Abiotic Conversion of Extracellular NH2OH Contributes to N2O Emission during Ammonia Oxidation

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.

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.

Low yield and abiotic origin of N2O formed by the complete nitrifier Nitrospira inopinata

Nitrous oxide (N2O) and nitric oxide (NO) are atmospheric trace gases that contribute to climate change and affect stratospheric and ground-level ozone concentrations. Ammonia oxidizing bacteria (AOB) and archaea (AOA) are key players in the nitrogen cycle and major producers of N2O and NO globally. However, nothing is known about N2O and NO production by the recently discovered and widely distributed complete ammonia oxidizers (comammox). Here, we show that the comammox bacterium Nitrospira inopinata is sensitive to inhibition by an NO scavenger, cannot denitrify to N2O, and emits N2O at levels that are comparable to AOA but much lower than AOB. Furthermore, we demonstrate that N2O formed by N. inopinata formed under varying oxygen regimes originates from abiotic conversion of hydroxylamine. Our findings indicate that comammox microbes may produce less N2O during nitrification than AOB.

Abiotic Nitrous Oxide (N2O) Production Is Strongly pH Dependent, but Contributes Little to Overall N2O Emissions in Biological Nitrogen Removal Systems

Hydroxylamine (NH₂OH) and nitrite (NO₂^-), intermediates during the nitritation process, can engage in chemical (abiotic) reactions that lead to nitrous oxide (N₂O) generation. Here, we quantify the kinetics and stoichiometry of the relevant abiotic reactions in a series of batch tests under different and relevant conditions, including pH, absence/presence of oxygen, and reactant concentrations. The highest N₂O production rates were measured from NH₂OH reaction with HNO₂, followed by HNO₂ reduction by Fe²⁺, NH₂OH oxidation by Fe³⁺, and finally NH₂OH disproportionation plus oxidation by O₂. Compared to other examined factors, pH had the strongest effect on N₂O formation rates. Acidic pH enhanced N₂O production from the reaction of NH₂OH with HNO₂ indicating that HNO₂ instead of NO₂^- was the reactant. In departure from previous studies, we estimate that abiotic N₂O production contributes little (< 3% of total N₂O production) to total N₂O emissions in typical nitritation reactor systems between pH 6.5 and 8. Abiotic contributions would only become important at acidic pH (≤ 5). In consideration of pH effects on both abiotic and biotic N₂O production pathways, circumneutral pH set-points are suggested to minimize overall N₂O emissions from nitritation systems.

Nitrification inhibitors effectively target N2 O-producing Nitrosospira spp. in tropical soil

The nitrification inhibitors (NIs) 3,4-dimethylpyrazole (DMPP) and dicyandiamide (DCD) can effectively reduce N2 O emissions; however, which species are targeted and the effect of these NIs on the microbial nitrifier community is still unclear. Here, we identified the ammonia oxidizing bacteria (AOB) species linked to N2 O emissions and evaluated the effects of urea and urea with DCD and DMPP on the nitrifying community in a 258 day field experiment under sugarcane. Using an amoA AOB amplicon sequencing approach and mining a previous dataset of 16S rRNA sequences, we characterized the most likely N2 O-producing AOB as a Nitrosospira spp. and identified Nitrosospira (AOB), Nitrososphaera (archaeal ammonia oxidizer) and Nitrospira (nitrite-oxidizer) as the most abundant, present nitrifiers. The fertilizer treatments had no effect on the alpha and beta diversities of the AOB communities. Interestingly, we found three clusters of co-varying variables with nitrifier operational taxonomic units (OTUs): the N2 O-producing AOB Nitrosospira with N2 O, NO3 - , NH4 + , water-filled pore space (WFPS) and pH; AOA Nitrososphaera with NO3 - , NH4 + and pH; and AOA Nitrososphaera and NOB Nitrospira with NH4 + , which suggests different drivers. These results support the co-occurrence of non-N2 O-producing Nitrososphaera and Nitrospira in the unfertilized soils and the promotion of N2 O-producing Nitrosospira under urea fertilization. Further, we suggest that DMPP is a more effective NI than DCD in tropical soil under sugarcane.

Overdose fertilization induced ammonia-oxidizing archaea producing nitrous oxide in intensive vegetable fields

Little is known about the effects of nitrogen (N) fertilization rates on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their differential contribution to nitrous oxide (N₂O) production, particularly in greenhouse based high N input vegetable soils. Six N treatments (N1, N2, N3, N4, N5 and N6 representing 0, 293, 587, 880, 1173 and 1760 kg N ha^-1 yr^-1, respectively) were continuously managed for three years in a typically intensified vegetable field in China. The aerobic incubation experiment involving these field-treated soils was designed to evaluate the relative contributions of AOA and AOB to N₂O production by using acetylene or 1-octyne as inhibitors. The results showed that the soil pH and net nitrification rate gradually declined with increasing the fertilizer N application rates. The AOA were responsible for 44-71% of the N₂O production with negligible N₂O from AOB in urea unamended control soils. With urea amendment, the AOA were responsible for 48-53% of the N₂O production in the excessively fertilized soils, namely the N5-N6 soils, while the AOB were responsible for 42-55% in the conventionally fertilized soils, namely the N1-N4 soils. Results indicated that overdose fertilization induced higher AOA-dependent N₂O production than AOB, whereas urea supply led to higher AOB-dependent N₂O production than AOA in conventionally fertilized soils. Additionally, a positive relationship existed between N₂O production and NO₂^- accumulation during the incubation. Further mechanisms for NO₂^--dependent N₂O production in intensive vegetable soils therefore deserve urgent attention.

Free nitrous acid (FNA) induced transformation of sulfamethoxazole in the enriched nitrifying culture

The sulfonamide antibiotics sulfamethoxazole (SMX) has been frequently detected in the wastewater. It has been reported that part of SMX can be transformed by the co-metabolism of ammonia oxidizing bacteria (AOB) during nitrifying process. However, previous studies reported inconsistent or even contradictory results in terms of SMX degradation and/or transformation. Literature study revealed that nitrite may play certain role in SMX transformation, which has been neglected previously. In this study, the transformation behavior of SMX was investigated with and without the presence of nitrite in an enriched nitrifying culture. The results clearly show that the elimination of SMX occurred with the presence/accumulation of nitrite, and a linear regression was observed between SMX elimination efficiency and free nitrous acid (FNA) concentration, indicating that FNA was the major factor responsible for the SMX transformation. By reacting with FNA, SMX transformation products, such as 4-nitro-SMX, desamino-SMX and hydroxylated SMX, were detected. However, when FNA concentration decreased, these intermediates may be retransformed back to SMX. These findings improved our understanding on SMX transformation in a biological system and highlighted the role of nitrite/FNA in the sulfonamide antibiotics degradation.

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

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

Planktonic Marine Archaea

Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group-the marine Thaumarchaeota-has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done.

Nitritation, nitrous oxide emission pathways and in situ microbial community in a modified University of Cape Town process

Achieving nitritation is a prerequisite to promote nutrients removal and save energy, but emission of nitrous oxide as a greenhouse gas cannot be ignored. This study established the nitritation in a continuous-flow MUCT process and investigated the mechanism of N₂O generation. The nitrite accumulation ratio (NAR) reached 95% by controlling the low DO of 0.3-0.5 mg/L and short HRT of 8 h. The ¹⁵N-isotope tracer experiment indicated that the percentage of nitrifier-denitrification (ND) pathway increased by 12.7% under the limited-aeration mode, improving the stable operating of nitritation. Meanwhile, the autotrophic anammox pathway increased with the contribution ratio of 14.7% to N₂ emission under the nitritation mode. The ¹⁵N-DNA-SIP revealed that the Nitrosomonas executed the ND pathway and the Planctomycetes conducted the anammox process, respectively. The integration of autotrophic and heterotrophic process based on nitritation technique has potential to solve the carbon-limited issue for total nitrogen removal in mainstream WWTPs.

Abiotic hydroxylamine nitrification involving manganese- and iron-bearing minerals

Hydroxylamine (NH₂OH) undergoes biotic and abiotic transformation processes in soil, producing nitrous oxide gas (N₂O(g)). Little is known about the magnitude of the abiotic chemical processes in the global N cycle, and the role of abiotic nitrification is still neglected in most current nitrogen trace gas studies. The abiotic fate of NH₂OH in soil systems is often focused on transition metals including manganese (Mn) and iron (Fe), and empirical correlations of nitrogen residual species including nitrite (NO₂^-), nitrate (NO₃^-), and N₂O(g). In this study, abiotic NH₂OH nitrification by well-characterized manganese (Mn)- and iron (Fe)-bearing minerals (pyrolusite, amorphous MnO₂(s), goethite, amorphous FeOOH(s)) was investigated. A nitrogen mass balance analysis involving NH₂OH, and the abiotic nitrification residuals, N₂O(g), N₂O(aq), NO₂^-, NO₃^-, was used, and specific reactions and mechanisms were investigated. Rapid and complete NH₂OH nitrification occurred (4-5 h) in the presence of pyrolusite and amorphous MnO₂(s), achieving a 95-96% mass balance of N byproducts. Conversely, NH₂OH nitrification was considerably slower by amorphous FeOOH(s) (14.5%) and goethite (1.1%). Direct reactions between the Mn- and Fe-bearing mineral species and NO₂^- and NO₃^- were not detected. Brunauer-Emmett-Teller surface area and energy dispersive X-ray measurements for elemental composition were used to determine the specific concentrations of Mn and Fe. Despite similar specific concentrations of Mn and Fe in crystalline and amorphous minerals, the rate of NH₂OH nitrification was much greater in the Mn-bearing minerals. Results underscore the intrinsically faster NH₂OH nitrification by Mn minerals than Fe minerals.

Nitrite accumulation inside sludge flocs significantly influencing nitrous oxide production by ammonium-oxidizing bacteria

This work aims to clarify the role of potential nitrite (NO₂^-) accumulation inside sludge flocs in N₂O production by ammonium-oxidizing bacteria (AOB) at different dissolved oxygen (DO) levels with focus on the conditions of no significant bulk NO₂^- accumulation (<0.2 mg N/L). To this end, an augmented nitrifying sludge with much higher abundance of nitrite-oxidizing bacteria (NOB) than AOB was enriched and then used for systematically designed batch tests, which targeted a range of DO levels from 0 to 3.0 mg O₂/L at a fixed ammonium concentration of 10 mg N/L. A two-pathway N₂O model was applied to facilitate the interpretation of batch experimental data, thus shedding light on the relationships between N₂O production pathways and key process parameters (i.e., DO and NO₂^- accumulation inside sludge flocs). The results demonstrated (i) the biomass specific N₂O production rate firstly increased and then decreased with DO, with the maximum value of 3.03 ± 0.05 mg N/h/g VSS obtained at DO level of 0.75 mg O₂/L, (ii) the AOB denitrification pathway for N₂O production was dominant (98.0%) at all DO levels tested even without significant bulk NO₂^- accumulation (<0.2 mg N/L) observed in the system, but its contribution decreased with DO, (iii) DO had a positive impact on the hydroxylamine pathway for N₂O production which therefore increased with DO, and (iv) the nitrite accumulation existed inside the sludge flocs and induced significant N₂O production from the AOB denitrification pathway.

Ammonia Monooxygenase-Mediated Cometabolic Biotransformation and Hydroxylamine-Mediated Abiotic Transformation of Micropollutants in an AOB/NOB Coculture

Biotransformation of various micropollutants (MPs) has been found to be positively correlated with nitrification in activated sludge communities. To further elucidate the roles played by ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), we investigated the biotransformation capabilities of an NOB pure culture ( Nitrobacter sp.) and an AOB ( Nitrosomonas europaea)/NOB ( Nitrobacter sp.) coculture for 15 MPs, whose biotransformation was reported previously to be associated with nitrification. The NOB pure culture did not biotransform any investigated MP, whereas the AOB/NOB coculture was capable of biotransforming six MPs (i.e., asulam, bezafibrate, fenhexamid, furosemide, indomethacin, and rufinamide). Transformation products (TPs) were identified, and tentative structures were proposed. Inhibition studies with octyne, an ammonia monooxygenase (AMO) inhibitor, suggested that AMO was the responsible enzyme for MP transformation that occurred cometabolically. For the first time, hydroxylamine, a key intermediate of all aerobic ammonia oxidizers, was found to react with several MPs at concentrations typically occurring in AOB batch cultures. All of these MPs were also biotransformed by the AOB/NOB coculture. Moreover, the same asulam TPs were detected in both biotransformation and hydroxylamine-treated abiotic transformation experiments, whereas rufinamide TPs formed from biological transformation were not detected during hydroxylamine-mediated abiotic transformation, which was consistent with the inability of rufinamide abiotic transformation by hydroxylamine. Thus, in addition to cometabolism likely carried out by AMO, an abiotic transformation route indirectly mediated by AMO might also contribute to MP biotransformation by AOB.

The cycle of nitrogen in river systems: sources, transformation, and flux

Nitrogen is a requisite and highly demanded element for living organisms on Earth. However, increasing human activities have greatly altered the global nitrogen cycle, especially in rivers and streams, resulting in eutrophication, formation of hypoxic zones, and increased production of N2O, a powerful greenhouse gas. This review focuses on three aspects of the nitrogen cycle in streams and rivers. We firstly introduce the distributions and concentrations of nitrogen compounds in streams and rivers as well as the techniques for tracing the sources of nitrogen pollution. Secondly, the overall picture of nitrogen transformations in rivers and streams conducted by organisms is described, especially focusing on the roles of suspended particle-water surfaces in overlying water, sediment-water interfaces, and riparian zones in the nitrogen cycle of streams and rivers. The coupling of nitrogen and other element (C, S, and Fe) cycles in streams and rivers is also briefly covered. Finally, we analyze the nitrogen budget of river systems as well as nitrogen loss as N2O and N2 through the fluvial network and give a summary of the effects and consequences of human activities and climate change on the riverine nitrogen cycle. In addition, future directions for the research on the nitrogen cycle in river systems are outlined.

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

Nitrous acid (HONO) is an important precursor of the hydroxyl radical (OH), the atmosphere´s primary oxidant. An unknown strong daytime source of HONO is required to explain measurements in ambient air. Emissions from soils are one of the potential sources. Ammonia-oxidizing bacteria (AOB) have been identified as possible producers of these HONO soil emissions. However, the mechanisms for production and release of HONO in soils are not fully understood. In this study, we used a dynamic soil-chamber system to provide direct evidence that gaseous emissions from nitrifying pure cultures contain hydroxylamine (NH₂OH), which is subsequently converted to HONO in a heterogeneous reaction with water vapor on glass bead surfaces. In addition to different AOB species, we found release of HONO also in ammonia-oxidizing archaea (AOA), suggesting that these globally abundant microbes may also contribute to the formation of atmospheric HONO and consequently OH. Since biogenic NH₂OH is formed by diverse organisms, such as AOB, AOA, methane-oxidizing bacteria, heterotrophic nitrifiers, and fungi, we argue that HONO emission from soil is not restricted to the nitrifying bacteria, but is also promoted by nitrifying members of the domains Archaea and Eukarya.