Mass Spectrometric Studies of the Effect of pH on the Accumulation of Intermediates in Denitrification by Paracoccus denitrificans

Sustained bacterial N2O reduction at acidic pH

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

Effect of free ammonia on partial denitrification: Long-term performance, mechanism, and feasibility of PD/Anammox-FBBR for mature landfill leachate treatment

As a stable and effective approach for NO2--N accumulation, partial denitrification (PD) could significantly cut down operation cost, and PD/Anammox (PD/A) is a promising nitrogen removal process in wastewater treatment. The biotoxicity of free ammonia (FA) to nitrifying bacteria and anammox bacteria has been demonstrated, while whether FA affects PD bacteria is an open question. Here, long-term operation of PD-fixed bed biofilm reactor (PD-FBBR) treating synthetic wastewater and mature landfill leachate was conducted to reveal the mechanism concerning the effect of FA on PD bacteria. Stable NO2--N accumulation was achieved with NO3--N to NO2--N transformation ratio (NTR) of 60-70% during 280-day operation with FA ranged from 0 to 20.71 ± 0.23 mg/L, while NTR decreased and maintained at ∼30% when FA reached 40.59 ± 0.19 mg/L. Specific NOx--N reduction rate improved at low FA concentration (< 12 mg/L), while high FA level (> 25 mg/L) had inhibitory effect on PD bacteria. Under FA stress, more extracellular polymeric substances (EPS) were secreted, and the glnA gene abundance, glutamine synthase concentration, and glutamine concentration in cell and EPS significantly increased, indicating the enhancement of glutamine biosynthesis in PD bacteria for ammonia assimilation played an important role in response to FA stress. Metagenomic sequencing showed that FA stimulated the upregulation of narK (NO3--N/NO2--N antiporter) gene abundance and enhanced uptake of NO3--N and extrusion of NO2--N. Comamonas, unclassified_f__Comamonadaceae and Thauera were highly enriched in biofilm, which played a key role in the stable NO2--N accumulation. Furthermore, a novel two stage PD/A-FBBR was applied to mature landfill leachate treatment, and satisfactory total inorganic nitrogen removal efficiency ranged from 81.38 ± 3.56% to 89.16 ± 1.57% was obtained at relatively low COD/NO3--N of 2.57-2.84. Overall, these findings demonstrated how PD bacteria respond to FA stress and confirmed the feasibility of PD/A process in high FA wastewater treatment.

Effect of COD/ NO3−-N ratio on nitrite accumulation and microbial behavior in glucose-driven partial denitrification system

COD/NO₃ ^--N ratio was considered to be one of the key factors achieving effective nitrite accumulation during partial denitrification. In two parallel reactors incubated with glucose as carbon source at COD/NO₃ ^--N of 3 and 5, respectively, the microbial community structure shift and the nitrite accumulation performance during long-term operation were investigated. The maximum nitrite accumulation ratios at COD/NO₃ ^--N of 3 and 5 were 17.9% and 47.04%, respectively. Thauera was the dominant genus in both reactors on day 220 with the relative abundance of 18.67% and 64.01%, respectively. Batch experiments with different electron acceptors suggested that the distinction in nitrite accumulation at COD/NO₃ ^--N of 3 and 5 might be caused by the differences in the abundance of Thauera.

Effects of liming on oxic and anoxic N2O and CO2 production in different horizons of boreal acid sulfate soil and non-acid soil under controlled conditions

In acid sulfate (AS) soils, organic rich topsoil and subsoil horizons with highly variable acidity and moisture conditions and interconnected reactions of sulfur and nitrogen make them potential sources of greenhouse gases (GHGs). Subsoil liming can reduce the acidification of sulfidic subsoils in the field. However, the mitigation of GHG production in AS subsoils by liming, and the mechanisms involved, are still poorly known. We limed samples from different horizons of AS and non-AS soils to study the effects of liming on the N₂O and CO₂ production during a 56-day oxic and subsequent 72-h anoxic incubation. Liming to pH ≥ 7 decreased oxic N₂O production by 97-98 % in the Ap1 horizon, 38-50 % in the Bg1 horizon, and 34-36 % in the BC horizon, but increased it by 136-208 % in the C horizon, respectively. Liming decreased anoxic N₂O production by 86-94 % and 78-91 % in Ap1 and Bg1 horizons, but increased it by 100-500 % and 50-162 % in BC and C horizons, respectively. Liming decreased N₂O/(N₂O + N₂) in anoxic denitrification in most horizons of both AS and non-AS soils. Liming significantly increased the cumulative oxic and anoxic CO₂ production in AS soil, but less so in non-AS soil due to the initial high soil pH. Higher carbon and nitrogen contents in AS soil compared to non-AS soil agreed with the respectively higher cumulative oxic N₂O production in all horizons, and the higher CO₂ production in the subsoil horizons of all lime treatments. Overall, liming reduced the proportion of N₂O in the GHGs produced in most soil horizons under oxic and anoxic conditions but reduced the total GHG production (as CO₂ equivalents) only in the Ap1 horizon of both soils. The results suggest that liming of subsoils may not always effectively mitigate GHG emissions due to concurrently increased CO₂ production and denitrification.

Propionibacterium freudenreichii-Assisted Approach Reduces N2O Emission and Improves Denitrification via Promoting Substrate Uptake and Metabolism

N₂O emission is often encountered during biodenitrification. In this paper, a new approach of using microorganisms to promote substrate uptake and metabolism to reduce denitrification intermediate accumulation was reported. With the introduction of Propionibacterium freudenreichii to a biodenitrification system, N₂O and nitrite accumulation was, respectively, decreased by 74 and 60% and the denitrification efficiency was increased by 150% at the time of 24 h with P. freudenreichii/groundwater denitrifier of 1/5 (OD₆₀₀). Propionate, produced by P. freudenreichii, only accelerated nitrate removal and was not the main reason for the decreased intermediate accumulation. The proteomic and enzyme analyses revealed that P. freudenreichii stimulated biofilm formation by upregulating proteins involved in porin forming, putrescine biosynthesis, spermidine/putrescine transport, and quorum sensing and upregulated transport proteins, which facilitated the uptake of the carbon source, nitrate, and Fe and Mo (the required catalytic sites of denitrification enzymes). Further investigation revealed that P. freudenreichii activated the methylmalonyl-CoA pathway in the denitrifier and promoted it to synthesize heme/heme d1, the groups of denitrification enzymes and electron transfer proteins, which upregulated the expression of denitrifying enzyme proteins and enhanced the ratio of NosZ to NorB, resulting in the increase of generation, transfer, and consumption of electrons in biodenitrification. Therefore, a significant reduction in the denitrification intermediate accumulation and an improvement in the denitrification efficiency were observed.

Assessing Intermediate Formation and Electron Competition during Thiosulfate-Driven Denitrification: An Experimental and Modeling Study

There is increasing interest in thiosulfate-driven denitrification for low C/N wastewater treatment, but the denitrification performance varies with the thiosulfate oxidation pathways. Models have been developed to predict the products of denitrification, but few consider thiosulfate reduction to elemental sulfur (S⁰), an undesirable reaction that can intensify electron competition with denitrifying enzymes. In this study, the model using indirect coupling of electrons (ICE) was developed to predict S⁰ formation and electron competition during thiosulfate-driven denitrification. Kinetic data were obtained from sulfur-oxidizing bacteria (SOB) dominated by the branched pathway and were used to calibrate and validate the model. Electron competition was investigated under different operating conditions. Modeling results reveal that electrons produced in the first step of thiosulfate oxidation typically prioritize thiosulfate reduction, then nitrate reduction, and finally nitrite reduction. However, the electron consumption rate for S⁰ formation decreases sharply with the decline of thiosulfate concentration. Thus, a continuous feeding strategy was effective in alleviating the competition between thiosulfate reduction and denitrifying enzymes. Electron competition leads to nitrite accumulation, which could be a reliable substrate for anammox. The model was further evaluated with anammox integration. Results suggested that the branched pathway and continuous supply of thiosulfate are favorable to create a symbiotic relationship between SOB and anammox.

Revisiting the involvement of ammonia oxidizers and denitrifiers in nitrous oxide emission from cropland soils

Nitrous oxide (N₂O), an ozone-depleting greenhouse gas, is generally produced by soil microbes, particularly NH₃ oxidizers and denitrifiers, and emitted in large quantities after N fertilizer application in croplands. N₂O can be produced via multiple processes, and reduced, with the involvement of more diverse microbes with different physiological constraints than previously thought; therefore, there is a lack of consensus on the production processes and microbes involved under different agricultural practices. In this study, multiple approaches were applied, including N₂O isotopocule analyses, microbial gene transcript measurements, and selective inhibition assays, to revisit the involvement of NH₃ oxidizers and denitrifiers, including the previously-overlooked taxa, in N₂O emission from a cropland, and address the biological and environmental factors controlling the N₂O production processes. Then, we synthesized the results from those approaches and revealed that the overlooked denitrifying bacteria and fungi were more involved in N₂O production than the long-studied ones. We also demonstrated that the N₂O production processes and soil microbes involved were different based on fertilization practices (plowing or surface application) and fertilization types (manure or urea). In particular, we identified the following intensified activities: (1) N₂O production by overlooked denitrifying fungi after manure fertilization onto soil surface; (2) N₂O production by overlooked denitrifying bacteria and N₂O reduction by long-studied N₂O-reducing bacteria after manure fertilization into the plowed layer; and (3) N₂O production by NH₃-oxidizing bacteria and overlooked denitrifying bacteria and fungi when urea fertilization was applied into the plowed layer. We finally propose the conceptual scheme of N flow after fertilization based on distinct physiological constraints among the diverse NH₃ oxidizers and denitrifiers, which will help us understand the environmental context-dependent N₂O emission processes.

Primary sludge fermentate as carbon source for mainstream partial denitrification-anammox (PdNA)

Primary sludge fermentate, a concentrated hydrolyzed wastewater carbon, was evaluated for use as an alternative carbon source for mainstream partial denitrification-anammox (PdNA) in a suspended growth activated sludge process in terms of partial denitrification (PdN) efficiency, PdNA nitrogen removal contributions, and final effluent quality. Fermenter operation at a 2-day sludge retention time (SRT) resulted in the maximum achievable yield of 0.14 ± 0.05 g sCOD/g VSS without release of excessive ammonia and phosphorus to the system. Based on the results of batch experiments, fermentate addition led to PdN efficiency of 93 ± 14%, which was similar to acetate at a nitrate residual of 2-3 mg N/L. In the pilot-scale mainstream deammonification reactor, PdN efficiency using fermentate was 49 ± 24%, which was lower than acetate (66 ± 24% during acetate period I and 70 ± 21% during acetate period II), most probably due to lower nitrate and ammonium kinetics in the PdN zone. Methanol cost-saving potential for the application of PdNA as the main short-cut nitrogen pathway was estimated to be 30% to 55% depending on the PdN efficiency achieved. PRACTITIONER POINTS: Primary sludge fermentate was evaluated as an alternative carbon source for mainstream partial denitrification-anammox (PdNA). Fermenter operated at a 1 to 2 day SRT resulted in the maximum achievable yield without the release of excessive ammonia and phosphorus to the system. Although 93% partial denitrification efficiency was achieved with fermentate in batch experiments, around 49% PdN efficiency was achieved in pilot studies. Application of PdNA with fermentate can result in significant methanol cost savings.

Nitrate and nitrite bacterial reduction at alkaline pH and high nitrate concentrations, comparison of acetate versus dihydrogen as electron donors

This study assesses bacterial denitrification at alkaline pH, up to 12, and high nitrate concentration, up to 400 mM. Two types of electron donors organic (acetate) and inorganic (dihydrogen) were compared. With both types of electron donors, nitrite reduction was the key step, likely to increase the pH and lead to nitrite accumulation. Firstly, an acclimation process was used: nitrate was progressively increased in three cultures set at pH 9, 10, or 11. This method allowed to observe for the first time nitrate reduction up to pH 10 and 100 mM nitrate with dihydrogen, or up to pH 10 and 400 mM nitrate with acetate. Nitrate reduction kinetics were faster in the presence of acetate. To investigate further the impact of the type of electron donor, a transition from acetate to dihydrogen was tested, and the pH evolution was modelled. Denitrification with dihydrogen strongly increases the pH while with acetate the pH evolution depends on the initial pH. The main difference is the production of acidifying CO₂ during the acetate oxidation. Finally, the use of long duration cultures with a highly alkaline pH allowed a nitrate reduction up to pH 11.5 with acetate. However, no reduction was possible in hydrogenotrophy as it would have increased the pH further. Instead, bacteria used organic matter from inoculum to reduce nitrate at pH 11.5. Therefore, considering bacterial denitrification in a context of alkaline pH and high nitrate concentration an organic electron donor such as acetate is advantageous.

Nitrogen stocks and flows in an acid sulfate soil

Besides causing acidification, acid sulfate (AS) soils contain large nitrogen (N) stocks and are a potential source of N loading to waters and nitrous oxide (N₂O) emissions. We quantified the stocks and flows of N, including crop yields, N leaching, and N₂O emissions, in a cultivated AS soil in western Finland. We also investigated whether controlled drainage (CD) and sub-irrigation (CDI) to keep the sulfidic horizons inundated can alleviate N losses. Total N stock at 0-100 cm (19.5 Mg ha^-1) was smaller than at 100-200 cm (26.6 Mg ha^-1), and the mineral N stock was largest below 170 cm. Annual N leaching (31-91 kg N ha^-1) plus N in harvested grain (74-122 kg N ha^-1) was 148% (range 118-189%) of N applied in fertilizers (90-125 kg N ha^-1) in 2011-2017, suggesting substantial N supply from soil reserves. Annual emissions of N₂O measured during 2 years were 8-28 kg N ha^-1. The most probable reasons for high N₂O emission rates in AS soils are concomitant large mineral N pools with fluctuating redox conditions and low pH in the oxidized subsoil, all favoring formation of N₂O in nitrification and denitrification. Although the groundwater level was higher in CD and CDI than in conventional drainage, N load and crop offtake did not differ between the drainage methods, but there were differences in emissions. Nitrogen flows to the atmosphere and drainage water were clearly larger than those in non-AS mineral soils indicating that AS soils are potential hotspots of environmental impacts.

Application of acidic conditions and inert-gas sparging to achieve high-efficiency nitrous oxide recovery during nitrite denitrification

Nitrogen removal with energy recovery through denitrification dependent N₂O production is garnering recent attention due to its cost advantages. The most effective current method requires alternating COD and nitrite to achieve high N₂O production making it incompatible with typical wastewaters and consequently difficult to use in most settings. The work described here introduces a robust and highly efficient N₂O recovery approach which has the potential to work with wastewaters containing COD and nitrite simultaneously. This method relies on low pH incubation and inert gas sparging (IGS) to shift a community of mainly N₂ producing nitrite denitrifiers to a community that accumulates N₂O when incubated in the absence of IGS. Before experiencing IGS, samples from activated sludge incubated at a pH of 4.5 and 6.0 only achieved a maximum N₂O production efficiency (PE_N₂O) of ∼26%. After IGS the PE_N₂O values increased to ∼97.5% and ∼80.2% for samples from these same pH 4.5 and pH 6.0 reactors, respectively. IGS did not lead to N₂O production in a pH 7.5 bioreactor. Meta-omics analysis revealed that IGS resulted in an increase in bacteria utilizing the clade I nitrous oxide reductase (nosZ_I) relative to bacteria utilizing the clade II nitrous oxide reductase (nosZ_II). This likely results from IGS flushing out N₂O leaving nitrite as the principal nitrogen oxide available for respiration, favoring nosZ_I utilizing bacteria which are more likely to be complete denitrifiers. Metatranscriptomic analysis suggested that the high PE_N₂O values that occurred after stopping IGS result from the NO generated by chemodenitrification accumulating to levels that inactivate [4Fe:4S] clusters in the NosR protein essential for N₂O reduction in the nosZ_I denitrifiers. This study provides an efficient and straightforward method for N₂O recovery, widening the options for energy recovery from nitrogen-based wastes.

Crop yield and N2O emission affected by long-term organic manure substitution fertilizer under winter wheat-summer maize cropping system

Application of organic manure combined with synthetic fertilizer can maintain crop yield and improve soil fertility, but the long-term effects of substituting different proportions of synthetic fertilizers with organic manure on N₂O emission remain unclear. In this study, field experiments and DNDC model simulations were used to study the long-term effects of substituting synthetic fertilizers with organic manure on crop yield and N₂O emission. The field experiment was conducted at Guanzhong Plain, northern China, under a wheat-maize cropping system. Six treatments were included: no fertilization (CK); synthetic nitrogen (N), phosphorus (P) and potassium (K) fertilizers (NPK); and 25%, 50%, 75% and 100% of the synthetic N substituted by dairy manure (25%M, 50%M, 75%M, and 100%M), respectively. The DNDC model was calibrated using the field data from the NPK treatment from 2014 to 2017 and was validated for the other treatments. The results showed that the DNDC model can successfully simulate the crop yield (e.g. nRMSE < 5%) and annual N₂O emission (nRMSE < 20%). In addition, a 30-year simulation found that organic manure substitution treatments could maintain wheat yield well, and the yield variation between different years was small. However, relative to the NPK treatment, the maize yields for the first 6 and 7 years were lower under 50%M and 75%M, and under 100%M maize yields were reduced for the first 15 years. The long-term simulation showed that N₂O emission of fertilized treatment had an increasing trend over time, especially the 75%M treatment where the N₂O emission was higher than that of NPK treatment after 25 years of fertilization. The annual mean N₂O emission under different treatments was, in decreasing order, NPK > 25%M > 50%M > 75%M > 100%M > CK. The yield-scale N₂O emission and emission factor were highest for the NPK treatment. Considering crop yield, yield stability and N₂O emission, substitution of 25% synthetic fertilizer by organic manure can simultaneously ensure crop productivity and environmental protection under the tested environment.

Involvement of the cbb3-Type Terminal Oxidase in Growth Competition of Bacteria, Biofilm Formation, and in Switching between Denitrification and Aerobic Respiration

Paracoccus denitrificans has a branched electron transport chain with three terminal oxidases transferring electrons to molecular oxygen, namely aa₃-type and cbb₃-type cytochrome c oxidases and ba₃-type ubiquinol oxidase. In the present study, we focused on strains expressing only one of these enzymes. The competition experiments showed that possession of cbb₃-type oxidase confers significant fitness advantage during oxygen-limited growth and supports the biofilm lifestyle. The aa₃-type oxidase was shown to allow rapid aerobic growth at a high oxygen supply. Activity of the denitrification pathway that had been expressed in cells grown anaerobically with nitrate was fully inhibitable by oxygen only in wild-type and cbb₃ strains, while in strains aa₃ and ba₃ dinitrogen production from nitrate and oxygen consumption occurred simultaneously. Together, the results highlight the importance of the cbb₃-type oxidase for the denitrification phenotype and suggest a way of obtaining novel bacterial strains capable of aerobic denitrification.

Microbial community structures and functions of hypersaline heterotrophic denitrifying process: Lab-scale and pilot-scale studies

High-nitrate wastewaters are known pose substantial risks to human and environmental health, while their effective treatment remains difficult. The denitrification of saline, high-NO₃^- wastewaters was investigated at the laboratory- and pilot-scale experiment. Complete denitrification was achieved for three different realistic wastewaters, and the maximum influent [NO₃^-]₀ and salinity were as high as 20,500 mg/L and 7.8%, respectively. The results of microbial community structure analyses revealed that the sequences of denitrifying functional bacteria accounted for 96.2% of all sequences, and the functional genes for denitrification in bacteria were enriched with elevated salinity and [NO₃^-]₀. A significant difference was observed in the dominant bacterial genus between synthetic and realistic wastewaters. Thauera and Halomonas species evolved to be the most common dominant genera contributing to the processes of nitrate, nitrite, and nitrous oxide reductase. This study is practically valuable for the treatment of realistic, saline, high-NO₃^- wastewaters via denitrification by heterotrophic bacteria.

Characterization of eubacterial communities by Denaturing Gradient Gel Electrophoresis (DGGE) and Next Generation Sequencing (NGS) in a desulfurization biotrickling filter using progressive changes of nitrate and nitrite as final electron acceptors

Anoxic biotrickling filters (BTFs) represent a technology with high H₂S elimination capacity and removal efficiencies widely studied for biogas desulfurization. Three changes in the final electron acceptors were made using nitrate and nitrite during an operating period of 520 days. The stability and performance of the anoxic BTF were maintained when a significant perturbation was applied to the system that involved the progressive change of nitrate to nitrite and vice versa. Here the impact of electron acceptor changes on the microbial community was characterized by denaturing gel gradient electrophoresis (DGGE) and next generation sequencing (NGS). Both platforms revealed that the community underwent changes during the perturbations but was resilient because the removal capacity did not significantly change. Proteobacteria and Bacteroidetes were the main Phyla and Sulfurimonas and Thiobacillus the main nitrate-reducing sulfide-oxidizing bacteria (NR-SOB) genera involved in the biodesulfurization process.

Modeling Denitrification as an Electric Circuit Accurately Captures Electron Competition between Individual Reductive Steps: The Activated Sludge Model-Electron Competition Model

Heterotrophic denitrification consists of the four-step sequential reduction of nitrate to dinitrogen gas over nitrite, nitric oxide, and nitrous oxide. Oxidation processes, commonly of organic compounds, provide the electrons needed for the sequential reaction steps. The intracellular electron distribution is a competitive process among the four reduction steps. In this study, a model describing organic carbon oxidation and four-step denitrification through electron competition is proposed [Activated Sludge Model-Electron Competition (ASM-EC)]. The model describes denitrification rates as an analogy to how current intensity varies through a parallel set of resistors in electric circuits. The ASM-EC model was calibrated with data from batch experiments with heterotrophic denitrifying communities, where reduction of mixtures of nitrogen oxides was monitored, while different carbon sources were supplied in excess. The carbon sources included methanol, ethanol, acetate, and their ternary mixture. The electron distribution preference and electron uptake rates varied between the carbon sources and were captured by the model structure for most of the experiments. The ASM-EC model uses fewer parameters compared to existing state-of-the-art denitrification models and performed equally well in the tested scenarios. We advocate the use of this model for denitrification in the activated sludge model, which can easily be integrated in existing model structures, because it provides a parsimonious description of electron competition during denitrification.

Adaptation of neutrophilic Paracoccus denitrificans to denitrification at highly alkaline pH

Bacterial denitrification is widely documented at neutral pH in order to improve the removal of nitrate in wastewater treatment processes. However, certain industrial contexts generate alkaline waste and effluent containing nitrate that must be denitrified. To obtain more information on denitrification at alkaline pH, this study evaluated the possibility of adapting a neutrophilic denitrifying strain, Paracoccus denitrificans, to alkaline pH. Firstly, P. denitrificans' denitrifying activity was evaluated without acclimation in batch bioreactors at pH 7.0, 8.0, 9.0 and 10.0. Then, two acclimation methods using successive batch bioreactors and a continuous bioreactor allowed P. denitrificans to be gradually exposed to alkaline pH: from 8.5 to 11.2 in 26 and 72 days respectively. Results showed that P. denitrificans could grow and catalyse nitrate reduction (i) at pH 9.0 without acclimation, (ii) at pH 10.5 in successive batch cultures with progressively increasing pH and (iii) at pH 10.8 in continuously fed culture with a hydraulic retention time (HRT) of 8 days. It was shown that denitrification affected the pH despite the presence of carbonate buffering of the P. denitrificans growth medium. With acetate as an electron donor, the pH of a carbonate buffered medium tends towards pH 10 during the process of denitrification. Graphical abstract.

Bioelectrochemical Ammoniation Coupled with Microbial Electrolysis for Nitrogen Recovery from Nitrate in Wastewater

Nitrate-N in wastewaters is hard to be recovered because it is difficult to volatilize with an opposite charge to ammonium. Here, we have proved the feasibility of dissimilatory nitrate reduction to ammonia (DNRA) by the easy-acclimated mixed electroactive bacteria, achieving the highest DNRA efficiency of 44%. It was then coupled with microbial electrolysis to concentrate ammonium by a factor of 4 in the catholyte for recovery. The abundance of electroactive bacteria in the biofilm before nitrate addition, especially Geobacter spp., was found to determine the DNRA efficiency. As the main competitors of DNRA bacteria, the growth of denitrifiers was more sensitive to C/N ratios. The DNRA microbial community contrarily showed a stable and recoverable ammoniation performance over C/N ratios ranging from 0.5 to 8.0. A strong competition of the electrode and nitrate on electron donors was observed at the early stage (15 d) of electroactive biofilm formation, which can be weakened when the biofilm was mature on 40 d. Quantitative PCR showed a significant increase in nirS and nrfA transcripts in the ammoniation process. nirS was inhibited significantly after nitrate depletion while nrfA was still upregulated. These findings provided a novel way to recover nitrate-N using organic wastes as both electron donor and power, which has broader implications on the sustainable wastewater treatment and the ecology of nitrogen cycling.

Biochar Enhances Nitrous Oxide Reduction in Acidic but Not in Near-Neutral pH Soil

We quantified nitrous oxide (N2O) fluxes and total denitrification (N2O + N2) in an acidic (Ferralsol) and a near-neutral pH soil (Cambisol) to determine whether biochar’s alkalinization effect could be the mechanism inducing potential reductions in N2O fluxes. In Ferralsol, decreases in N2O emissions and in the N2O to N2O + N2 ratio were observed in both biochar and lime treatments. In Cambisol, neither biochar nor lime decreased N2O emissions, despite significantly increasing soil pH. The abundance and community structure of nosZ gene-bearing microorganisms indicated that gene abundances did not explain biochar effects, but a higher diversity of nosZ gene-bearing microorganisms correlated to lower total denitrification. Overall, our results suggest that biochar’s potential to decrease N2O emissions, through soil alkalinization, may be more effective in acidic soils.

Influence of Hydrogen Electron Donor, Alkaline pH, and High Nitrate Concentrations on Microbial Denitrification: A Review

Bacterial respiration of nitrate is a natural process of nitrate reduction, which has been industrialized to treat anthropic nitrate pollution. This process, also known as “microbial denitrification”, is widely documented from the fundamental and engineering points of view for the enhancement of the removal of nitrate in wastewater. For this purpose, experiments are generally conducted with heterotrophic microbial metabolism, neutral pH and moderate nitrate concentrations (<50 mM). The present review focuses on a different approach as it aims to understand the effects of hydrogenotrophy, alkaline pH and high nitrate concentration on microbial denitrification. Hydrogen has a high energy content but its low solubility, 0.74 mM (1 atm, 30 °C), in aqueous medium limits its bioavailability, putting it at a kinetic disadvantage compared to more soluble organic compounds. For most bacteria, the optimal pH varies between 7.5 and 9.5. Outside this range, denitrification is slowed down and nitrite (NO₂⁻) accumulates. Some alkaliphilic bacteria are able to express denitrifying activity at pH levels close to 12 thanks to specific adaptation and resistance mechanisms detailed in this manuscript, and some bacterial populations support nitrate concentrations in the range of several hundred mM to 1 M. A high concentration of nitrate generally leads to an accumulation of nitrite. Nitrite accumulation can inhibit bacterial activity and may be a cause of cell death.

Substrate Diffusion within Biofilms Significantly Influencing the Electron Competition during Denitrification

A common and long-existing operational issue of wastewater denitrification is the unexpected accumulation of nitrite (NO₂^-) that could suppress the activity of various microorganisms involved in biological wastewater treatment process and nitrous oxide (N₂O) that could emit as a potent greenhouse gas. Recently, it has been confirmed that the accumulation of these denitrification intermediates in biological wastewater treatment process is greatly influenced by the electron competition between the four denitrification steps. However, little is known about this in biofilm systems. In this work, we applied a mathematical model that links carbon oxidation and nitrogen reduction processes through a pool of electron carriers, to assess electron competition in denitrifying biofilms. Simulations were performed comprehensively at seven combinations of electron acceptor addition scheme (i.e., simultaneous addition of one, two or three among nitrate (NO₃^-), NO₂^-, and N₂O) to compare the effect of electron competition on NO₃^-, NO₂^- and N₂O reduction. Overall, the effects of substrate loading, biofilm thickness and effective diffusion coefficients on electron competition are not always intuitive. Model simulations show that electron competition was intensified due to the substrate load limitation (from 120 to 20 mg COD/L) and increasing biofilm thicknesses (from 0.1 to 1.6 mm) in most cases, where electrons were prioritized to nitrite reductase because of the insufficient electron donor availability in the biofilm. In contrast, increasing effective diffusion coefficients did not pose a significant effect on electron competition and only increased electrons distributed to nitrite reductase when both NO₂^- and N₂O are added.

Use of Cotton as a Carbon Source for Denitrification in Biofilters for Groundwater Remediation

This study is part of a comprehensive research aimed at the development and application of the “Water Sensitive Cities” idea in Israel. This is a sustainable concept, incorporating among others the harvesting, treatment, and reuse of storm-water. The use of engineered biofiltration systems for the harvesting and treatment of storm-water in Israel is complicated due to the prolonged dry climate period, spanning 7–8 months of the year. Therefore, the tactic suggested is to use a hybrid biofiltration system for both storm-water harvesting/polishing during winter, and for remediation of nitrate-contaminated groundwater during summer. This paper focuses on the summer design (denitrification) configuration. In preliminary experiments, it was found that crude cotton could serve as an effective carbon source for denitrification. Further results are reported herein regarding the design and operation of biofilter columns applied for the treatment of synthetic mixtures simulating nitrate-contaminated groundwater. The columns were composed of crude cotton wool and polyethylene beads, which prevented the effect of cotton compression. This application was shown to enable controlled removal of nitrate to low levels, while emitting very low concentrations of total organic carbon (TOC) and nitrite. It was also concluded that a biofilter requires judicious design and operation, since complete removal of nitrogen oxides might lead to the formation of undesired compounds such as sulfides due to the development of anaerobic conditions.

Citric acid application for denitrification process support in biofilm reactor

The study demonstrated that citric acid, as an organic carbon source, can improve denitrification in Anaerobic Sequencing Batch Biofilm Reactor (AnSBBR). The consumption rate of the organic substrate and the denitrification rate were lower during the period of the reactor's acclimatization (cycles 1-60; 71.5 mgCOD L^-1 h^-1 and 17.81 mgN L^-1 h^-1, respectively) than under the steady state conditions (cycles 61-180; 143.8 mgCOD L^-1 h^-1 and 24.38 mgN L^-1 h^-1). The biomass yield coefficient reached 0.04 ± 0.02 mgTSS· mgCOD_re^-1 (0.22 ± 0.09 mgTSS mgN_re^-1). Observations revealed the diversified microbiological ecology of the denitrifying bacteria. Citric acid was used mainly by bacteria representing the Trichoccocus genus, which represented above 40% of the sample during the first phase of the process (cycles 1-60). In the second phase (cycles 61-180) the microorganisms the genera that consumed the acetate and formate, as the result of citric acid decomposition were Propionibacterium (5.74%), Agrobacterium (5.23%), Flavobacterium (1.32%), Sphaerotilus (1.35%), Erysipelothrix (1.08%).

Segregating metabolic processes into different microbial cells accelerates the consumption of inhibitory substrates

Different microbial cell types typically specialize at performing different metabolic processes. A canonical example is substrate cross-feeding, where one cell type consumes a primary substrate into an intermediate and another cell type consumes the intermediate. While substrate cross-feeding is widely observed, its consequences on ecosystem processes is often unclear. How does substrate cross-feeding affect the rate or extent of substrate consumption? We hypothesized that substrate cross-feeding eliminates competition between different enzymes and reduces the accumulation of growth-inhibiting intermediates, thus accelerating substrate consumption. We tested this hypothesis using isogenic mutants of the bacterium Pseudomonas stutzeri that either completely consume nitrate to dinitrogen gas or cross-feed the intermediate nitrite. We demonstrate that nitrite cross-feeding eliminates inter-enzyme competition and, in turn, reduces nitrite accumulation. We further demonstrate that nitrite cross-feeding accelerates substrate consumption, but only when nitrite has growth-inhibiting effects. Knowledge about inter-enzyme competition and the inhibitory effects of intermediates could therefore be important for deciding how to best segregate different metabolic processes into different microbial cell types to optimize a desired biotransformation.

Transient Accumulation of NO2- and N2O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes

Denitrifying bacteria accumulate NO2−, NO, and N₂O, the amounts depending on transcriptional regulation of core denitrification genes in response to O₂-limiting conditions. The genes include nar, nir, nor and nosZ, encoding NO3−-, NO2−-, NO- and N₂O reductase, respectively. We previously constructed a dynamic model to simulate growth and respiration in batch cultures of Paracoccus denitrificans. The observed denitrification kinetics were adequately simulated by assuming a stochastic initiation of nir-transcription in each cell with an extremely low probability (0.5% h^-1), leading to product- and substrate-induced transcription of nir and nor, respectively, via NO. Thus, the model predicted cell diversification: after O₂ depletion, only a small fraction was able to grow by reducing NO2−. Here we have extended the model to simulate batch cultivation with NO3−, i.e., NO2−, NO, N₂O, and N₂ kinetics, measured in a novel experiment including frequent measurements of NO2−. Pa. denitrificans reduced practically all NO3− to NO2− before initiating gas production. The NO2− production is adequately simulated by assuming stochastic nar-transcription, as that for nirS, but with a higher probability (0.035 h^-1) and initiating at a higher O₂ concentration. Our model assumes that all cells express nosZ, thus predicting that a majority of cells have only N₂O-reductase (A), while a minority (B) has NO2−-, NO- and N₂O-reductase. Population B has a higher cell-specific respiration rate than A because the latter can only use N₂O produced by B. Thus, the ratio BA is low immediately after O₂ depletion, but increases throughout the anoxic phase because B grows faster than A. As a result, the model predicts initially low but gradually increasing N₂O concentration throughout the anoxic phase, as observed. The modelled cell diversification neatly explains the observed denitrification kinetics and transient intermediate accumulations. The result has major implications for understanding the relationship between genotype and phenotype in denitrification research.

Denitrifiers generally respire O₂, but if O₂ becomes limiting, they may switch to anaerobic respiration (denitrification) by producing NO3−-, NO2−-, NO- and/or N₂O reductase, encoded by nar, nir, nor, and nosZ genes, respectively. Denitrification causes transient accumulation of NO2− and NO/N₂O emissions, depending on the activity of the four reductases. Denitrifiers lacking nosZ produce ~100% N₂O, whereas organisms with only nosZ are net consumers of N₂O. Full-fledged denitrifiers are equipped with all four reductases, genetic regulation of which determines NO2− accumulation and NO/N₂O emissions. Paracoccus denitrificans is a full-fledged denitrifying bacterium, and here we present a modelling approach to understand its gene regulation. We found that the observed transient accumulation of NO2− and N₂O can be neatly explained by assuming cell diversification: all cells expressing nosZ, while a minority expressing nar and nir+nor. Thus, the model predicts that in a batch culture of this organism, only a minor sub-population is full-fledged denitrifier. The cell diversification is a plausible outcome of stochastic initiation of nar- and nir transcription, which then becomes autocatalytic by NO2−and NO, respectively. The findings are important for understanding the regulation of denitrification in bacteria: product-induced transcription of denitrification genes is common, and we surmise that diversification in response to anoxia is widespread.

Effect of self-alkalization on nitrite accumulation in a high-rate denitrification system: Performance, microflora and enzymatic activities

The self-alkalization of denitrifying automatic circulation (DAC) reactor resulted in a large increase of pH up to 9.20 and caused a tremendous accumulation of nitrite up to 451.1 ± 49.0 mgN L(-1) at nitrate loading rate (NLR) from 35 kgN m(-3) d(-1) to 55 kgN m(-3) d(-1). The nitrite accumulation was greatly relieved even at the same NLR once the pH was maintained at 7.6 ± 0.2 in the system. Enzymatic assays indicated that the long-term bacterial exposure to high pH significantly inhibited the activity of copper type nitrite reductase (NirK) rather than the cytochrome cd1 type nitrite reductase (NirS). The terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that the dominant denitrifying bacteria shifted from the NirS-containing Thauear sp. 27 to the NirK-containing Hyphomicrobium nitrativorans strain NL23 during the self-alkalization. The significant nitrite accumulation in the high-rate denitrification system could be therefore, due to the inhibition of Cu-containing NirK by high pH from the self-alkalization. The results suggest that the NirK-containing H. nitrativorans strain NL23 could be an ideal functional bacterium for the conversion of nitrate to nitrite, i.e. denitritation, which could be combined with anaerobic ammonium oxidation (Anammox) to develop a new process for nitrogen removal from wastewater.

Modeling nitrous oxide production and reduction in soil through explicit representation of denitrification enzyme kinetics

An enzyme-explicit denitrification model with representations for pre- and de novo synthesized enzymes was developed to improve predictions of nitrous oxide (N2O) accumulations in soil and emissions from the surface. The metabolic model of denitrification is based on dual-substrate utilization and Monod growth kinetics. Enzyme synthesis/activation was incorporated into each sequential reduction step of denitrification to regulate dynamics of the denitrifier population and the active enzyme pool, which controlled the rate function. Parameterizations were developed from observations of the dynamics of N2O production and reduction in soil incubation experiments. The model successfully reproduced the dynamics of N2O and N2 accumulation in the incubations and revealed an important regulatory effect of denitrification enzyme kinetics on the accumulation of denitrification products. Pre-synthesized denitrification enzymes contributed 20, 13, 43, and 62% of N2O that accumulated in 48 h incubations of soil collected from depths of 0-5, 5-10, 10-15, and 15-25 cm, respectively. An enzyme activity function (E) was defined to estimate the relative concentration of active enzymes and variation in response to environmental conditions. The value of E allows for activities of pre-synthesized denitrification enzymes to be differentiated from de novo synthesized enzymes. Incorporating explicit representations of denitrification enzyme kinetics into biogeochemical models is a promising approach for accurately simulating dynamics of the production and reduction of N2O in soils.

Aerobic and anaerobic nitrogen transformation processes in N2-fixing cyanobacterial aggregates

Colonies of N(2)-fixing cyanobacteria are key players in supplying new nitrogen to the ocean, but the biological fate of this fixed nitrogen remains poorly constrained. Here, we report on aerobic and anaerobic microbial nitrogen transformation processes that co-occur within millimetre-sized cyanobacterial aggregates (Nodularia spumigena) collected in aerated surface waters in the Baltic Sea. Microelectrode profiles showed steep oxygen gradients inside the aggregates and the potential for nitrous oxide production in the aggregates' anoxic centres. (15)N-isotope labelling experiments and nutrient analyses revealed that N(2) fixation, ammonification, nitrification, nitrate reduction to ammonium, denitrification and possibly anaerobic ammonium oxidation (anammox) can co-occur within these consortia. Thus, N. spumigena aggregates are potential sites of nitrogen gain, recycling and loss. Rates of nitrate reduction to ammonium and N(2) were limited by low internal nitrification rates and low concentrations of nitrate in the ambient water. Presumably, patterns of N-transformation processes similar to those observed in this study arise also in other phytoplankton colonies, marine snow and fecal pellets. Anoxic microniches, as a pre-condition for anaerobic nitrogen transformations, may occur within large aggregates (⩾1 mm) even when suspended in fully oxygenated waters, whereas anoxia in small aggregates (<1 to ⩾0.1 mm) may only arise in low-oxygenated waters (⩽25 μM). We propose that the net effect of aggregates on nitrogen loss is negligible in NO(3)(-)-depleted, fully oxygenated (surface) waters. In NO(3)(-)-enriched (>1.5 μM), O(2)-depleted water layers, for example, in the chemocline of the Baltic Sea or the oceanic mesopelagic zone, aggregates may promote N-recycling and -loss processes.

Biogas biodesulfurization in an anoxic biotrickling filter packed with open-pore polyurethane foam

Biogas biodesulfurization by an anoxic biotrickling filter packed with open pore polyurethane foam at the laboratory scale (packed volume 2.4L) has been studied. The biotrickling system was operated for 620 days with biogas supplied continuously and two nitrate feeding regimes were tested (manual and programmed). Biomass immobilization was carried out under the manual nitrate feeding regime and a study was then carried out on the effects on removal efficiency of the following parameters: nitrate source, H2S inlet load, nitrate concentration, sulfate accumulation, temperature, pH and trickling liquid velocity. The effect of increased H2S inlet load was studied under the programmed nitrate feeding regime. The results show that a removal efficiency of 99% can be obtained when working under the following conditions: inlet loads below 130gSm(-3)h(-1), a programmed nitrate feeding system, temperature of 30°C, sulfate concentration below 33gL(-1), a pH between 7.3 and 7.5, and a trickling liquid velocity higher than 4.6mh(-1).

Denitrification and N2O:N2 production in temperate grasslands: processes, measurements, modelling and mitigating negative impacts

In this review we explore the biotic transformations of nitrogenous compounds that occur during denitrification, and the factors that influence denitrifier populations and enzyme activities, and hence, affect the production of nitrous oxide (N2O) and dinitrogen (N2) in soils. Characteristics of the genes related to denitrification are also presented. Denitrification is discussed with particular emphasis on nitrogen (N) inputs and dynamics within grasslands, and their impacts on the key soil variables and processes regulating denitrification and related gaseous N2O and N2 emissions. Factors affecting denitrification include soil N, carbon (C), pH, temperature, oxygen supply and water content. We understand that the N2O:N2 production ratio responds to the changes in these factors. Increased soil N supply, decreased soil pH, C availability and water content generally increase N2O:N2 ratio. The review also covers approaches to identify and quantify denitrification, including acetylene inhibition, (15)N tracer and direct N2 quantification techniques. We also outline the importance of emerging molecular techniques to assess gene diversity and reveal enzymes that consume N2O during denitrification and the factors affecting their activities and consider a process-based approach that can be used to quantify the N2O:N2 product ratio and N2O emissions with known levels of uncertainty in soils. Finally, we explore strategies to reduce the N2O:N2 product ratio during denitrification to mitigate N2O emissions. Future research needs to focus on evaluating the N2O-reducing ability of the denitrifiers to accelerate the conversion of N2O to N2 and the reduction of N2O:N2 ratio during denitrification.

Modeling the effect of copper availability on bacterial denitrification

When denitrifying bacteria such as Paracoccus denitrificans respire anaerobically they convert nitrate to dinitrogen gas via a pathway which includes the potent greenhouse gas, nitrous oxide (N₂O). The copper-dependent enzyme Nitrous Oxide reductase (Nos) catalyzes the reduction of N₂O to dinitrogen. In low-copper conditions, recent experiments in chemostats have demonstrated that Nos efficiency decreases resulting in significant N₂O emissions. For the first time, a chemostat-based mathematical model is developed that describes the anaerobic denitrification pathway based on Michaelis–Menten kinetics and published kinetic parameters. The model predicts steady-state enzyme levels from experimental data. For low copper concentrations, the predicted Nos level is significantly reduced, whereas the levels for the non copper-dependent reductases in the pathway remain relatively unaffected. The model provides time courses for the pathway metabolites that accurately reflect previously published experimental data. In the absence of experimental data purely predictive analyses can also be readily performed by calculating the relative Nos level directly from the copper concentration. Here, the model quantitatively estimates the increasing level of emitted N₂O as the copper level decreases.

Nitrate-dependent ferrous iron oxidation by anaerobic ammonium oxidation (anammox) bacteria

We examined nitrate-dependent Fe(2+) oxidation mediated by anaerobic ammonium oxidation (anammox) bacteria. Enrichment cultures of "Candidatus Brocadia sinica" anaerobically oxidized Fe(2+) and reduced NO3(-) to nitrogen gas at rates of 3.7 ± 0.2 and 1.3 ± 0.1 (mean ± standard deviation [SD]) nmol mg protein(-1) min(-1), respectively (37°C and pH 7.3). This nitrate reduction rate is an order of magnitude lower than the anammox activity of "Ca. Brocadia sinica" (10 to 75 nmol NH4(+) mg protein(-1) min(-1)). A (15)N tracer experiment demonstrated that coupling of nitrate-dependent Fe(2+) oxidation and the anammox reaction was responsible for producing nitrogen gas from NO3(-) by "Ca. Brocadia sinica." The activities of nitrate-dependent Fe(2+) oxidation were dependent on temperature and pH, and the highest activities were seen at temperatures of 30 to 45°C and pHs ranging from 5.9 to 9.8. The mean half-saturation constant for NO3(-) ± SD of "Ca. Brocadia sinica" was determined to be 51 ± 21 μM. Nitrate-dependent Fe(2+) oxidation was further demonstrated by another anammox bacterium, "Candidatus Scalindua sp.," whose rates of Fe(2+) oxidation and NO3(-) reduction were 4.7 ± 0.59 and 1.45 ± 0.05 nmol mg protein(-1) min(-1), respectively (20°C and pH 7.3). Co-occurrence of nitrate-dependent Fe(2+) oxidation and the anammox reaction decreased the molar ratios of consumed NO2(-) to consumed NH4(+) (ΔNO2(-)/ΔNH4(+)) and produced NO3(-) to consumed NH4(+) (ΔNO3(-)/ΔNH4(+)). These reactions are preferable to the application of anammox processes for wastewater treatment.

Effects of pH on nitrite accumulation during wastewater denitrification

The characteristics of nitrite accumulation during denitrification in mixed liquors with different pH values were studied. The mixed liquors were prepared by adding acclimated denitrifying activated sludge to synthetic wastewater with methanol (CH3OH) as the carbon source (chemical oxygen demand = 600 mg/L) and sodium nitrate (NaNO3) as the nitrogen source (NO3(-)-N = 50 mg/L). The results showed that the pH during denitrification could be kept constant using buffer solutions composed of KH2PO4, Na2HPO4 x 12H2O and Na2B4O7 x 10H2O. Nitrite accumulation was more serious at low pH than at high pH, regardless of whether the pH of the mixed liquor was stabilized during denitrification. The specific rates of nitrate and nitrite reduction were both inhibited by increased pH. The specific rate of nitrate reduction was more vulnerable than that of nitrite reduction to higher pH. Nitrite accumulation during these experiments resulted from different reduction rates for nitrate and nitrite. Nitrite reduction rates were inhibited by the presence of nitrate, which stimulated nitrite accumulation during denitrification.

Soil nitrate reducing processes - drivers, mechanisms for spatial variation, and significance for nitrous oxide production

The microbial processes of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two important nitrate reducing mechanisms in soil, which are responsible for the loss of nitrate ([Formula: see text]) and production of the potent greenhouse gas, nitrous oxide (N(2)O). A number of factors are known to control these processes, including O(2) concentrations and moisture content, N, C, pH, and the size and community structure of nitrate reducing organisms responsible for the processes. There is an increasing understanding associated with many of these controls on flux through the nitrogen cycle in soil systems. However, there remains uncertainty about how the nitrate reducing communities are linked to environmental variables and the flux of products from these processes. The high spatial variability of environmental controls and microbial communities across small sub centimeter areas of soil may prove to be critical in determining why an understanding of the links between biotic and abiotic controls has proved elusive. This spatial effect is often overlooked as a driver of nitrate reducing processes. An increased knowledge of the effects of spatial heterogeneity in soil on nitrate reduction processes will be fundamental in understanding the drivers, location, and potential for N(2)O production from soils.

Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

Nitrous oxide (N(2)O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N(2)O is formed biologically from the oxidation of hydroxylamine (NH(2)OH) or the reduction of nitrite (NO(-) (2)) to NO and further to N(2)O. Our review of the biological pathways for N(2)O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO(-) (2) to NO and the further reduction of NO to N(2)O, while N(2)O formation from NH(2)OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N(2)O formation due to the reactivity of NO(-) (2), NH(2)OH, and nitroxyl (HNO). Moreover, biological N(2)O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N(2)O build-up are key to understand mechanisms of N(2)O release. Here, we discuss novel technologies that allow experiments on NO and N(2)O formation at high temporal resolution, namely NO and N(2)O microelectrodes and the dynamic analysis of the isotopic signature of N(2)O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N(2)O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N(2)O build-up.

Metabolic modeling of denitrification in Agrobacterium tumefaciens: a tool to study inhibiting and activating compounds for the denitrification pathway

A metabolic network model for facultative denitrification was developed based on experimental data obtained with Agrobacterium tumefaciens. The model includes kinetic regulation at the enzyme level and transcription regulation at the enzyme synthesis level. The objective of this work was to study the key factors regulating the metabolic response of the denitrification pathway to transition from oxic to anoxic respiration and to find parameter values for the biological processes that were modeled. The metabolic model was used to test hypotheses that were formulated based on the experimental results and offers a structured look on the processes that occur in the cell during transition in respiration. The main phenomena that were modeled are the inhibition of the cytochrome c oxidase by nitric oxide (NO) and the (indirect) inhibition of oxygen on the denitrification enzymes. The activation of transcription of nitrite reductase and NO reductase by their respective substrates were hypothesized. The general assumption that nitrite and NO reduction are controlled interdependently to prevent NO accumulation does not hold for A. tumefaciens. The metabolic network model was demonstrated to be a useful tool for unraveling the different factors involved in the complex response of A. tumefaciens to highly dynamic environmental conditions.

Nitrite accumulation under constant temperature in anoxic denitrification process: The effects of carbon sources and COD/NO(3)-N

Effects of external carbon sources and COD/NO(3)-N on nitrite accumulation through denitrification were studied at a temperature of 28±2.0 °C using mixed activated sludge. Nitrite accumulation was observed for each type of carbon source studied. Glucose resulted in the greatest nitrite accumulation and production rate, which were 14.51±2.41 mg/L and 0.121±0.013 g N/(g VSS d), respectively. Moreover, a higher COD/NO(3)-N ratio ranging from 1.0 to 15.0 increased accumulation to the maximum value of 0.34±0.03 g N/(g VSS d). It was assumed that the competition for electrons between nitrite reductase and nitrate reductase led to different reduction rates and finally caused the accumulation. In addition, it was reasonable to use the pH and ORP as proxies for monitoring the real endpoint of the denitrification process with the addition of carbon sources.

Biological sources and sinks of nitrous oxide and strategies to mitigate emissions

Nitrous oxide (N(2)O) is a powerful atmospheric greenhouse gas and cause of ozone layer depletion. Global emissions continue to rise. More than two-thirds of these emissions arise from bacterial and fungal denitrification and nitrification processes in soils, largely as a result of the application of nitrogenous fertilizers. This article summarizes the outcomes of an interdisciplinary meeting, 'Nitrous oxide (N(2)O) the forgotten greenhouse gas', held at the Kavli Royal Society International Centre, from 23 to 24 May 2011. It provides an introduction and background to the nature of the problem, and summarizes the conclusions reached regarding the biological sources and sinks of N(2)O in oceans, soils and wastewaters, and discusses the genetic regulation and molecular details of the enzymes responsible. Techniques for providing global and local N(2)O budgets are discussed. The findings of the meeting are drawn together in a review of strategies for mitigating N(2)O emissions, under three headings, namely: (i) managing soil chemistry and microbiology, (ii) engineering crop plants to fix nitrogen, and (iii) sustainable agricultural intensification.

Genetic characterization of denitrifier communities with contrasting intrinsic functional traits

Microorganisms capable of denitrification are polyphyletic and exhibit distinct denitrification regulatory phenotypes (DRP), and thus, denitrification in soils could be controlled by community composition. In a companion study (Dörsch et al., 2012) and preceding work, ex situ denitrification assays of three organic soils demonstrated profoundly different functional traits including N(2) O/N(2) ratios. Here, we explored the composition of the underlying denitrifier communities by analyzing the abundance and structure of denitrification genes (nirK, nirS, and nosZ). The relative abundance of nosZ (vs. nirK + nirS) was similar for all communities, and hence, the low N(2) O reductase activity in one of the soils was not because of the lack of organisms with this gene. Similarity in community composition between the soils was generally low for nirK and nirS, but not for nosZ. The community with the most robust denitrification (consistently low N(2) O/N(2) ) had the highest diversity/richness of nosZ and nirK, but not of nirS. Contrary results found for a second soil agreed with impaired denitrification (low overall denitrification activity, high N(2) O/N(2) ). In conclusion, differences in community composition and in the absolute abundance of denitrification genes clearly reflected the functional differences observed in laboratory studies and may shed light on differences in in situ N(2) O emission of the soils.

Decreased N2O reduction by low soil pH causes high N2O emissions in a riparian ecosystem

Quantification of harmful nitrous oxide (N(2)O) emissions from soils is essential for mitigation measures. An important N(2)O producing and reducing process in soils is denitrification, which shows deceased rates at low pH. No clear relationship between N(2)O emissions and soil pH has yet been established because also the relative contribution of N(2)O as the denitrification end product decreases with pH. Our aim was to show the net effect of soil pH on N(2)O production and emission. Therefore, experiments were designed to investigate the effects of pH on NO(3)(-) reduction, N(2)O production and reduction and N(2) production in incubations with pH values set between 4 and 7. Furthermore, field measurements of soil pH and N(2)O emissions were carried out. In incubations, NO(3)(-) reduction and N(2) production rates increased with pH and net N(2)O production rate was highest at pH 5. N(2)O reduction to N(2) was halted until NO(3)(-) was depleted at low pH values, resulting in a built up of N(2)O. As a consequence, N(2)O:N(2) production ratio decreased exponentially with pH. N(2)O reduction appeared therefore more important than N(2)O production in explaining net N(2)O production rates. In the field, a negative exponential relationship for soil pH against N(2)O emissions was observed. Soil pH could therefore be used as a predictive tool for average N(2)O emissions in the studied ecosystem. The occurrence of low pH spots may explain N(2)O emission hotspot occurrence. Future studies should focus on the mechanism behind small scale soil pH variability and the effect of manipulating the pH of soils.

Denitrifying Bacteria in the Earthworm Gastrointestinal Tract and In Vivo Emission of Nitrous Oxide (N(inf2)O) by Earthworms

Earthworms (Lumbricus rubellus and Octolasium lacteum) and gut homogenates did not produce CH(inf4), and methanogens were not readily culturable from gut material. In contrast, the numbers of culturable denitrifiers averaged 7 x 10(sup7) and 9 x 10(sup6) per g (dry weight) of gut material for L. rubellus and O. lacteum, respectively; these values were 256- and 35-fold larger than the numbers of culturable denitrifiers in the soil from which the earthworms were obtained. Anaerobically incubated earthworm gut homogenates supplemented with nitrate produced N(inf2)O at rates exceeding that of soil homogenates. Furthermore, living earthworms emitted N(inf2)O under aerobic conditions, and N(inf2)O emission was stimulated by acetylene. For earthworms collected from a mildly acidic (pH 6) beech forest soil, the rates of N(inf2)O emission for earthworms and soil averaged 884 and 2 pmol per h per g (fresh weight), respectively. In contrast, for earthworms collected from a more acidic (pH 4.6) oak-beech forest soil, N(inf2)O emission by earthworms and soil averaged 145 and 45 pmol per h per g (fresh weight), respectively. Based on the extrapolation of this data, earthworms accounted for an estimated 16 and 0.25% of the total N(inf2)O produced at the stand level of these beech and oak-beech forest soils, respectively.

Influence of Volatile Fatty Acids on Nitrite Accumulation by a Pseudomonas stutzeri Strain Isolated from a Denitrifying Fluidized Bed Reactor

Intermediate nitrite accumulation during denitrification by Pseudomonas stutzeri isolated from a denitrifying fluidized bed reactor was examined in the presence of different volatile fatty acids. Nitrite accumulated when acetate or propionate served as the carbon and electron source but did not accumulate in the presence of butyrate, valerate, or caproate. Nitrite accumulation in the presence of acetate was caused by differences in the rates of nitrate and nitrite reduction and, in addition, by competition between nitrate and nitrite reduction pathways for electrons. Incubation of the cells with butyrate resulted in a slower nitrate reduction rate and a faster nitrite reduction rate than incubation with acetate. Whereas nitrate inhibited the nitrite reduction rate in the presence of acetate, no such inhibition was found in butyrate-supplemented cells. Cytochromes b and c were found to mediate electron transport during nitrate reduction by the cells. Cytochrome c was reduced via a different pathway when nitrite-reducing cells were incubated with acetate than when they were incubated with butyrate. Furthermore, addition of antimycin A to nitrite-reducing cells resulted in partial inhibition of electron transport to cytochrome c in acetate-supplemented cells but not in butyrate-supplemented cells. On the basis of these findings, we propose that differences in intermediate nitrite accumulation are caused by differences in electron flow to nitrate and nitrite reductases during oxidation of either acetate or butyrate.

Denitrification gene pools, transcription and kinetics of NO, N2O and N2 production as affected by soil pH

The N(2)O : N(2) product ratio of denitrification is negatively correlated with soil pH, but the mechanisms involved are not clear. We compared soils from field experiments where the pH had been maintained at different levels (pH 4.0-8.0) by liming (> or = 20 years), and quantified functional gene pools (nirS, nirK and nosZ), their transcription and gas kinetics (NO, N(2)O and N(2)) of denitrification as induced by anoxic incubation with and without a carbon substrate (glutamate). Denitrification in unamended soil appeared to be based largely on the activation of a pre-existing denitrification proteome, because constant rates of N(2) and N(2)O production were observed, and the transcription of functional genes was below the detection level. In contrast, glutamate-amended soils showed sharp peaks in the transcripts of nirS and nosZ, increasing the rates of denitrification and pH-dependent transient accumulation of N(2)O. The results indicate that the high N(2)O : N(2) product ratio at low pH is a post-transcriptional phenomenon, because the transcription rate of nosZ relative to that of nirS was higher at pH 6.1 than at pH 8.0. The most plausible explanation is that the translation/assembly of N(2)O reductase is more sensitive to low pH than that of the other reductases involved in denitrification.