Expression of nitrite reductase in Nitrosomonas europaea involves NsrR, a novel nitrite-sensitive transcription repressor

AOB Nitrosospira cluster 3a.2 (D11) dominates N2O emissions in fertilised agricultural soils

Ammonia-oxidation process directly contribute to soil nitrous oxide (N2O) emissions in agricultural soils. However, taxonomy of the key nitrifiers (within ammonia oxidising bacteria (AOB), archaea (AOA) and complete ammonia oxidisers (comammox Nitrospira)) responsible for substantial N2O emissions in agricultural soils is unknown, as is their regulation by soil biotic and abiotic factors. In this study, cumulative N2O emissions, nitrification rates, abundance and community structure of nitrifiers were investigated in 16 agricultural soils from major crop production regions of China using microcosm experiments with amended nitrogen (N) supplemented or not with a nitrification inhibitor (nitrapyrin). Key nitrifier groups involved in N2O emissions were identified by comparative analyses of the different treatments, combining sequencing and random forest analyses. Soil cumulative N2O emissions significantly increased with soil pH in all agricultural soils. However, they decreased with soil organic carbon (SOC) in alkaline soils. Nitrapyrin significantly inhibited soil cumulative N2O emissions and AOB growth, with a significant inhibition of the AOB Nitrosospira cluster 3a.2 (D11) abundance. One Nitrosospira multiformis-like OTU phylotype (OTU34), which was classified within the AOB Nitrosospira cluster 3a.2 (D11), had the greatest importance on cumulative N2O emissions and its growth significantly depended on soil pH and SOC contents, with higher growth at high pH and low SOC conditions. Collectively, our results demonstrate that alkaline soils with low SOC contents have high N2O emissions, which were mainly driven by AOB Nitrosospira cluster 3a.2 (D11). Nitrapyrin can efficiently reduce nitrification-related N2O emissions by inhibiting the activity of AOB Nitrosospira cluster 3a.2 (D11). This study advances our understanding of key nitrifiers responsible for high N2O emissions in agricultural soils and their controlling factors, and provides vital knowledge for N2O emission mitigation in agricultural ecosystems.

Initial evidence on the effect of copper on global cropland nitrogen cycling: A meta-analysis

Copper (Cu) is a key cofactor in ammonia monooxygenase functioning responsible for the first step of nitrification, but its excess availability impairs soil microbial functions and plant growth. Yet, the impact of Cu on nitrogen (N) cycling and process-related variables in cropland soils remains unexplored globally. Through a meta-analysis of 1209-paired and 319-single observations from 94 publications, we found that Cu (Cu addition or Cu-polluted soil) reduced soil potential nitrification by 33.8% and nitrite content by 73.5% due to reduced soil enzyme activities of nitrification and urease, microbial biomass content, and ammonia oxidizing archaea abundance. The response ratio of potential nitrification decreased with increasing Cu concentration, soil total N, and clay content. We further noted that soil potential nitrification inhibited by 46.5% only when Cu concentration was higher than 150 mg kg-1, while low Cu concentration (less than 150 mg kg-1) stimulated soil nitrate by 99.0%. Increasing initial soil Cu content stimulated gross N mineralization rate due to increased soil organic carbon and total N, but inhibited gross nitrification rate, which ultimately stimulated gross N immobilization rate as a result of increased the residence time of ammonium. This resulted in a lower ratio of gross nitrification rate to gross N immobilization rate, implying a lower potential risk of N loss as evidenced by decreased nitrous oxide emissions with increasing initial soil Cu content. Our analysis offers initial global evidence that Cu has an important role in controlling soil N availability and loss through its effect on N production and consumption.

Global patterns in gene content of soil microbiomes emerge from microbial interactions

Microbial metabolism sustains life on Earth. Sequencing surveys of communities in hosts, oceans, and soils have revealed ubiquitous patterns linking the microbes present, the genes they possess, and local environmental conditions. One prominent explanation for these patterns is environmental filtering: local conditions select strains with particular traits. However, filtering assumes ecological interactions do not influence patterns, despite the fact that interactions can and do play an important role in structuring communities. Here, we demonstrate the insufficiency of the environmental filtering hypothesis for explaining global patterns in topsoil microbiomes. Using denitrification as a model system, we find that the abundances of two characteristic genotypes trade-off with pH; nar gene abundances increase while nap abundances decrease with declining pH. Contradicting the filtering hypothesis, we show that strains possessing the Nar genotype are enriched in low pH conditions but fail to grow alone. Instead, the dominance of Nar genotypes at low pH arises from an ecological interaction with Nap genotypes that alleviates nitrite toxicity. Our study provides a roadmap for dissecting how global associations between environmental variables and gene abundances arise from environmentally modulated community interactions.

Comparison of typical nitrite oxidizing bacteria suppression strategies and the effect on nitrous oxide emissions in a biofilm reactor

In mainstream partial nitritation/anammox (PN/A), suppression of nitrite oxidizing bacteria (NOB) and mitigation of N2O emissions are two essential operational goals. The N2O emissions linked to three typical NOB suppression strategies were tested in a covered rotating biological contactor (RBC) biofilm system at 21 °C: (i) low dissolved oxygen (DO) concentrations, and treatments with (ii) free ammonia (FA), and (iii) free nitrous acids (FNA). Low emerged DO levels effectively minimized NOB activity and decreased N2O emissions, but NOB adaptation appeared after 200 days of operation. Further NOB suppression was successfully achieved by periodic (3 h per week) treatments with FA (29.3 ± 2.6 mg NH3-N L-1) or FNA (3.1 ± 0.3 mg HNO2-N L-1). FA treatment, however, promoted N2O emissions, while FNA did not affect these. Hence, biofilm PN/A should be operated at relatively low DO levels with periodic FNA treatment to maximize nitrogen removal efficiency while avoiding high greenhouse gas emissions.

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.

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.

Understory species composition mediates soil greenhouse gas fluxes by affecting bacterial community diversity in boreal forests

Introduction

Plant species composition in forest ecosystems can alter soil greenhouse gas (GHG) budgets by affecting soil properties and microbial communities. However, little attention has been paid to the forest types characterized by understory vegetation, especially in boreal forests where understory species contribute significantly to carbon and nitrogen cycling.

Method

In the present study, soil GHG fluxes, soil properties and bacterial community, and soil environmental conditions were investigated among three types of larch forest [Rhododendron simsii-Larix gmelinii forest (RL), Ledum palustre-Larix gmelinii forest (LL), and Sphagnum-Bryum-Ledum palustre-Larix gmelinii forest (SLL)] in the typical boreal region of northeast China to explore whether the forest types characterized by different understory species can affect soil GHG fluxes.

Results

The results showed that differences in understory species significantly affected soil GHG fluxes, properties, and bacterial composition among types of larch forest. Soil CO₂ and N₂O fluxes were significantly higher in LL (347.12 mg m^-2 h^-1 and 20.71 μg m^-2 h^-1) and RL (335.54 mg m^-2 h^-1 and 20.73 μg m^-2 h^-1) than that in SLL (295.58 mg m^-2 h^-1 and 17.65 μg m^-2 h^-1), while lower soil CH₄ uptake (-21.07 μg m^-2 h^-1) were found in SLL than in RL (-35.21 μg m^-2 h^-1) and LL (-35.85 μg m^-2 h^-1). No significant differences between LL and RL were found in soil CO₂, CH₄, and N₂O fluxes. Soil bacterial composition was mainly dominated by Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi among the three types of larch forest, while their abundances differed significantly. Soil environmental variables, soil properties, bacterial composition, and their interactions significantly affected the variations in GHG fluxes with understory species. Specifically, structural equation modeling suggested that soil bacterial composition and temperature had direct close links with variations in soil GHG fluxes among types of larch forest. Moreover, soil NO₃ ^--N and NH₄ ⁺ - N content also affected soil CO₂, CH₄, and N₂O fluxes indirectly, via their effects on soil bacterial composition.

Discussion

Our study highlights the importance of understory species in regulating soil GHG fluxes in boreal forests, which furthers our understanding of the role of boreal forests in sustainable development and climate change mitigation.

Mechanisms of NO and N2O production by enriched nitrifying sludge in a sequencing batch reactor: Effects of hydroxylamine

NO and N₂O as important greenhouse gases andtheir production mechanisms during nitrification are not completely understood. This study aimed to analyze the effect of hydroxylamine (NH₂OH) on NO and N₂O produced by nitrifying bacteria from activated sludge in a sequencing batch reactor (SBR). Experimental results showed that when nitrite (NO₂^-) accumulated during aerobic ammonia (NH₄⁺) oxidation, N₂O was the main product. The total amount of NO and N₂O produced by NH₂OH oxidation was positively correlated with dissolved oxygen (DO) levels. The imbalance of NH₄⁺ oxidation caused by NH₂OH addition was more conducive to the generation of NO and N₂O under high DO conditions. When NH₂OH was added into the reactor with NO₂^- as the substrate, the production of NO and N₂O under high DO levels was mainly related to NH₂OH oxidation. Under low DO conditions, NO and N₂O from the biotic/abiotic hybrid pathways were more significant in the reactor of the coexistence of NO₂^- and NH₂OH, which could be mainly caused by the pathways of nitrifier denitrification and abiotic reaction. Besides, limited amount of NO and N₂O was generated by heterotrophic denitrification pathway during autotrophic nitrification. The implications for the above results are important for understanding the production of NO and N₂O under NH₂OH stress in nitrifying sludge reactor.

An investigation into the optimal granular sludge size for simultaneous nitrogen and phosphate removal

An aerobic granular sludge (AGS) pilot plant fed with a mixture of acetate amended centrate and secondary effluent was used to investigate the optimal granule size range for simultaneous nitrification and denitrification (SND) and ortho-phosphate removal. The anaerobic phase was mixed to understand how AGS will perform if integrated with a continuous flow activated sludge system that cannot feed the influent through the settled sludge bed. Five different granule size fractions were taken from the pilot (operated at DO setpoint of 2mgO₂/L) and each size was subjected to activity tests in a well-controlled lab-scale AGS reactor at four dissolved oxygen (DO) concentrations of 1, 2, 3, and 4 mgO₂/L. The size fractions were: 212 - 600 µm, 600 - 1000 µm, 1000 - 1400 µm, 1400 - 2000 µm, and >2000 µm. The smallest size range (212 - 600 µm) had the highest nitrification and phosphate removal rates at DO setpoints from 1 - 3 mgO₂/L, which was attributed to the higher aerobic volume fraction in small granules and hence a higher abundance of phosphorus accumulating organisms (PAO) and ammonia oxidizing bacteria (AOB). In comparison, large granules (>1000 µm) had 1.4 - 4.7 times lower ammonia oxidation rates than the smallest size range, which aligned with their lower AOB abundance relative to granule biomass. The granules with the highest anoxic volume fraction had the highest abundance of nitrite reductase genes (nir gene) but did not show the highest specific nitrogen removal rate. Instead, smaller granules (212 - 600 and 600 - 1000 µm), which had a lower nir gene abundance, had the highest specific nitrogen removal rates (1.2 - 3.1 times higher than larger granules) across all DO values except at 4 mgO₂/L. At a DO setpoint of 4 mgO₂/L, nitrite production by ammonia oxidation (ammonia monooxygenase) exceeded nitrite reduction by nitrite reductase in granules smaller than 1000 µm, in addition, some denitrifying heterotrophs switched to oxygen utilization in deeper layers hence suppressing denitrification activity. At the DO range of 2 - 4 mg/L, granular size had a greater effect on nutrient removal than DO. Therefore, for AGS developed at an average DO setpoint of 2 mgO₂/L, selecting for size fractions in the range of 212 - 1000 µm and avoiding DO values higher than 3 mgO₂/L can achieve both a higher nitrogen removal capacity and energy savings. This study is the first to investigate the influence of different DO values on SND and biological phosphorus removal performance of different aerobic granular sludge sizes.

Long-Term Low Dissolved Oxygen Operation Decreases N2O Emissions in the Activated Sludge Process

Nitrous oxide (N₂O) is an important greenhouse gas and a dominant ozone-depleting substance. Nitrification in the activated sludge process (ASP) is an important N₂O emission source. This study demonstrated that a short-term low dissolved oxygen (DO) increased the N₂O emissions by six times, while long-term low DO operation decreased the N₂O emissions by 54% (P < 0.01). Under long-term low DO, the ammonia oxidizer abundance in the ASP increased significantly, and thus, complete nitrification was recovered and no NH₃ or nitrite accumulated. Moreover, long-term low DO decreased the abundance of ammonia-oxidizing bacteria (AOB) by 28%, while increased the abundance of ammonia-oxidizing archaea (AOA) by 507%, mainly due to their higher oxygen affinity. As a result, AOA outnumbered AOB with the AOA/AOB amoA gene ratio increasing to 19.5 under long-term low DO. The efficient nitrification and decreased AOB abundance might not increase N₂O production via AOB under long-term low DO conditions. The enriched AOA could decrease the N₂O emissions because they were reported to lack canonical nitric oxide (NO) reductase genes that convert NO to N₂O. Probably because of AOA enrichment, the positive and significant (P = 0.02) correlation of N₂O emission and nitrite concentration became insignificant (P = 0.332) after 80 days of low DO operation. Therefore, ASPs can be operated with low DO and extended sludge age to synchronously reduce N₂O production and carbon dioxide emissions owing to lower aeration energy without compromising the nitrification efficiency.

Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration

Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.

Return-Sludge Treatment with Endogenous Free Nitrous Acid Limits Nitrate Production and N2O Emission for Mainstream Partial Nitritation/Anammox

Nitrite oxidizing bacteria (NOB) and nitrous oxide (N₂O) hinder the development of mainstream partial nitritation/anammox. To overcome these, endogenous free ammonia (FA) and free nitrous acid (FNA), which can be produced in the sidestream, were used for return-sludge treatment for two integrated-film activated sludge reactors containing biomass in flocs and on carriers. The repeated exposure of biomass from one reactor to FA shocks had a limited impact on NOB suppression but inhibited anammox bacteria (AnAOB). In the other reactor, repeated FNA shocks to the separated flocs failed to limit the system's nitrate production since NOB activity was still high on the biofilms attached to the unexposed carriers. In contrast, the repeated FNA treatment of flocs and carriers favored aerobic ammonium-oxidizing bacteria (AerAOB) over NOB activity with AnAOB negligibly affected. It was further revealed that return-sludge treatment with higher FNA levels led to lower N₂O emissions under similar effluent nitrite concentrations. On this basis, weekly 4 h FNA shocks of 2.0 mg of HNO₂-N/L were identified as an optimal and realistic treatment, which not only enabled nitrogen removal efficiencies of ∼65% at nitrogen removal rates of ∼130 mg of N/L/d (20 °C) but also yielded the lowest cost and carbon footprint.

Genomic Analysis of Bacillus megaterium NCT-2 Reveals Its Genetic Basis for the Bioremediation of Secondary Salinization Soil

Bacillus megaterium NCT-2 is a nitrate-uptake bacterial, which shows high bioremediation capacity in secondary salinization soil, including nitrate-reducing capacity, phosphate solubilization, and salinity adaptation. To gain insights into the bioremediation capacity at the genetic level, the complete genome sequence was obtained by using a multiplatform strategy involving HiSeq and PacBio sequencing. The NCT-2 genome consists of a circular chromosome of 5.19 Mbp and ten indigenous plasmids, totaling 5.88 Mbp with an average GC content of 37.87%. The chromosome encodes 5,606 genes, 142 tRNAs, and 53 rRNAs. Genes involved in the features of the bioremediation in secondary salinization soil and plant growth promotion were identified in the genome, such as nitrogen metabolism, phosphate uptake, the synthesis of organic acids and phosphatase for phosphate-solubilizing ability, and Trp-dependent IAA synthetic system. Furthermore, strain NCT-2 has great ability of adaption to environments due to the genes involved in cation transporters, osmotic stress, and oxidative stress. This study sheds light on understanding the molecular basis of using B. megaterium NCT-2 in bioremediation of the secondary salinization soils.

Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth

Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.

Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium Nitrosomonas europaea is the best-characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of N. europaea, e.g., by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on N. europaea have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole-genome transcriptomics to investigate the overall effect of oxygen limitation on N. europaea. Under oxygen-limited conditions, growth yield was reduced and ammonia-to-nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper-containing cytochrome c oxidases encoded by N. europaea were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of N. europaea’s sNOR with regard to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in N. europaea and other ammonia-oxidizing bacteria.

IMPORTANCE Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.

Archaeal nitrification is constrained by copper complexation with organic matter in municipal wastewater treatment plants

Consistent with the observation that ammonia-oxidizing bacteria (AOB) outnumber ammonia-oxidizing archaea (AOA) in many eutrophic ecosystems globally, AOB typically dominate activated sludge aeration basins from municipal wastewater treatment plants (WWTPs). In this study, we demonstrate that the growth of AOA strains inoculated into sterile-filtered wastewater was inhibited significantly, in contrast to uninhibited growth of a reference AOB strain. In order to identify possible mechanisms underlying AOA-specific inhibition, we show that complex mixtures of organic compounds, such as yeast extract, were highly inhibitory to all AOA strains but not to the AOB strain. By testing individual organic compounds, we reveal strong inhibitory effects of organic compounds with high metal complexation potentials implying that the inhibitory mechanism for AOA can be explained by the reduced bioavailability of an essential metal. Our results further demonstrate that the inhibitory effect on AOA can be alleviated by copper supplementation, which we observed for pure AOA cultures in a defined medium and for AOA inoculated into nitrifying sludge. Our study offers a novel mechanistic explanation for the relatively low abundance of AOA in most WWTPs and provides a basis for modulating the composition of nitrifying communities in both engineered systems and naturally occurring environments.

Indications for enzymatic denitrification to N2O at low pH in an ammonia-oxidizing archaeon

Nitrous oxide (N₂O) is a key climate change gas and nitrifying microbes living in terrestrial ecosystems contribute significantly to its formation. Many soils are acidic and global change will cause acidification of aquatic and terrestrial ecosystems, but the effect of decreasing pH on N₂O formation by nitrifiers is poorly understood. Here, we used isotope-ratio mass spectrometry to investigate the effect of acidification on production of N₂O by pure cultures of two ammonia-oxidizing archaea (AOA; Nitrosocosmicus oleophilus and Nitrosotenuis chungbukensis) and an ammonia-oxidizing bacterium (AOB; Nitrosomonas europaea). For all three strains acidification led to increased emission of N₂O. However, changes of ¹⁵N site preference (SP) values within the N₂O molecule (as indicators of pathways for N₂O formation), caused by decreasing pH, were highly different between the tested AOA and AOB. While acidification decreased the SP value in the AOB strain, SP values increased to a maximum value of 29‰ in N. oleophilus. In addition, ¹⁵N-nitrite tracer experiments showed that acidification boosted nitrite transformation into N₂O in all strains, but the incorporation rate was different for each ammonia oxidizer. Unexpectedly, for N. oleophilus more than 50% of the N₂O produced at pH 5.5 had both nitrogen atoms from nitrite and we demonstrated that under these conditions expression of a putative cytochrome P450 NO reductase is strongly upregulated. Collectively, our results indicate that N. oleophilus might be able to enzymatically denitrify nitrite to N₂O at low pH.

Enhancing the digestion of waste activated sludge through nitrite addition: insight on mechanism through profiles of extracellular polymeric substances (EPS) and microbial communities

Extracellular nitrite has been used to improve the digestion of waste activated sludge (WAS). However, the underlying mechanism remains largely unknown. In this study, WAS was treated with 0.2 gNO₂^--N/gVSS for 7 days and its performance was compared to that of aerobic and anaerobic treatments. The addition of nitrite had a distinct effect on the reduction of VSS/SS and the accumulation of soluble organics compared to the control reactors. As evident by the variations of extracellular polymeric substances (EPS), nitrite addition had a positive effect on decreasing protein. In particular, the decrease of protein mainly occurred in tightly bound EPS (TB-EPS), which caused sludge disintegration and enhanced sludge reduction. Additionally, the decrease of microbial diversity with nitrite addition was significant compared to the control reactors, accompany with a decrease of live/dead cells ratio and an increase of supernatant DNA concentration. This suggests that nitrite could cause cell death and lysis, resulting in sludge degradation. Thus, nitrite addition enhanced sludge treatment through the combined effect of TB-EPS disintegration and cell lysis. These findings will be useful for the optimization of sludge treatment process based on nitrite addition.

Integrated Omic Analyses Provide Evidence that a "Candidatus Accumulibacter phosphatis" Strain Performs Denitrification under Microaerobic Conditions

The ability of "Candidatus Accumulibacter phosphatis" to grow and remove phosphorus from wastewater under cycling anaerobic and aerobic conditions has also been investigated as a metabolism that could lead to simultaneous removal of nitrogen and phosphorus by a single organism. However, although phosphorus removal under cyclic anaerobic and anoxic conditions has been demonstrated, clarifying the role of "Ca. Accumulibacter phosphatis" in this process has been challenging, since (i) experimental research describes contradictory findings, (ii) none of the published "Ca. Accumulibacter phosphatis" genomes show the existence of a complete respiratory pathway for denitrification, and (iii) some genomes lacking a complete respiratory pathway have genes for assimilatory nitrate reduction. In this study, we used an integrated omics analysis to elucidate the physiology of a "Ca. Accumulibacter phosphatis" strain enriched in a reactor operated under cyclic anaerobic and microaerobic conditions. The reactor's performance suggested the ability of the enriched "Ca. Accumulibacter phosphatis" strain (clade IC) to simultaneously use oxygen and nitrate as electron acceptors under microaerobic conditions. A draft genome of this organism was assembled from metagenomic reads ("Ca. Accumulibacter phosphatis" UW-LDO-IC) and used as a reference to examine transcript abundance throughout one reactor cycle. The genome of UW-LDO-IC revealed the presence of a full pathway for respiratory denitrification. The observed transcript abundance patterns showed evidence of coregulation of the denitrifying genes along with a cbb ₃ cytochrome, which has been characterized as having high affinity for oxygen. Furthermore, we identified an FNR-like binding motif upstream of the coregulated genes, suggesting transcription-level regulation of both denitrifying and respiratory pathways in UW-LDO-IC. Taking the results together, the omics analysis provides strong evidence that "Ca. Accumulibacter phosphatis" UW-LDO-IC uses oxygen and nitrate simultaneously as electron acceptors under microaerobic conditions. IMPORTANCE "Candidatus Accumulibacter phosphatis" is widely found in full-scale wastewater treatment plants, where it has been identified as the key organism for biological removal of phosphorus. Since aeration can account for 50% of the energy use during wastewater treatment, microaerobic conditions for wastewater treatment have emerged as a cost-effective alternative to conventional biological nutrient removal processes. Our report provides strong genomics-based evidence not only that "Ca. Accumulibacter phosphatis" is the main organism contributing to phosphorus removal under microaerobic conditions but also that this organism simultaneously respires nitrate and oxygen in this environment, consequently removing nitrogen and phosphorus from the wastewater. Such activity could be harnessed in innovative designs for cost-effective and energy-efficient optimization of wastewater treatment systems.

Metabolic and Proteomic Responses to Salinity in Synthetic Nitrifying Communities of Nitrosomonas spp. and Nitrobacter spp

Typically, nitrification is a two-stage microbial process and is key in wastewater treatment and nutrient recovery from waste streams. Changes in salinity represent a major stress factor that can trigger response mechanisms, impacting the activity and the physiology of bacteria. Despite its pivotal biotechnological role, little information is available on the specific response of nitrifying bacteria to varying levels of salinity. In this study, synthetic communities of ammonia-oxidizing bacteria (AOB Nitrosomonas europaea and/or Nitrosomonas ureae) and nitrite-oxidizing bacteria (NOB Nitrobacter winogradskyi and/or Nitrobacter vulgaris) were tested at 5, 10, and 30 mS cm^-1 by adding sodium chloride to the mineral medium (0, 40, and 200 mM NaCl, respectively). Ammonia oxidation activity was less affected by salinity than nitrite oxidation. AOB, on their own or in combination with NOB, showed no significant difference in the ammonia oxidation rate among the three conditions. However, N. winogradskyi improved the absolute ammonia oxidation rate of both N. europaea and N. ureae. N. winogradskyi’s nitrite oxidation rate decreased to 42% residual activity upon exposure to 30 mS cm^-1, also showing a similar behavior when tested with Nitrosomonas spp. The nitrite oxidation rate of N. vulgaris, as a single species, was not affected when adding sodium chloride up to 30 mS cm^-1, however, its activity was completely inhibited when combined with Nitrosomonas spp. in the presence of ammonium/ammonia. The proteomic analysis of a co-culture of N. europaea and N. winogradskyi revealed the production of osmolytes, regulation of cell permeability and an oxidative stress response in N. europaea and an oxidative stress response in N. winogradskyi, as a result of increasing the salt concentration from 5 to 30 mS cm^-1. A specific metabolic response observed in N. europaea suggests the role of carbon metabolism in the production of reducing power, possibly to meet the energy demands of the stress response mechanisms, induced by high salinity. For the first time, metabolic modifications and response mechanisms caused by the exposure to salinity were described, serving as a tool toward controllability and predictability of nitrifying systems exposed to salt fluctuations.

Anaerobic Bacterial Response to Nitrosative Stress

This chapter provides an overview of current knowledge of how anaerobic bacteria protect themselves against nitrosative stress. Nitric oxide (NO) is the primary source of this stress. Aerobically its removal is an oxidative process, whereas reduction is required anaerobically. Mechanisms required to protect aerobic and anaerobic bacteria are therefore different. Several themes recur in the review. First, how gene expression is regulated often provides clues to the physiological function of the gene products. Second, the physiological significance of reports based upon experiments under extreme conditions that bacteria do not encounter in their natural environment requires reassessment. Third, responses to the primary source of stress need to be distinguished from secondary consequences of chemical damage due to failure of repair mechanisms to cope with extreme conditions. NO is generated by many mechanisms, some of which remain undefined. An example is the recent demonstration that the hybrid cluster protein combines with YtfE (or RIC protein, for repair of iron centres damaged by nitrosative stress) in a new pathway to repair key iron-sulphur proteins damaged by nitrosative stress. The functions of many genes expressed in response to nitrosative stress remain either controversial or are completely unknown. The concentration of NO that accumulates in the bacterial cytoplasm is essentially unknown, so dogmatic statements cannot be made that damage to transcription factors (Fur, FNR, SoxRS, MelR, OxyR) occurs naturally as part of a physiologically relevant signalling mechanism. Such doubts can be resolved by simple experiments to meet six proposed criteria.

Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of Nitrosomonas europaea and Nitrobacter winogradskyi

Modern agriculture is sustained by application of inorganic nitrogen (N) fertilizer in the form of ammonium (NH₄⁺). Up to 60% of NH₄⁺-based fertilizer can be lost through leaching of nitrifier-derived nitrate (NO₃⁻), and through the emission of N oxide gases (i.e., nitric oxide [NO], N dioxide [NO₂], and nitrous oxide [N₂O] gases), the latter being a potent greenhouse gas. Our approach to modeling of nitrification suggests that both biotic and abiotic mechanisms function as important sources and sinks of N oxides during microaerobic conditions and that previous models might have underestimated gross NO production during nitrification.

Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, emits nitrogen (N) oxide gases (NO, NO₂, and N₂O), which are potentially hazardous compounds that contribute to global warming. To better understand the dynamics of nitrification-derived N oxide production, we conducted culturing experiments and used an integrative genome-scale, constraint-based approach to model N oxide gas sources and sinks during complete nitrification in an aerobic coculture of two model nitrifying bacteria, the ammonia-oxidizing bacterium Nitrosomonas europaea and the nitrite-oxidizing bacterium Nitrobacter winogradskyi. The model includes biotic genome-scale metabolic models (iFC578 and iFC579) for each nitrifier and abiotic N oxide reactions. Modeling suggested both biotic and abiotic reactions are important sources and sinks of N oxides, particularly under microaerobic conditions predicted to occur in coculture. In particular, integrative modeling suggested that previous models might have underestimated gross NO production during nitrification due to not taking into account its rapid oxidation in both aqueous and gas phases. The integrative model may be found at https://github.com/chaplenf/microBiome-v2.1.

IMPORTANCE Modern agriculture is sustained by application of inorganic nitrogen (N) fertilizer in the form of ammonium (NH₄⁺). Up to 60% of NH₄⁺-based fertilizer can be lost through leaching of nitrifier-derived nitrate (NO₃⁻), and through the emission of N oxide gases (i.e., nitric oxide [NO], N dioxide [NO₂], and nitrous oxide [N₂O] gases), the latter being a potent greenhouse gas. Our approach to modeling of nitrification suggests that both biotic and abiotic mechanisms function as important sources and sinks of N oxides during microaerobic conditions and that previous models might have underestimated gross NO production during nitrification.

Smart operation of nitritation/denitritation virtually abolishes nitrous oxide emission during treatment of co-digested pig slurry centrate

The implementation of nitritation/denitritation (Nit/DNit) as alternative to nitrification/denitrification (N/DN) is driven by operational cost savings, e.g. 1.0-1.8 EUR/ton slurry treated. However, as for any biological nitrogen removal process, Nit/DNit can emit the potent greenhouse gas nitrous oxide (N₂O). Challenges remain in understanding formation mechanisms and in mitigating the emissions, particularly at a low ratio of organic carbon consumption to nitrogen removal (COD_rem/N_rem). In this study, the centrate (centrifuge supernatant) from anaerobic co-digestion of pig slurry was treated in a sequencing batch reactor. The process removed approximately 100% of ammonium a satisfactory nitrogen loading rate (0.4 g N/L/d), with minimum nitrite and nitrate in the effluent. Substantial N₂O emission (around 17% of the ammonium nitrogen loading) was observed at the baseline operational condition (dissolved oxygen, DO, levels averaged at 0.85 mg O₂/L; COD_rem/N_rem of 2.8) with ∼68% of the total emission contributed by nitritation. Emissions increased with higher nitrite accumulation and lower organic carbon to nitrogen ratio. Yet, higher DO levels (∼2.2 mg O₂/L) lowered the aerobic N₂O emission and weakened the dependency on nitrite concentration, suggesting a shift in N₂O production pathway. The most effective N₂O mitigation strategy combined intermittent patterns of aeration, anoxic feeding and anoxic carbon dosage, decreasing emission by over 99% (down to ∼0.12% of the ammonium nitrogen loading). Without anaerobic digestion, mitigated Nit/DNit decreases the operational carbon footprint with about 80% compared to N/DN. With anaerobic digestion included, about 4 times more carbon is sequestered. In conclusion, the low COD_rem/N_rem feature of Nit/DNit no longer offsets its environmental sustainability provided the process is smartly operated.

Hierarchical Control of Nitrite Respiration by Transcription Factors Encoded within Mobile Gene Clusters of Thermus thermophilus

Denitrification in Thermus thermophilus is encoded by the nitrate respiration conjugative element (NCE) and nitrite and nitric oxide respiration (nic) gene clusters. A tight coordination of each cluster’s expression is required to maximize anaerobic growth, and to avoid toxicity by intermediates, especially nitric oxides (NO). Here, we study the control of the nitrite reductases (Nir) and NO reductases (Nor) upon horizontal acquisition of the NCE and nic clusters by a formerly aerobic host. Expression of the nic promoters PnirS, PnirJ, and PnorC, depends on the oxygen sensor DnrS and on the DnrT protein, both NCE-encoded. NsrR, a nic-encoded transcription factor with an iron–sulfur cluster, is also involved in Nir and Nor control. Deletion of nsrR decreased PnorC and PnirJ transcription, and activated PnirS under denitrification conditions, exhibiting a dual regulatory role never described before for members of the NsrR family. On the basis of these results, a regulatory hierarchy is proposed, in which under anoxia, there is a pre-activation of the nic promoters by DnrS and DnrT, and then NsrR leads to Nor induction and Nir repression, likely as a second stage of regulation that would require NO detection, thus avoiding accumulation of toxic levels of NO. The whole system appears to work in remarkable coordination to function only when the relevant nitrogen species are present inside the cell.

Contributions of nitrification and denitrification to N2O emissions from aged refuse bioreactor at different feeding loads of ammonia substrates

Nitrous oxide (N₂O) is a strong greenhouse gas, and its emissions from microbial nitrification (NF) and denitrification (DNF) are a threat to the environment. In the present study, a combined approach consisting of ¹⁵N stable isotope and molecular biology (qPCR) was used to determine the contributions of autotrophic nitrification (ANF), heterotrophic nitrification (HNF), and DNF to N₂O emissions in laboratory incubations of aged refuse for different ammonia (NH₄⁺-N) loads (200, 400, and 800mg·NH₄⁺-N/kg·aged refuse) and incubation times (2-144h). Experimental results showed that the N₂O emissions increased with the increase in applied amount of NH₄⁺-N substrates. Simultaneous nitrification and denitrification (SND) were demonstrated to be present in the incubations of aged refuse. The results of ¹⁵N stable isotope labelling experiment indicated that NF (54.60%-68.8%) and DNF (83.38%-85.90%) contributed to majority of N₂O emissions in the incubations of 24h and 72h, respectively. The results of functional genes (amoA and nosZ) quantification experiments indicated that the high gene copies of amoA and nosZ were present at 24h and 72h, respectively. The study also demonstrated the utility of a combined stable isotope and molecular biology approach. The approaches not only provide similar inferences about the N₂O emissions, but also enable the determination of relative contributions of ANF, HNF, and DNF to N₂O emissions. The results of the study are important in providing guidance to artificially optimize the operating conditions for alleviating N₂O emissions in aged refuse bioreactors.

Hybrid Nitrous Oxide Production from a Partial Nitrifying Bioreactor: Hydroxylamine Interactions with Nitrite

The goal of this study was to elucidate the mechanisms of nitrous oxide (N₂O) production from a bioreactor for partial nitrification (PN). Ammonia-oxidizing bacteria (AOB) enriched from a sequencing batch reactor (SBR) were subjected to N₂O production pathway tests. The N₂O pathway test was initiated by supplying an inorganic medium to ensure an initial NH₄⁺-N concentration of 160 mg-N/L, followed by ¹⁵NO₂^- (20 mg-N/L) and dual ¹⁵NH₂OH (each 17 mg-N/L) spikings to quantify isotopologs of gaseous N₂O (⁴⁴N₂O, ⁴⁵N₂O, and ⁴⁶N₂O). N₂O production was boosted by ¹⁵NH₂OH spiking, causing exponential increases in mRNA transcription levels of AOB functional genes encoding hydroxylamine oxidoreductase (haoA), nitrite reductase (nirK), and nitric oxide reductase (norB) genes. Predominant production of ⁴⁵N₂O among N₂O isotopologs (46% of total produced N₂O) indicated that coupling of ¹⁵NH₂OH with ¹⁴NO₂^- produced N₂O via N-nitrosation hybrid reaction as a predominant pathway. Abiotic hybrid N₂O production was also observed in the absence of the AOB-enriched biomass, indicating multiple pathways for N₂O production in a PN bioreactor. The additional N₂O pathway test, where ¹⁵NH₄⁺ was spiked into 400 mg-N/L of NO₂^- concentration, confirmed that the hybrid N₂O production was a dominant pathway, accounting for approximately 51% of the total N₂O production.

Isotopocule analysis of biologically produced nitrous oxide in various environments

Natural abundance ratios of isotopocules, molecules that have the same chemical constitution and configuration, but that only differ in isotope substitution, retain a record of a compound's origin and reactions. A method to measure isotopocule ratios of nitrous oxide (N₂ O) has been established by using mass analysis of molecular ions and fragment ions. The method has been applied widely to environmental samples from the atmosphere, ocean, fresh water, soils, and laboratory-simulation experiments. Results show that isotopocule ratios, particularly the ¹⁵ N-site preference (difference between isotopocule ratios ¹⁴ N¹⁵ N¹⁶ O/¹⁴ N¹⁴ N¹⁶ O and ¹⁵ N¹⁴ N¹⁶ O/¹⁴ N¹⁴ N¹⁶ O), have a wide range that depends on their production and consumption processes. Observational and laboratory studies of N₂ O related to biological processes are reviewed and discussed to elucidate complex material cycles of this trace gas, which causes global warming and stratospheric ozone depletion. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:135-160, 2017.

Bacterial Responses to Glyoxal and Methylglyoxal: Reactive Electrophilic Species

Glyoxal (GO) and methylglyoxal (MG), belonging to α-oxoaldehydes, are produced by organisms from bacteria to humans by glucose oxidation, lipid peroxidation, and DNA oxidation. Since glyoxals contain two adjacent reactive carbonyl groups, they are referred to as reactive electrophilic species (RES), and are damaging to proteins and nucleotides. Therefore, glyoxals cause various diseases in humans, such as diabetes and neurodegenerative diseases, from which all living organisms need to be protected. Although the glyoxalase system has been known for some time, details on how glyoxals are sensed and detoxified in the cell have not been fully elucidated, and are only beginning to be uncovered. In this review, we will summarize the current knowledge on bacterial responses to glyoxal, and specifically focus on the glyoxal-associated regulators YqhC and NemR, as well as their detoxification mediated by glutathione (GSH)-dependent/independent glyoxalases and NAD(P)H-dependent reductases. Furthermore, we will address questions and future directions.

Acidification Enhances Hybrid N2O Production Associated with Aquatic Ammonia-Oxidizing Microorganisms

Ammonia-oxidizing microorganisms are an important source of the greenhouse gas nitrous oxide (N₂O) in aquatic environments. Identifying the impact of pH on N₂O production by ammonia oxidizers is key to understanding how aquatic greenhouse gas fluxes will respond to naturally occurring pH changes, as well as acidification driven by anthropogenic CO₂. We assessed N₂O production rates and formation mechanisms by communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in a lake and a marine environment, using incubation-based nitrogen (N) stable isotope tracer methods with ¹⁵N-labeled ammonium (¹⁵NH4+) and nitrite (¹⁵NO2−), and also measurements of the natural abundance N and O isotopic composition of dissolved N₂O. N₂O production during incubations of water from the shallow hypolimnion of Lake Lugano (Switzerland) was significantly higher when the pH was reduced from 7.54 (untreated pH) to 7.20 (reduced pH), while ammonia oxidation rates were similar between treatments. In all incubations, added NH4+ was the source of most of the N incorporated into N₂O, suggesting that the main N₂O production pathway involved hydroxylamine (NH₂OH) and/or NO2− produced by ammonia oxidation during the incubation period. A small but significant amount of N derived from exogenous/added ¹⁵NO2− was also incorporated into N₂O, but only during the reduced-pH incubations. Mass spectra of this N₂O revealed that NH4+ and ¹⁵NO2− each contributed N equally to N₂O by a “hybrid-N₂O” mechanism consistent with a reaction between NH₂OH and NO2−, or compounds derived from these two molecules. Nitrifier denitrification was not an important source of N₂O. Isotopomeric N₂O analyses in Lake Lugano were consistent with incubation results, as ¹⁵N enrichment of the internal N vs. external N atoms produced site preferences (25.0–34.4‰) consistent with NH₂OH-dependent hybrid-N₂O production. Hybrid-N₂O formation was also observed during incubations of seawater from coastal Namibia with ¹⁵NH4+ and NO2−. However, the site preference of dissolved N₂O here was low (4.9‰), indicating that another mechanism, not captured during the incubations, was important. Multiplex sequencing of 16S rRNA revealed distinct ammonia oxidizer communities: AOB dominated numerically in Lake Lugano, and AOA dominated in the seawater. Potential for hybrid N₂O formation exists among both communities, and at least in AOB-dominated environments, acidification may accelerate this mechanism.

Nitrous oxide as a function of oxygen and archaeal gene abundance in the North Pacific

Oceanic oxygen minimum zones are strong sources of the potent greenhouse gas N₂O but its microbial source is unclear. We characterized an exponential response in N₂O production to decreasing oxygen between 1 and 30 μmol O₂ l⁻¹ within and below the oxycline using ¹⁵NO₂⁻, a relationship that held along a 550 km offshore transect in the North Pacific. Differences in the overall magnitude of N₂O production were accounted for by archaeal functional gene abundance. A one-dimensional (1D) model, parameterized with our experimentally derived exponential terms, accurately reproduces N₂O profiles in the top 350 m of water column and, together with a strong ⁴⁵N₂O signature indicated neither canonical nor nitrifier–denitrification production while statistical modelling supported production by archaea, possibly via hybrid N₂O formation. Further, with just archaeal N₂O production, we could balance high-resolution estimates of sea-to-air N₂O exchange. Hence, a significant source of N₂O, previously described as leakage from bacterial ammonium oxidation, is better described by low-oxygen archaeal production at the oxygen minimum zone's margins.

Understanding the production processes behind oceanic sources of nitrous oxide (N₂O), a potent greenhouse gas, is of critical importance. Here, the authors reveal an archaeal-mediated N₂O production pathway in the North Pacific, which increases exponentially with decreasing oxygen.

Nitrous oxide emissions from one-step partial nitritation/anammox processes

Measurements of nitrous oxide were made at pilot- and full-scale plants to evaluate greenhouse gas emissions from one-step partial nitritation/anammox processes applied in moving bed biofilm reactors treating reject water. It was found that 0.51-1.29% and 0.35-1.33% of the total nitrogen loads in the pilot- and full-scale reactor, respectively, were emitted as nitrous oxide. Between 80 and 90% of nitrous oxide emissions were in gaseous form and the rest amount was found in the reactor effluent; over 90% of nitrous oxide emissions occurred in the aerated period and less than 8% in the non-aerated period in the full-scale study. Nitrous oxide productions/consumptions were closely related to aeration and the nitrogen loads applied in the system.

Quorum Quenching of Nitrobacter winogradskyi Suggests that Quorum Sensing Regulates Fluxes of Nitrogen Oxide(s) during Nitrification

Quorum sensing (QS) is a widespread process in bacteria used to coordinate gene expression with cell density, diffusion dynamics, and spatial distribution through the production of diffusible chemical signals. To date, most studies on QS have focused on model bacteria that are amenable to genetic manipulation and capable of high growth rates, but many environmentally important bacteria have been overlooked. For example, representatives of proteobacteria that participate in nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, produce QS signals called acyl-homoserine lactones (AHLs). Nitrification emits nitrogen oxide gases (NO, NO₂, and N₂O), which are potentially hazardous compounds that contribute to global warming. Despite considerable interest in nitrification, the purpose of QS in the physiology/ecology of nitrifying bacteria is poorly understood. Through a quorum quenching approach, we investigated the role of QS in a well-studied AHL-producing nitrite oxidizer, Nitrobacter winogradskyi We added a recombinant AiiA lactonase to N. winogradskyi cultures to degrade AHLs to prevent their accumulation and to induce a QS-negative phenotype and then used mRNA sequencing (mRNA-Seq) to identify putative QS-controlled genes. Our transcriptome analysis showed that expression of nirK and nirK cluster genes (ncgABC) increased up to 19.9-fold under QS-proficient conditions (minus active lactonase). These data led to us to query if QS influenced nitrogen oxide gas fluxes in N. winogradskyi Production and consumption of NO_x increased and production of N₂O decreased under QS-proficient conditions. Quorum quenching transcriptome approaches have broad potential to identify QS-controlled genes and phenotypes in organisms that are not genetically tractable.

IMPORTANCE

Bacterial cell-cell signaling, or quorum sensing (QS), is a method of bacterial communication and gene regulation that is well studied in bacteria. However, little is known about the purpose of QS in many environmentally important bacteria. Here, we demonstrate quorum quenching coupled with mRNA-Seq to identify QS-controlled genes and phenotypes in Nitrobacter winogradskyi, a nitrite-oxidizing bacterium. Nitrite oxidizers play an important role in the nitrogen cycle though their participation in nitrification, the aerobic oxidation of ammonia to nitrate via nitrite. Our quorum quenching approach revealed that QS influences production and consumption of environmentally important nitrogen oxide gases (NO, NO₂, and N₂O) in N. winogradskyi This study demonstrated a novel technique for studying QS in difficult-to-work-with microorganisms and showed that nitrite oxidizers might also contribute to nitrification-dependent production of nitrogen oxide gases that contribute to global warming.

Atmospheric emission of nitric oxide and processes involved in its biogeochemical transformation in terrestrial environment

Nitric oxide (NO) is an intra- and intercellular gaseous signaling molecule with a broad spectrum of regulatory functions in biological system. Its emissions are produced by both natural and anthropogenic sources; however, soils are among the most important sources of NO. Nitric oxide plays a decisive role in environmental-atmospheric chemistry by controlling the tropospheric photochemical production of ozone and regulates formation of various oxidizing agents such as hydroxyl radical (OH), which contributes to the formation of acid of precipitates. Consequently, for developing strategies to overcome the deleterious impact of NO on terrestrial ecosystem, it is mandatory to have reliable information about the exact emission mechanism and processes involved in its transformation in soil-atmospheric system. Although the formation process of NO is a complex phenomenon and depends on many physicochemical characteristics, such as organic matter, soil pH, soil moisture, soil temperature, etc., this review provides comprehensive updates about the emission characteristics and biogeochemical transformation mechanism of NO. Moreover, this article will also be helpful to understand the processes involved in the consumption of NO in soils. Further studies describing the functions of NO in biological system are also discussed.

Reducing N2O Emission from a Domestic-Strength Nitrifying Culture by Free Nitrous Acid-Based Sludge Treatment

An increase of nitrite in the domestic-strength range is generally recognized to stimulate nitrous oxide (N2O) production by ammonia-oxidizing bacteria (AOB). It was found in this study, however, that N2O emission from a mainstream nitritation system (cyclic nitrite = 25-45 mg of N/L) that was established by free nitrous acid (FNA)-based sludge treatment was not higher but much lower than that from the initial nitrifying system with full conversion of NH4(+)-N to NO3(-)-N. Under dissolved oxygen (DO) levels of 2.5-3.0 mg/L, N2O emission from the nitritation stage was 76% lower than that from the initial stage. Even when the DO level was reduced to 0.3-0.8 mg/L, N2O emission from the nitritation stage was still 40% lower. An investigation of the mechanism showed that FNA treatment caused a shift of the stimulation threshold of nitrite on N2O emission. At the nitritation stage, the maximal N2O emission factor occurred at ∼16 mg of N/(L of nitrite). However, it increased with increasing nitrite in the range of 0-56 mg of N/L at the initial stage. FNA treatment decreased the biomass-specific N2O production rate, suggesting that the enzymes relevant to nitrifier denitrification were inhibited. Microbial analysis revealed that FNA treatment decreased the microbial community diversity but increased the abundances of AOB and denitrifiers.

Bacterial iron-sulfur cluster sensors in mammalian pathogens

Iron-sulfur clusters act as important cofactors for a number of transcriptional regulators in bacteria, including many mammalian pathogens. The sensitivity of iron-sulfur clusters to iron availability, oxygen tension, and reactive oxygen and nitrogen species enables bacteria to use such regulators to adapt their gene expression profiles rapidly in response to changing environmental conditions. In this review, we discuss how the [4Fe-4S] or [2Fe-2S] cluster-containing regulators FNR, Wbl, aconitase, IscR, NsrR, SoxR, and AirSR contribute to bacterial pathogenesis through control of both metabolism and classical virulence factors. In addition, we briefly review mammalian iron homeostasis as well as oxidative/nitrosative stress to provide context for understanding the function of bacterial iron-sulfur cluster sensors in different niches within the host.

The combined effect of dissolved oxygen and nitrite on N2O production by ammonia oxidizing bacteria in an enriched nitrifying sludge

Both nitrite [Formula: see text] and dissolved oxygen (DO) play important roles in nitrous oxide (N2O) production by ammonia oxidizing bacteria (AOB). However, few studies focused on the combined effect of them on N2O production by AOB as well as the corresponding mechanisms. In this study, N2O production by an enriched nitrifying sludge, consisting of both AOB and nitrite-oxidizing bacteria (NOB), was investigated under various [Formula: see text] and DO concentrations. At each investigated DO level, both the biomass specific N2O production rate and the N2O emission factor (the ratio between N2O nitrogen emitted and the ammonium nitrogen converted) increased as [Formula: see text] concentration increased from 3 mg N/L to 50 mg N/L. However, at each investigated [Formula: see text] level, the maximum biomass specific N2O production rate occurred at DO of 0.85 mg O2/L, while the N2O emission factor decreased as DO increased from 0.35 to 3.5 mg O2/L. The analysis of the process data using a mathematical N2O model incorporating both the AOB denitrification and hydroxylamine (NH2OH) oxidation pathways indicated that the contribution of AOB denitrification pathway increased as [Formula: see text] concentration increased, but decreased as DO concentration increased, accompanied by a corresponding change in the contribution of NH2OH oxidation pathway to N2O production. The AOB denitrification pathway was predominant in most cases, with the NH2OH oxidation pathway making a comparable contribution only at high DO level (e.g. 3.5 mg O2/L).

Genomic and proteomic characterization of "Candidatus Nitrosopelagicus brevis": an ammonia-oxidizing archaeon from the open ocean

Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name "Candidatus Nitrosopelagicus brevis" str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean.

Neisserial Molecular Adaptations to the Nasopharyngeal Niche

The exclusive reservoir of the genus Neisseria is the human. Of the broad range of species that comprise the Neisseria, only two are frequently pathogenic, and only one of those is a resident of the nasopharynx. Although Neisseria meningitidis can cause severe disease if it invades the bloodstream, the vast majority of interactions between humans and Neisseria are benign, with the bacteria inhabiting its mucosal niche as a non-invasive commensal. Understandably, with the exception of Neisseria gonorrhoeae, which preferentially colonises the urogenital tract, the neisseriae are extremely well adapted to survival in the human nasopharynx, their sole biological niche. The purpose of this review is to provide an overview of the molecular mechanisms evolved by Neisseria to facilitate colonisation and survival within the nasopharynx, focussing on N. meningitidis. The organism has adapted to survive in aerosolised transmission and to attach to mucosal surfaces. It then has to replicate in a nutrition-poor environment and resist immune and competitive pressure within a polymicrobial complex. Temperature and relative gas concentrations (nitric oxide and oxygen) are likely to be potent initial signals of arrival within the nasopharyngeal environment, and this review will focus on how N. meningitidis responds to these to increase the likelihood of its survival.

An introduction to nitric oxide sensing and response in bacteria

Nitric oxide (NO) is a radical gas that has been intensively studied for its role as a bacteriostatic agent. NO reacts in complex ways with biological molecules, especially metal centers and other radicals, to generate other bioactive compounds that inhibit enzymes, oxidize macromolecules, and arrest bacterial growth. Bacteria encounter not only NO derived from the host during infection but also NO derived from other bacteria and inorganic sources. The transcriptional responses used by bacteria to respond to NO are diverse but usually involve an iron-containing transcription factor that binds NO and alters its affinity for either DNA or factors involved in transcription, leading to the production of enzymatic tolerance systems. Some of these systems, such as flavohemoglobin and flavorubredoxin, directly remove NO. Some do not but are still important for NO tolerance through other mechanisms. The targets of NO that are protected by these systems include many metabolic pathways such as the tricarboxylic acid cycle and branched chain amino acid synthesis. This chapter discusses these topics and others and serves as a general introduction to microbial NO biology.

Nitrous oxide reduction genetic potential from the microbial community of an intermittently aerated partial nitritation SBR treating mature landfill leachate

This study investigates the microbial community dynamics in an intermittently aerated partial nitritation (PN) SBR treating landfill leachate, with emphasis to the nosZ encoding gene. PN was successfully achieved and high effluent stability and suitability for a later anammox reactor was ensured. Anoxic feedings allowed denitrifying activity in the reactor. The influent composition influenced the mixed liquor suspended solids concentration leading to variations of specific operational rates. The bacterial community was low diverse due to the stringent conditions in the reactor, and was mostly enriched by members of Betaproteobacteria and Bacteroidetes as determined by 16S rRNA sequencing from excised DGGE melting types. The qPCR analysis for nitrogen cycle-related enzymes (amoA, nirS, nirK and nosZ) demonstrated high amoA enrichment but being nirS the most relatively abundant gene. nosZ was also enriched from the seed sludge. Linear correlation was found mostly between nirS and the organic specific rates. Finally, Bacteroidetes sequenced in this study by 16S rRNA DGGE were not sequenced for nosZ DGGE, indicating that not all denitrifiers deal with complete denitrification. However, nosZ encoding gene bacteria was found during the whole experiment indicating the genetic potential to reduce N2O.