This study provided new insights into the broad distribution and diversity of comammox Nitrospira in agricultural soils, which could potentially play an important role in the microbial nitrogen cycle in soils.

Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies

Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N₂ O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia-based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle. Direct N₂ O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N₂ O production, vary within and between ammonia-oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N₂ O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow-release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N₂ O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N₂ O emissions.

Biochar Is Comparable to Dicyandiamide in the Mitigation of Nitrous Oxide Emissions from Camellia oleifera Abel. Fields

Research Highlights: Intensive nitrogen (N) application for agricultural purposes has substantially increased soil nitrous oxide (N2O) emissions. Agricultural soil has great potential in the reduction of N2O emissions, and applications of biochar and nitrification inhibitors may be useful for mitigating agricultural soil N2O emissions. Background and Objectives: Camellia oleifera Abel. is an important woody oil plant in China. However, intensive N input in C. oleifera silviculture has increased the risk of soil N2O emissions. As an important greenhouse gas, N2O is characterized by a global warming potential at a 100-year scale that is 265 times that of carbon dioxide. Thus, mitigation of soil N2O emissions, especially fertilized soils, will be crucial for reducing climate change. Materials and Methods: Here, we conducted an in situ study over 12 months to examine the effects of C. oleifera fruit shell-derived biochar and dicyandiamide (DCD) on soil N2O emissions from a C. oleifera field with intensive N application. Results: A three-fold increase of cumulative soil N2O emissions was observed following N application. Cumulative N2O emissions from the field with N fertilization were reduced by 36% and 44% with biochar and DCD, respectively. While N2O emissions were slightly deceased by biochar, the decrease was comparable to that by DCD. Conclusions: Results indicated that biochar may mitigate soil N2O emissions substantially and similarly to DCD under specific conditions. This result should be examined by prolonged and multi-site studies before it can be generalized to broader scales.

High NO and N2O accumulation during nitrite denitrification in lab-scale sequencing batch reactor: influencing factors and mechanism

Nitrous oxide (N₂O) accumulation in biological nitrogen removal has drawn much attention in recent years; however, nitric oxide (NO) accumulation in denitrification was rarely studied. In this study, NO and N₂O accumulation during nitrite denitrification in a lab-scale sequencing batch reactor (SBR) were investigated. Results showed that low pH (< 7) and high influent loading (> 360:90) (COD:NO₂^--N) caused serious NO and N₂O accumulation. The maximal NO accumulation of 4.96 mg L^-1 was observed at influent loading of 720:180 and the maximal N₂O accumulation of 46.29 mg L^-1 was found at pH of 6. The NO accumulation was far higher than the values reported in previous studies. In addition, the high NO accumulation could completely inhibit the activities of reductases involved in denitrification. High NO and N₂O accumulation were mainly caused by significant free nitrous acid (FNA) and NO inhibition at low pH and high influent loading. There were significant differences on NO and N₂O accumulation at different carbon to nitrogen (COD/N). Low COD/N (≤ 4) could mitigate NO accumulation, but led to high N₂O accumulation. It is speculated that NO accumulation is related to the rapid denitrification with accumulated electron in anaerobic stage at high COD/N. N₂O accumulation is attributed to intense electron competition at low COD/N. High dissolved oxygen (DO) of 4.04 mg L^-1 was detected during NO detoxification in this experiment, which is speculated to be partly caused by NO dismutation.

Long-term harvesting of reeds affects greenhouse gas emissions and microbial functional genes in alkaline wetlands

Reed (Phragmites australis) is dominant vegetation in alkaline wetlands that is harvested annually due to its economic value. To reveal the effects of harvesting reeds on the emission of greenhouse gases (GHG), the annual soil physicochemical characteristics and flux of GHGs in a reed wetland without harvesting (NHRW) and with harvesting (HRW) were measured. The results showed that after the harvesting of reeds, the total organic carbon (TOC) and total nitrogen (TN) significantly decreased, and soil temperature significantly increased. The annual cumulative N₂O emissions decreased from 0.73 ± 0.20 kg ha^-1 to -0.57 ± 0.49 kg ha^-1 with the harvesting of reeds. The annual cumulative CH₄ emissions also decreased from 561.88 ± 18.61 kg ha^-1 to 183.13 ± 18.77 kg ha^-1 with the harvesting of reeds. However, harvesting of reeds had only a limited influence on the annual cumulative CO₂ emissions. A Pearson correlation analysis revealed that the CO₂ and N₂O emissions were more sensitive to temperature than the CH₄ emissions. Both structural equation modeling (SEM) analysis and slurry incubation confirmed that higher temperatures offset the reduction of CO₂ emissions after reed harvesting. Metagenomics showed that the abundance of functional genes involved in both GHG sink and source decreased with reed harvesting. This study presents a comprehensive view of reed harvesting on GHG emissions in alkaline wetlands, yielding new insight into the microbial response and offering a novel perspective on the potential impacts of wetland management.

The effect of pH on N2O production in intermittently-fed nitritation reactors

The effect of pH on nitrous oxide (N₂O) production rates was quantified in an intermittently-fed lab-scale sequencing batch reactor performing high-rate nitritation. N₂O and other nitrogen (N) species (e.g. ammonium (NH₄⁺), nitrite, hydroxylamine and nitric oxide) were monitored to identify in-cycle dynamics and determine N conversion rates at controlled pH set-points (6.5, 7, 7.5, 8 and 8.5). Operational conditions and microbial compositions remained similar during long-term reactor-scale pH campaigns. The specific ammonium removal rates and nitrite accumulation rates varied little with varying pH levels (p > 0.05). The specific net N₂O production rates and net N₂O yield of NH₄⁺ removed (ΔN₂O/ΔNH₄⁺) increased up to seven-fold from pH 6.5 to 8, and decreased slightly with further pH increase to 8.5 (p < 0.05). Best-fit model simulations predicted nitrifier denitrification as the dominant N₂O production pathway (≥87% of total net N₂O production) at all examined pH. Our study highlights the effect of pH on biologically mediated N₂O emissions in nitrogen removal systems and its importance in the design of N₂O mitigation strategies.

Coal chemical reverse osmosis concentrate treatment by membrane-aerated biofilm reactor system

Coal chemical reverse osmosis concentrate (ROC), which is characterized by high salinity and high organics, remains as a serious environmental problem. In this study, a lab-scale three-stage membrane-aerated biofilm reactor (MABR) system was designed to treat such a ROC. The effects of influent salinity and operating parameters (pH, DO and HRT) on the treatment efficiency were discussed. The removal efficiencies of COD, NH₄-N and TN under the optimal operating parameters reached to 81.01%, 92.31% and 70.72%, respectively. Simultaneous nitrification and denitrification (SND) as well as shortcut nitrogen removal were achieved. The salinity less than 3% did not induce significant decrease in treatment efficiency and microbial communities. Moreover, the dominant phyla in biofilms were Proteobacteria and Bacteroidetes. This work demonstrated MABR had great potential in ROC treatment.