Denitrification: production and consumption of nitric oxide

A comprehensive review of flue gas bio-mitigation: chemolithotrophic interactions with flue gas in bio-reactors as a sustainable possibility for technological advancements

Flue gas mitigation technologies aim to reduce the environmental impact of flue gas emissions, particularly from industrial processes and power plants. One approach to mitigate flue gas emissions involves bio-mitigation, which utilizes microorganisms to convert harmful gases into less harmful or inert substances. The review thus explores the bio-mitigation efficiency of chemolithotrophic interactions with flue gas and their potential application in bio-reactors. Chemolithotrophs are microorganisms that can derive energy from inorganic compounds, such as carbon dioxide (CO2), nitrogen oxides (NOx), and sulfur dioxide (SO2), present in the flue gas. These microorganisms utilize specialized enzymatic pathways to oxidize these compounds and produce energy. By harnessing the metabolic capabilities of chemolithotrophs, flue gas emissions can be transformed into value-added products. Bio-reactors provide controlled environments for the growth and activity of chemolithotrophic microorganisms. Depending on the specific application, these can be designed as suspended or immobilized reactor systems. The choice of bio-reactor configuration depends on process efficiency, scalability, and ease of operation. Factors influencing the bio-mitigation efficiency of chemolithotrophic interactions include the concentration and composition of the flue gas, operating conditions (such as temperature, pH, and nutrient availability), and reactor design. Chemolithotrophic interactions with flue gas in bio-reactors offer a potentially efficient approach to mitigating flue gas emissions. Continued research and development in this field are necessary to optimize reactor design, microbial consortia, and operating conditions. Advances in understanding the metabolism and physiology of chemolithotrophic microorganisms will contribute to developing robust and scalable bio-mitigation technologies for flue gas emissions.

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.

Bacterial nitric oxide reductase (NorBC) models employing click chemistry

Bacterial NO Reductase (NorBC or cNOR) is a membrane-bound enzyme found in denitrifying bacteria that catalyzes the two-electron reduction of NO to N₂O and water. The mechanism by which NorBC operates is highly debated, due to the fact that this enzyme is difficult to work with, and no intermediates of the NO reduction reaction could have been identified so far. The unique active site of NorBC consists of a heme b₃/non-heme Fe_B diiron center. Synthetic model complexes provide the opportunity to obtain insight into possible mechanistic alternatives for this enzyme. In this paper, we present three new synthetic model systems for NorBC, consisting of a tetraphenylporphyrin-derivative clicked to modified BMPA-based ligands (BMPA = bis(methylpyridyl)amine) that model the non-heme site in the enzyme. These complexes have been characterized by EPR, IR and UV-Vis spectroscopy. The reactivity with NO was then investigated, and it was found that the complex with the BMPA-carboxylate ligand as the non-heme component has a very low affinity for NO at the non-heme iron site. If the carboxylate functional group is replaced with a phenolate or pyridine group, reactivity is restored and formation of a diiron dinitrosyl complex was observed. Upon one-electron reduction of the nitrosylated complexes, following the semireduced pathway for NO reduction, formation of dinitrosyl iron complexes (DNICs) was observed in all three cases, but no N₂O could be detected.

Mechanistic insights into polyhydroxyalkanoate-enhanced denitrification capacity of microbial community: Evolution of community structure and intracellular electron transfer of nitrogen metabolism

Denitrification is the key driving force of nitrogen cycle in surface water and plays an important role in eutrophication water remediation. Compared with some other common carbon sources, such as glucose and sodium acetate, polyhydroxyalkanoates (PHAs) were found to have the distinguished advantages in screening specific denitrifying bacteria of natural surface water bodies. In this study, the large ensembles of taxa were obtained from surface water samples and then sub-cultured with PHA or glucose as the sole carbon source. The microbial community that could be screened by PHA was identified, and the environmental functions of these bacteria were analyzed. At the genus level, the main communities regulated by PHA included Pseudomonas (56.30 %), Acinetobacter (27.75 %), Flavobacterium (10.19 %) and Comamonas (3.14 %), which all had good denitrification ability. The changes in carbon source, nitrogen source and biomass (expressed by DNA) were simultaneously monitored when culturing the model strain (P. stuzeri) with PHA or glucose. Compared with the glucose group, less PHA was consumed to remove the same amount of nitrate within a shorter incubation time, and there was no significant difference in bacterial growth with PHA or glucose as the carbon source (glucose:ΔN:ΔC:ΔDNA = 1:18:0.072; PHA:ΔN:ΔC:ΔDNA = 1:11:0.063). PHA improved the denitrification efficiency by increasing the expression of NarGHI, NirB, NirK and NorB, i.e., the key enzymes in the denitrification process. In addition, PHA accelerated the assimilating rate of extracellular nitrate by bacteria through increasing the expression of NarK. Finally, PHA-regulated electron transfer during denitrification was studied by observing the changes in NADH and NAD⁺. PHA could use a large proportion of NADH to offer electrons for denitrification, which increased the rate of denitrification. Improved mechanistic insights into the PHA-enhanced denitrification capacity of the microbial community can provide novel options for the in-situ remediation of eutrophic surface water.

Bacterial nitric oxide synthase in colorizing meat products: Current development and future directions

Nitrite has been widely used in meat products for its abilities including color formation, antimicrobial properties, flavor formation and preventing lipid oxidation. However, the possible generation of N-nitrosamines through reaction of nitrite with secondary amines arises many concerns in the usage of nitrite. For a long time, nitrite substitution is unsettled issue in the meat industry. Many attempts have been tried, however, the alternative solutions are often ephemeral and palliative. In recent years, bacterial nitric oxide synthase (bNOS) has received attention for its critical roles, especially in reddening meat products. This comprehensive background study summarizes the application of bNOS in colorizing meat products, its functions in bacteria, and methods of regulating the bNOS pathway. Based on this information, some strategies for promoting the nitric oxide yield for effectively substituting nitrite are presented, such as changing the environmental conditions for bacterial survival and adding substrate. Thus, bNOS is a promising nitrite substitute for color formation, and further research on its other roles in meat needs to be carried out to obtain the complete picture.

Mechanistic understanding of the pollutant removal and transformation processes in the constructed wetland system

Constructed wetland systems (CWs) are biologically and physically engineered systems to mimic the natural wetlands which can potentially treat the wastewater from the various point and nonpoint sources of pollution. The present study aims to review the various mechanisms involved in the different types of CWs for wastewater treatment and to elucidate their role in the effective functioning of the CWs. Several physical, chemical, and biological processes substantially influence the pollutant removal efficiency of CWs. Plants species Phragmites australis, Typha latifolia, and Typha angustifolia are most widely used in CWs. The rate of nitrogen (N) removal is significantly affected by emergent vegetation cover and type of CWs. Hybrid CWs (HCWS) removal efficiency for nutrients, metals, pesticides, and other pollutants is higher than a single constructed wetland. The contaminant removal efficiency of the vertical subsurface flow constructed wetlands (VSSFCW) commonly used for the treatment of domestic and municipal wastewater ranges between 31% and 99%. Biochar/zeolite addition as substrate material further enhances the wastewater treatment of CWs. Innovative components (substrate materials, plant species) and factors (design parameters, climatic conditions) sustaining the long-term sink of the pollutants, such as nutrients and heavy metals in the CWs should be further investigated in the future. PRACTITIONER POINTS: Constructed wetland systems (CWs) are efficient natural treatment system for on-site contaminants removal from wastewater. Denitrification, nitrification, microbial and plant uptake, sedimentation and adsorption are crucial pollutant removal mechanisms. Phragmites australis, Typha latifolia, and Typha angustifolia are widely used emergent plants in constructed wetlands. Hydraulic retention time (HRT), water flow regimes, substrate, plant, and microbial biomass substantially affect CWs treatment performance.

Activation of O2 and NO in heme-copper oxidases - mechanistic insights from computational modelling

Heme-copper oxidases are transmembrane enzymes involved in aerobic and anaerobic respiration. The largest subgroup contains the cytochrome c oxidases (CcO), which reduce molecular oxygen to water. A significant part of the free energy released in this exergonic process is conserved as an electrochemical gradient across the membrane, via two processes, electrogenic chemistry and proton pumping. A deviant subgroup is the cytochrome c dependent NO reductases (cNOR), which reduce nitric oxide to nitrous oxide and water. This is also an exergonic reaction, but in this case none of the released free energy is conserved. Computational studies applying hybrid density functional theory to cluster models of the bimetallic active sites in the heme-copper oxidases are reviewed. To obtain a reliable description of the reaction mechanisms, energy profiles of the entire catalytic cycles, including the reduction steps have to be constructed. This requires a careful combination of computational results with certain experimental data. Computational studies have elucidated mechanistic details of the chemical parts of the reactions, involving cleavage and formation of covalent bonds, which have not been obtainable from pure experimental investigations. Important insights regarding the mechanisms of energy conservation have also been gained. The computational studies show that the reduction potentials of the active site cofactors in the CcOs are large enough to afford electrogenic chemistry and proton pumping, i.e. efficient energy conservation. These results solve a conflict between different types of experimental data. A mechanism for the proton pumping, involving a specific and crucial role for the active site tyrosine, conserved in all CcOs, is suggested. For the cNORs, the calculations show that the low reduction potentials of the active site cofactors are optimized for fast elimination of the toxic NO molecules. At the same time, the low reduction potentials lead to endergonic reduction steps with high barriers. To prevent even higher barriers, which would lead to a too slow reaction, when the electrochemical gradient across the membrane is present, the chemistry must occur in a non-electrogenic manner. This explains why there is no energy conservation in cNOR.

Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling

Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O2, NO, and SO32-, respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. In this review, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations.

A new approach for the effective removal of NOx from flue gas by using an integrated system of oxidation-absorption-biological reduction

A new process of NO_x removal from flue gas, using an integrated system of oxidation-absorption-biological reduction (OABR), is introduced. The experimental results show that increasing the NO_x oxidation ratio in flue gas can effectively improve the NO_x removal efficiency of the OABR system. The NO_x removal efficiency could reach 98.8% with 0.02 M NaHCO₃ as the chemical absorbent and under the condition of the optimal NO_x oxidation ratio of 50%. During stable operation, the OABR system could maintain a high NO_x removal efficiency (above 94%) under the following conditions: 1-8 vol% (10⁴-8 × 10⁴ ppmv) O₂, 200-800 ppmv NO_x, 0.5-1.5 L/min gas flow rate and 100-800 ppmv SO₂. The nitrogen equilibrium results showed that about 59% of the nitrogen in the inlet NO_x were transformed to N₂ through microbial denitrification, 37% of the nitrogen were converted to biological nitrogen for microbial growth, and only 1.1% of the nitrogen remained in the liquid phase. This new approach has an excellent NO_x removal performance and great potential for industrial application.

Heme P460: A (Cross) Link to Nitric Oxide

Ammonia-oxidizing bacteria (AOB) convert ammonia (NH₃) to nitrite (NO₂^-) as their primary metabolism and thus provide a blueprint for the use of NH₃ as a chemical fuel. The first energy-producing step involves the homotrimeric enzyme hydroxylamine oxidoreductase (HAO), which was originally reported to oxidize hydroxylamine (NH₂OH) to NO₂^-. HAO uses the heme P460 cofactor as the site of catalysis. This heme is supported by seven other c hemes in each monomer that mediate electron transfer. Heme P460 cofactors are c-heme-based cofactors that have atypical protein cross-links between the peptide backbone and the porphyrin macrocycle. This cofactor has been observed in both the HAO and cytochrome (cyt) P460 protein families. However, there are differences; specifically, HAO uses a single tyrosine residue to form two covalent attachments to the macrocycle whereas cyt P460 uses a lysine residue to form one. In Nitrosomonas europaea, which expresses both HAO and cyt P460, these enzymes achieve the oxidation of NH₂OH and were both originally reported to produce NO₂^-. Each can inspire means to effect controlled release of chemical energy.Spectroscopically studying the P460 cofactors of HAO is complicated by the 21 non-P460 heme cofactors, which obscure the active site. However, monoheme cyt P460 is more approachable biochemically and spectroscopically. Thus, we have used cyt P460 to study biological NH₂OH oxidation. Under aerobic conditions substoichiometric production of NO₂^- was observed along with production of nitrous oxide (N₂O). Under anaerobic conditions, however, N₂O was the exclusive product of NH₂OH oxidation. We have advanced our understanding of the mechanism of this enzyme and have showed that a key intermediate is a ferric nitrosyl that can dissociate the bound nitric oxide (NO) molecule and react with O₂, thus producing NO₂^- abiotically. Because N₂O was the true product of one P460 cofactor-containing enzyme, this prompted us to reinvestigate whether NO₂^- is enzymatically generated from HAO catalysis. Like cyt P460, we showed that HAO does not produce NO₂^- enzymatically, but unlike cyt P460, its final product is NO, establishing it as an intermediate of nitrification. More broadly, NO can be recognized as a molecule common to the primary metabolisms of all organisms involved in nitrogen "defixation".Delving deeper into cyt P460 yielded insights broadly applicable to controlled biochemical redox processes. Studies of an inactive cyt P460 from Nitrosomonas sp. AL212 showed that this enzyme was unable to oxidize NH₂OH because it lacked a glutamate residue in its secondary coordination sphere that was present in the active N. europaea cyt P460 variant. Restoring the Glu residue imbued activity, revealing that a second-sphere base is Nature's key to controlled oxidation of NH₂OH. A key lesson of bioinorganic chemistry is reinforced: the polypeptide matrix is an essential part of dictating function. Our work also exposed some key functional contributions of noncanonical heme-protein cross-links. The heme-Lys cross-link of cyt P460 enforces the relative position of the cofactor and second-sphere residues. Moreover, the cross-link prevents the dissociation of the axial histidine residue, which stops catalysis, emphasizing the importance of this unique post-translational modification.

Electrochemical and spectroscopic characteristics of cytochrome P450 55A3 and its interaction with nitric oxide

Cytochrome P450 55A3 (CYP55A3) is an enzyme with the catalytic activity of nitric oxide (NO) to nitrous oxide using NADH or NADPH as the electron donor. Herein CYP55A3 has been expressed in E. coli and purified by His-tag columns. The electrochemical and spectroscopic characteristic of CYP55A3 and its interaction with NO has been studied. The direct electrochemistry of Fe³⁺/Fe²⁺ redox peaks in CYP55A3 was realized on the pyrolitic graphite electrode with the redox potential of -475 mV in pH 7.0 phosphate buffer. With the addition of NO a ferric nitroxyl complex (Fe³⁺-NO) formed with a new reduction peak at -0.78 V. The reduction peak current increased with the concentration of NO and showed typical Michaelis-Menten kinetic characteristics with the apparent Michaelis constant Kmapp 9.78 μM. The binding constant K calculated to be 3.93 × 10⁴ M by UV-vis method. The fluorescence emission spectra of iron porphyrin in CYP55A3 showed with the peak wavelength 633 nm, and its fluorescence intensity increased after binding with NO. The fluorescence analysis demonstrated that NADH can relay electrons to iron porphyrin and reduce NO. The reductive product of NO released and the iron porphyrin in CYP55A3 turned back to the original form.

Investigation of growth kinetics and partial denitrification performance in strain Acinetobacter johnsonii under different environmental conditions

A denitrifying strain ZY04 with a high nitrite-accumulating rate was isolated and purified from activated sludge in a laboratory-scale A2/O reactor. The strain was characterized and identified as Acinetobacter johnsonii by 16S rDNA phylogenetic analysis. The sequences of the key functional genes (napA, nirB, nirD) involved in partial denitrification were amplified via polymerase chain reaction, which provided a basis for exploring gene expression. The effects of different environmental factors (C/N ratio, pH and temperature) on the partial denitrification performance and transcriptional levels of the functional genes during the logarithmic growth phase were investigated by batch experiments. The results showed that the partial denitrification performance was optimal when the C/N ratio was 5, the pH value was 6-8 and the temperature was 25°C. The gene expression during the logarithmic growth phase indicated the good performance of partial denitrification under different environmental conditions. All three functional genes exhibited the highest expression levels at 25°C. The results of inhibitory kinetics analysis revealed that three biokinetic models (Aiba, Edwards and Andrews) simulated the growth pattern of strain ZY04 inhibited by a single substrate (nitrate or sodium acetate) well. In the double-substrate inhibitory model, five models of nine combinations successfully fitted the growth characteristics of the strain affected by the double substrate of nitrate and sodium acetate. The relevant semi-saturation parameters and substrate inhibition parameters were obtained, and the correlation coefficient (R 2) reached 98%.

INDISIM-Denitrification, an individual-based model for study the denitrification process

Denitrification is one of the key processes of the global nitrogen (N) cycle driven by bacteria. It has been widely known for more than 100 years as a process by which the biogeochemical N-cycle is balanced. To study this process, we develop an individual-based model called INDISIM-Denitrification. The model embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM and is designed to simulate in aerobic and anaerobic conditions the cell growth kinetics of denitrifying bacteria. INDISIM-Denitrification simulates a bioreactor that contains a culture medium with succinate as a carbon source, ammonium as nitrogen source and various electron acceptors. To implement INDISIM-Denitrification, the individual-based model INDISIM was used to give sub-models for nutrient uptake, stirring and reproduction cycle. Using a thermodynamic approach, the denitrification pathway, cellular maintenance and individual mass degradation were modeled using microbial metabolic reactions. These equations are the basis of the sub-models for metabolic maintenance, individual mass synthesis and reducing internal cytotoxic products. The model was implemented in the open-access platform NetLogo. INDISIM-Denitrification is validated using a set of experimental data of two denitrifying bacteria in two different experimental conditions. This provides an interactive tool to study the denitrification process carried out by any denitrifying bacterium since INDISIM-Denitrification allows changes in the microbial empirical formula and in the energy-transfer-efficiency used to represent the metabolic pathways involved in the denitrification process. The simulator can be obtained from the authors on request.

Nitrous oxide from chemodenitrification: A possible missing link in the Proterozoic greenhouse and the evolution of aerobic respiration

The potent greenhouse gas nitrous oxide (N₂ O) may have been an important constituent of Earth's atmosphere during Proterozoic (~2.5-0.5 Ga). Here, we tested the hypothesis that chemodenitrification, the rapid reduction of nitric oxide by ferrous iron, would have enhanced the flux of N₂ O from ferruginous Proterozoic seas. We empirically derived a rate law, d N 2 O d t = 7.2 × 10 - 5 [ Fe 2 + ] 0.3 [ NO ] 1 , and measured an isotopic site preference of +16‰ for the reaction. Using this empirical rate law, and integrating across an oceanwide oxycline, we found that low nM NO and μM-low mM Fe²⁺ concentrations could have sustained a sea-air flux of 100-200 Tg N₂ O-N year^-1 , if N₂ fixation rates were near-modern and all fixed N₂ was emitted as N₂ O. A 1D photochemical model was used to obtain steady-state atmospheric N₂ O concentrations as a function of sea-air N₂ O flux across the wide range of possible pO₂ values (0.001-1 PAL). At 100-200 Tg N₂ O-N year^-1 and >0.1 PAL O₂ , this model yielded low-ppmv N₂ O, which would produce several degrees of greenhouse warming at 1.6 ppmv CH₄ and 320 ppmv CO₂ . These results suggest that enhanced N₂ O production in ferruginous seawater via a previously unconsidered chemodenitrification pathway may have helped to fill a Proterozoic "greenhouse gap," reconciling an ice-free Mesoproterozoic Earth with a less luminous early Sun. A particularly notable result was that high N₂ O fluxes at intermediate O₂ concentrations (0.01-0.1 PAL) would have enhanced ozone screening of solar UV radiation. Due to rapid photolysis in the absence of an ozone shield, N₂ O is unlikely to have been an important greenhouse gas if Mesoproterozoic O₂ was 0.001 PAL. At low O₂ , N₂ O might have played a more important role as life's primary terminal electron acceptor during the transition from an anoxic to oxic surface Earth, and correspondingly, from anaerobic to aerobic metabolisms.

HN2 O2 - as a Ligand in Mononuclear Hydrogenhyponitrite-κ2 -N,O Ruthenium Complexes with Bisphosphane Co-Ligands

The hyponitrite anion is a tentative intermediate in the reduction of nitric oxide (NO) to nitrous oxide (N₂ O) catalyzed by nitric-oxide reductase (NOR) in the process of bacterial denitrification. Owing to the considerable number of known coordination modes for the hyponitrito ligand, its actual bonding form in the enzymatic cycle is a point of current discussion. Here, we contribute to the hardly known ligand properties of a key intermediate, the monoprotonated hyponitrite anion. Three air- and water-stable ruthenium complexes with hydrogenhyponitrite as the ligand were synthesized by using commercially available bisphosphane co-ligands (1,2-bis(diphenylphosphino)ethane (dppe), 1,3-bis(diphenylphosphino)propane (dppp), 1,2-bis(diphenylphosphino)ethene (dppv)). The starting compounds [Ru(dppe)₂ (tos)]BF₄ (1) and [Ru(dppp)₂ (tos)]BF₄ (2) contained the bidentate coordinating tosylate anion (tos) as a particularly well-suited leaving group. To confirm the protonated and deprotonated species, X-ray diffraction, IR, UV/Vis spectroscopy (solution and solid state), solid-state NMR spectroscopy, and high-resolution mass spectroscopy were used. DFT calculations give insight into the bonding situation. We report on [Ru(dppe)₂ (HN₂ O₂ )]BF₄ (5), [Ru(dppp)₂ (HN₂ O₂ )]BF₄ (6), [Ru(dppv)₂ (HN₂ O₂ )]BF₄ (7), [Ru(dppp)₂ (HN₂ O₂ )]BF₄ ⋅Imi (9; Imi=imidazole) as the first mononuclear trans-hydrogenhyponitrite complexes. Isolated deprotonated analogs are [Ru(dppe)₂ (N₂ O₂ )]⋅HImi(BF₄ ) (8) and [Ru(dppv)₂ (N₂ O₂ )] ⋅HImi(BF₄ )⋅Imi (10).

Response of greenhouse gas emissions and microbial community dynamics to temperature variation during partial nitrification

This study investigated the greenhouse gas emission characteristics and microbial community dynamics with the variation of temperature during partial nitrification. Low temperature weakened nitrite accumulation, and partial nitrification would shift to complete nitrification easily at 15 °C. Based on CO₂ equivalents (CO₂-eq), partial nitrification process released 2.7 g of greenhouse gases per gMLSS per cycle, and N₂O accounted for more than 98% of the total CO₂-eq emission. The total CO₂-eq emission amount at 35 °C was 45.6% and 153.4% higher than that at 25 °C and 15 °C, respectively. During partial nitrification, the microbial community diversity greatly declined compared with seed sludge. However, the diversity was enhanced at low temperature. The abundance of Betaproteobacteria at class level increased greatly during partial nitrification. Proteobacteria abundance declined while Nitrospira raised at low temperature. The nosZ community abundance was not affected by temperature, although N₂O emission was varied with the operating temperature.

Emerging Roles of Nitric Oxide Synthase in Bacterial Physiology

Nitric oxide (NO) is a potent inhibitor of diverse cellular processes in bacteria. Therefore, it was surprising to discover that several bacterial species, primarily Gram-positive organisms, harboured a gene encoding nitric oxide synthase (NOS). Recent attempts to characterize bacterial NOS (bNOS) have resulted in the discovery of structural features that may allow it to function as a NO dioxygenase and produce nitrate in addition to NO. Consistent with this characterization, investigations into the biological function of bNOS have also emphasized a role for NOS-dependent nitrate and nitrite production in aerobic and microaerobic respiration. In this review, we aim to compare, contrast, and summarize the structure, biochemistry, and biological role of bNOS with mammalian NOS and discuss how recent advances in our understanding of bNOS have enabled efforts at designing inhibitors against it.

Comparative gene expression analysis of Porphyromonas gingivalis ATCC 33277 in planktonic and biofilms states

Background and objective

Porphyromonas gingivalis is a keystone pathogen in the onset and progression of periodontitis. Its pathogenicity has been related to its presence and survival within the subgingival biofilm. The aim of the present study was to compare the genome-wide transcription activities of P. gingivalis in biofilm and in planktonic growth, using microarray technology.

Material and methods

P. gingivalis ATCC 33277 was incubated in multi-well culture plates at 37°C for 96 hours under anaerobic conditions using an in vitro static model to develop both the planktonic and biofilm states (the latter over sterile ceramic calcium hydroxyapatite discs). The biofilm development was monitored by Confocal Laser Scanning Microscopy (CLSM) and Scanning Electron Microscopy (SEM). After incubation, the bacterial cells were harvested and total RNA was extracted and purified. Three biological replicates for each cell state were independently hybridized for transcriptomic comparisons. A linear model was used for determining differentially expressed genes and reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to confirm differential expression. The filtering criteria of ≥ ±2 change in gene expression and significance p-values of <0.05 were selected.

Results

A total of 92 out of 1,909 genes (4.8%) were differentially expressed by P. gingivalis growing in biofilm compared to planktonic. The 54 up-regulated genes in biofilm growth were mainly related to cell envelope, transport, and binding or outer membranes proteins. Thirty-eight showed decreased expression, mainly genes related to transposases or oxidative stress.

Conclusion

The adaptive response of P. gingivalis in biofilm growth demonstrated a differential gene expression.

The effect of drip irrigation and drip fertigation on N2O and NO emissions, water saving and grain yields in a maize field in the North China Plain

N₂O and NO emissions, the water usage and grain yields of a maize field in the North China Plain (NCP) under traditional flood irrigation, drip irrigation and drip fertigation were compared. With respect to the flood irrigation treatment, N₂O emissions were reduced by 13.8% in the drip irrigation treatment and 7.7% in the drip fertigation treatment. NO emissions were reduced to 16.7% in the drip irrigation treatment but increased by 21.7% in the drip fertigation treatment. The molar ratios of NO/N₂O within 2days after each fertilization event were evidently greater from the drip fertigation treatment than from the flood irrigation treatment, indicating that nitrification was more intensive in the drip fertigation treatment than in the treatment of flood irrigation. Compared with the flood irrigation treatment, evident increase of the maize yields in the drip irrigation treatment (28%) and the drip fertigation treatment (3.7%) were found. Although the drip fertigation treatment could evidently increase NO emission, the 40% water reduction in drip fertigation is of great importance for the sustainable development of agriculture in the NCP where water resources are extremely limited. To mitigate NO emissions from agricultural fields in the NCP with drip fertigation, the addition of a nitrification inhibitor combined with N or nitrate fertilizer was recommended.

Pseudomonas aeruginosa Exhibits Deficient Biofilm Formation in the Absence of Class II and III Ribonucleotide Reductases Due to Hindered Anaerobic Growth

Chronic lung infections by the ubiquitous and extremely adaptable opportunistic pathogen Pseudomonas aeruginosa correlate with the formation of a biofilm, where bacteria grow in association with an extracellular matrix and display a wide range of changes in gene expression and metabolism. This leads to increased resistance to physical stress and antibiotic therapies, while enhancing cell-to-cell communication. Oxygen diffusion through the complex biofilm structure generates an oxygen concentration gradient, leading to the appearance of anaerobic microenvironments. Ribonucleotide reductases (RNRs) are a family of highly sophisticated enzymes responsible for the synthesis of the deoxyribonucleotides, and they constitute the only de novo pathway for the formation of the building blocks needed for DNA synthesis and repair. P. aeruginosa is one of the few bacteria encoding all three known RNR classes (Ia, II, and III). Class Ia RNRs are oxygen dependent, class II are oxygen independent, and class III are oxygen sensitive. A tight control of RNR activity is essential for anaerobic growth and therefore for biofilm development. In this work we explored the role of the different RNR classes in biofilm formation under aerobic and anaerobic initial conditions and using static and continuous-flow biofilm models. We demonstrated the importance of class II and III RNR for proper cell division in biofilm development and maturation. We also determined that these classes are transcriptionally induced during biofilm formation and under anaerobic conditions. The molecular mechanism of their anaerobic regulation was also studied, finding that the Anr/Dnr system is responsible for class II RNR induction. These data can be integrated with previous knowledge about biofilms in a model where these structures are understood as a set of layers determined by oxygen concentration and contain cells with different RNR expression profiles, bringing us a step closer to the understanding of this complex growth pattern, essential for P. aeruginosa chronic infections.

Silicon Nitride Bioceramics Induce Chemically Driven Lysis in Porphyromonas gingivalis

Organisms of Gram-negative phylum bacteroidetes, Porphyromonas gingivalis, underwent lysis on polished surfaces of silicon nitride (Si3N4) bioceramics. The antibacterial activity of Si3N4 was mainly the result of chemically driven principles. The lytic activity, although not osmotic in nature, was related to the peculiar pH-dependent surface chemistry of Si3N4. A buffering effect via the formation of ammonium ions (NH4(+)) (and their modifications) was experimentally observed by pH microscopy. Lysis was confirmed by conventional fluorescence spectroscopy, and the bacteria's metabolism was traced with the aid of in situ Raman microprobe spectroscopy. This latter technique revealed the formation of peroxynitrite within the bacterium itself. Degradation of the bacteria's nucleic acid, drastic reduction in phenilalanine, and reduction of lipid concentration were observed due to short-term exposure (6 days) to Si3N4. Altering the surface chemistry of Si3N4 by either chemical etching or thermal oxidation influenced peroxynitrite formation and affected bacteria metabolism in different ways. Exploiting the peculiar surface chemistry of Si3N4 bioceramics could be helpful in counteracting Porphyromonas gingivalis in an alkaline pH environment.

Nitric Oxide in the Offensive Strategy of Fungal and Oomycete Plant Pathogens

In the course of evolutionary changes pathogens have developed many invasion strategies, to which the host organisms responded with a broad range of defense reactions involving endogenous signaling molecules, such as nitric oxide (NO). There is evidence that pathogenic microorganisms, including two most important groups of eukaryotic plant pathogens, also acquired the ability to synthesize NO via non-unequivocally defined oxidative and/or reductive routes. Although the both kingdoms Chromista and Fungi are remarkably diverse, the experimental data clearly indicate that pathogen-derived NO is an important regulatory molecule controlling not only developmental processes, but also pathogen virulence and its survival in the host. An active control of mitigation or aggravation of nitrosative stress within host cells seems to be a key determinant for the successful invasion of plant pathogens representing different lifestyles and an effective mode of dispersion in various environmental niches.

Investigation of denitrifying microbial communities within an agricultural drainage system fitted with low-grade weirs

Enhancing wetland characteristics in agricultural drainage ditches with the use of low-grade weirs, has been identified as a best management practice (BMP) to mitigate nutrient runoff from agriculture landscapes. A major objective of utilizing low-grade weirs as a BMP includes fostering environments suitable for the biogeochemical removal of nitrogen via denitrification. This study examined the spatial resolution of microbial communities involved in denitrification in agricultural drainage systems fitted with low-grade weirs. Appropriate sampling scales of microbial communities were investigated using 16S rRNA and denitrification functional genes nosZ, nirS, and nirK via quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP) analysis. Genes 16S rRNA, nosZ, and nirS were all successfully detected in soil samples, while nirK was below the detection limit throughout the study. Utilizing a combination of three sampling regimes (management, reach, catchment) was found to be effective in capturing microbial community patterns, as ANOVA results revealed nosZ gene abundance was significantly greater at the management rather than reach scale (p = 0.045; F = 3.311), although, no significant differences were observed in 16S rRNA or nirS between sampling scales (p > 0.05). A Pearson correlation matrix confirmed that 16S rRNA and nosZ gene abundances were positively correlated with soil carbon (C), nitrogen (N), and moisture, while nirS abundance was only positively correlated with soil C and soil moisture. This highlights the potential for wetland-like characteristics to be recovered in agricultural drainage systems, as weir proximity is observed to enhance soil moisture and conditions for N remediation. This study provides the basis for additional investigations of these unique environments in the Mississippi Alluvial Valley and a starting point for adaptive management to enhance agricultural drainage systems for microbial communities towards nutrient remediation goals.

Bacterial nitric oxide reductase: a mechanism revisited by an ONIOM (DFT:MM) study

Bacterial nitric oxide reductase (cNOR) is an important binuclear iron enzyme responsible for the reduction of nitric oxide to nitrous oxide in the catalytic cycle of bacterial respiration. The reaction mechanism of cNOR as well as the key reactive intermediates of the reaction are still under debate. Here, we report a computational study based on ONIOM (DFT:MM) calculations aimed at investigating the reaction mechanism of cNOR. The results suggest that the reaction proceeds via the mono-nitrosyl mechanism which starts off by the binding of an NO molecule to the heme b3 center, N-N hyponitrite bond formation as a result of the reaction with a second NO molecule was found to proceed with an exothermic energy barrier to yield a hyponitrite adduct forming an open (incomplete) ring conformation with the non-heme FeB center (O-N-N-O-FeB). N-O bond cleavage to yield N2O was shown to be the rate-limiting step with an activation barrier of 22.6 kcal mol(-1). The dinitrosyl (trans) mechanism, previously proposed by several studies, was also examined and found unfavorable due to high activation barriers of the resulting intermediates.

Cysteine-mediated redox signalling in the mitochondria

This review represents a novel look at the many sources, cysteine targets, and signaling processes of ROS in the mitochondria.

Current advances of integrated processes combining chemical absorption and biological reduction for NO x removal from flue gas

Anthropogenic nitrogen oxides (NO x ) emitted from the fossil-fuel-fired power plants cause adverse environmental issues such as acid rain, urban ozone smoke, and photochemical smog. A novel chemical absorption-biological reduction (CABR) integrated process under development is regarded as a promising alternative to the conventional selective catalytic reduction processes for NO x removal from the flue gas because it is economic and environmentally friendly. CABR process employs ferrous ethylenediaminetetraacetate [Fe(II)EDTA] as a solvent to absorb the NO x following microbial denitrification of NO x to harmless nitrogen gas. Meanwhile, the absorbent Fe(II)EDTA is biologically regenerated to sustain the adequate NO x removal. Compared with conventional denitrification process, CABR not only enhances the mass transfer of NO from gas to liquid phase but also minimize the impact of oxygen on the microorganisms. This review provides the current advances of the development of the CABR process for NO x removal from the flue gas.

Effect of biochar on nitrous oxide emission and its potential mechanisms

Extensive use of biochar to mitigate nitrous oxide (N2O) emission is limited by the lack of understanding on the exact mechanisms altering N2O emission from biochar-amended soil. Biochars produced from rice straw and dairy manure at 350 and 500 degrees C by oxygen-limited pyrolysis were used to investigate their influence on N2O emission. A quadratic effect of biochar levels was observed on the N2O emissions. The potential mechanisms were explored by terminal restriction fragment length polymorphism (T-RFLP) and real-time polymerase chain reaction (qPCR). A lower relative abundance of bacteria, which included ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), was observed at 4% biochar application rate. Reduced copy numbers of the ammonia monooxygenase gene amoA and the nitrite reductase gene nirS coincided with decreased N2O emissions. Therefore, biochar may potentially alter N2O emission by affecting ammonia-oxidizing and denitrification bacteria, which is determined by the application rate of biochar in soil. Implications: Biochar research has received increased interest in recent years because of the potential beneficial effects of biochar on soil properties. Recent research shows that biochar can alter the rates of nitrogen cycling in soil systems by influencing nitrification and denitrification, which are key sources of the greenhouse gas nitrous oxide (N2O). However, there are still some controversial data. The purpose of this research was to (1) examine how applications of different dose of biochar to soil affect emission of N2O and (2) improve the understanding of the underlying mechanisms.

Nitric oxide: an effective weapon of the plant or the pathogen?

An explosion of research in plant nitric oxide (NO) biology during the last two decades has revealed that NO is a key signal involved in plant development, abiotic stress responses and plant immunity. During the course of evolutionary changes, microorganisms parasitizing plants have developed highly effective offensive strategies, in which NO also seems to be implicated. NO production has been demonstrated in several plant pathogens, including fungi, but the origin of NO seems to be as puzzling as in plants. So far, published studies have been spread over multiple species of pathogenic microorganisms in various developmental stages; however, the data clearly indicate that pathogen-derived NO is an important regulatory molecule involved not only in developmental processes, but also in pathogen virulence and its survival in the host. This review also focuses on the search for potential mechanisms by which pathogens convert NO messages into a physiological response or detoxify both endo- and exogenous NO. Finally, taking into account the data available from model bacteria and yeast, a basic draft for the mode of NO action in phytopathogenic microorganisms is proposed.

Nitric oxide removal by wastewater bacteria in a biotrickling filter

Nitric oxide (NO) is one of the most important air pollutants in atmosphere mainly emitted from combustion source. A biotrickling filter was designed and operated to remove NO from an air stream using bacteria extracted from the sewage sludge of a municipal sewage treatment plant. To obtain the best operation conditions for the biotrickling filter, orthogonal experiments (L9(3(4))) were designed. Inlet oxygen concentration was found to be the most significant factor of the biotrickling filter and has a significant negative effect on the system. The optimal conditions of the biotrickling filter occurred at a temperature of 40°C, a pH of 8.0 and a chemical oxygen demand of 165 mg/L in the recycled water with no oxygen in the system. The bacteria sample was detected by DNA sequencing technology and showed 93%-98% similarity to Pseudomonas mendocina. Moreover, a full gene sequencing results indicated the bacterium was a brand new strain and named as P. mendocina DLHK. This strain can transfer nitrate to organic nitrogen. The result suggested the assimilation nitrogen process in this system. Through the isotope experimental analysis, two intermediate products ((15)NO and (15)N2O) were found. The results indicated the denitrification function and capability of the biotrickling filter in removing NO.

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.

Fe(II) oxidation is an innate capability of nitrate-reducing bacteria that involves abiotic and biotic reactions

Phylogenetically diverse species of bacteria can catalyze the oxidation of ferrous iron [Fe(II)] coupled to nitrate (NO(3)(-)) reduction, often referred to as nitrate-dependent iron oxidation (NDFO). Very little is known about the biochemistry of NDFO, and though growth benefits have been observed, mineral encrustations and nitrite accumulation likely limit growth. Acidovorax ebreus, like other species in the Acidovorax genus, is proficient at catalyzing NDFO. Our results suggest that the induction of specific Fe(II) oxidoreductase proteins is not required for NDFO. No upregulated periplasmic or outer membrane redox-active proteins, like those involved in Fe(II) oxidation by acidophilic iron oxidizers or anaerobic photoferrotrophs, were observed in proteomic experiments. We demonstrate that while "abiotic" extracellular reactions between Fe(II) and biogenic NO(2)(-)/NO can be involved in NDFO, intracellular reactions between Fe(II) and periplasmic components are essential to initiate extensive NDFO. We present evidence that an organic cosubstrate inhibits NDFO, likely by keeping periplasmic enzymes in their reduced state, stimulating metal efflux pumping, or both, and that growth during NDFO relies on the capacity of a nitrate-reducing bacterium to overcome the toxicity of Fe(II) and reactive nitrogen species. On the basis of our data and evidence in the literature, we postulate that all respiratory nitrate-reducing bacteria are innately capable of catalyzing NDFO. Our findings have implications for a mechanistic understanding of NDFO, the biogeochemical controls on anaerobic Fe(II) oxidation, and the production of NO(2)(-), NO, and N(2)O in the environment.

Elucidating the regulon of multidrug resistance regulator RarA in Klebsiella pneumoniae

RarA is an AraC-type regulator in Klebsiella pneumoniae, which, when overexpressed, confers a low-level multidrug-resistant (MDR) phenotype linked to the upregulation of both the acrAB and oqxAB efflux genes. Increased rarA expression has also been shown to be integral in the development of tigecycline resistance in the absence of ramA in K. pneumoniae. Given its phenotypic role in MDR, microarray analyses were performed to determine the RarA regulon. Transcriptome analysis was undertaken using strains Ecl8ΔrarA/pACrarA-2 (rarA-expressing construct) and Ecl8ΔrarA/pACYC184 (vector-only control) using bespoke microarray slides consisting of probes derived from the genomic sequences of K. pneumoniae MGH 78578 (NC_009648.1) and Kp342 (NC_011283.1). Our results show that rarA overexpression resulted in the differential expression of 66 genes (42 upregulated and 24 downregulated). Under the COG (clusters of orthologous groups) functional classification, the majority of affected genes belonged to the category of cell envelope biogenesis and posttranslational modification, along with genes encoding the previously uncharacterized transport proteins (e.g., KPN_03141, sdaCB, and leuE) and the porin OmpF. However, genes associated with energy production and conversion and amino acid transport/metabolism (e.g., nuoA, narJ, and proWX) were found to be downregulated. Biolog phenotype analyses demonstrated that rarA overexpression confers enhanced growth of the overexpresser in the presence of several antibiotic classes (i.e., beta-lactams and fluoroquinolones), the antifungal/antiprotozoal compound clioquinol, disinfectants (8-hydroxyquinoline), protein synthesis inhibitors (i.e., minocycline and puromycin), membrane biogenesis agents (polymyxin B and amitriptyline), DNA synthesis (furaltadone), and the cytokinesis inhibitor (sanguinarine). Both our transcriptome and phenotypic microarray data support and extend the role of RarA in the MDR phenotype of K. pneumoniae.

Electrochemical behaviour of bacterial nitric oxide reductase-evidence of low redox potential non-heme Fe(B) gives new perspectives on the catalytic mechanism

Nitric oxide reductase (NOR) is a membrane bound enzyme involved in the metabolic denitrification pathway, reducing nitric oxide (NO) to nitrous oxide (N(2)O), subsequently promoting the formation of the NN bond. Three types of bacterial NOR are known, namely cNOR, qNOR and qCuNOR, that differ on the physiological electron donor. cNOR has been purified as a two subunit complex, the NorC, anchored to the cytoplasmic membrane, with a low-spin heme c, and the NorB subunit showing high structural homology with the HCuO subunit I, comprising a bis-histidine low-spin heme b and a binuclear iron centre. The binuclear iron centre is the catalytic site and it is formed by a heme b(3) coupled to a non-heme iron (Fe(B)) through a μ-oxo bridge. The catalytic mechanism is still under discussion and three hypotheses have been proposed: the trans-mechanism, the cis-Fe(B) and the cis-heme b(3) mechanisms. In the present work, the Pseudomonas nautica cNOR electrochemical behaviour was studied by cyclic voltammetry (CV), using a pyrolytic graphite electrode modified with the immobilised protein. The protein redox centres were observed and the formal redox potentials were determined. The binuclear iron centre presents the lowest redox potential value, and discrimination between the heme b(3) and Fe(B) redox processes was attained. Also, the number of electrons involved and correspondent surface electronic transfer rate constants were estimated. The pH dependence of the observed redox processes was determined and some new insights on the NOR catalytic mechanism are discussed.

Protection from nitrosative stress: a central role for microbial flavohemoglobin

Nitric oxide (NO) is an inevitable product of life in an oxygen- and nitrogen-rich environment. This reactive diatomic molecule exhibits microbial cytotoxicity, in large part by facilitating nitrosative stress and inhibiting heme-containing proteins within the aerobic respiratory chain. Metabolism of NO is therefore essential for microbial life. In many bacteria, fungi, and protozoa, the evolutionarily ancient flavohemoglobin (flavoHb) converts NO and O(2) to inert nitrate (NO(3)(-)) and undergoes catalytic regeneration via flavin-dependent reduction. Since its identification, widespread efforts have characterized roles for flavoHb in microbial nitrosative stress protection. Subsequent genomic studies focused on flavoHb have elucidated the transcriptional machinery necessary for inducible NO protection, such as NsrR in Escherichia coli, as well as additional proteins that constitute a nitrosative stress protection program. As an alternative strategy, flavoHb has been heterologously employed in higher eukaryotic organisms such as plants and human tumors to probe the function(s) of endogenous NO signaling. Such an approach may also provide a therapeutic route to in vivo NO depletion. Here we focus on the molecular features of flavoHb, the hitherto characterized NO-sensitive transcriptional machinery responsible for its induction, the roles of flavoHb in resisting mammalian host defense systems, and heterologous applications of flavoHb in plant/mammalian systems (including human tumors), as well as unresolved questions surrounding this paradigmatic NO-consuming enzyme.

Microbial removal of NOX at high temperature by a novel aerobic strain Chelatococcus daeguensis TAD1 in a biotrickling filter

The removal of NO(X) at high temperature by Chelatococcus daeguensis TAD1 in a biotrickling filter was studied. Media components of the recycling liquid were screened using Plackett-Burman design and then were optimized using response surface methodology, which enhanced the efficiency of nitrate removal by TAD1. The optimal medium was used to perform long-term experiments of NO(X) removal in a biotrickling filter under high concentrations of O(2) and NO in simulated flue gas. Results showed that the biotrickling filter was able to consistently remove 80.2-92.3% NO(X) when the inlet NO concentration was 600ppm under the conditions of oxygen concentration ranging between 2% and 20% and empty bed residence time (EBRT) being 112.5s. Analyses by polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) indicated that TAD1 was always predominant in the biofilm under a flue gas environment. Overall, the present study demonstrated that utilizing a biotrickling filter inoculated with the aerobic denitrifier TAD1 to remove NO(X) at high temperature was practically feasible.

Nitric oxide stress resistance in Porphyromonas gingivalis is mediated by a putative hydroxylamine reductase

Porphyromonas gingivalis, the causative agent of adult periodontitis, must maintain nitric oxide (NO) homeostasis and surmount nitric oxide stress from host immune responses or other oral bacteria to survive in the periodontal pocket. To determine the involvement of a putative hydroxylamine reductase (PG0893) and a putative nitrite reductase-related protein (PG2213) in P. gingivalis W83 NO stress resistance, genes encoding those proteins were inactivated by allelic exchange mutagenesis. The isogenic mutants P. gingivalis FLL455 (PG0893ermF) and FLL456 (PG2213ermF) were black pigmented and showed growth rates and gingipain and hemolytic activities similar to those of the wild-type strain. P. gingivalis FLL455 was more sensitive to NO than the wild type. Complementation of P. gingivalis FLL455 with the wild-type gene restored the level of NO sensitivity to a level similar to that of the parent strain. P. gingivalis FLL455 and FLL456 showed sensitivity to oxidative stress similar to that of the wild-type strain. DNA microarray analysis showed that PG0893 and PG2213 were upregulated 1.4- and 2-fold, respectively, in cells exposed to NO. In addition, 178 genes were upregulated and 201 genes downregulated more than 2-fold. The majority of these modulated genes were hypothetical or of unknown function. PG1181, predicted to encode a transcriptional regulator, was upregulated 76-fold. Transcriptome in silico analysis of the microarray data showed major metabolomic variations in key pathways. Collectively, these findings indicate that PG0893 and several other genes may play an important role in P. gingivalis NO stress resistance.

Flux of nitric oxide between the necrotrophic pathogen Botrytis cinerea and the host plant

Nitric oxide (NO) production by Botrytis cinerea and the effect of externally supplied NO were studied during saprophytic growth and plant infection. Fluorescence analysis with 4,5-diaminofluorescein diacetate and electrochemical studies were conducted in vitro between 4 and 20 h of incubation and in planta between 15 and 75 h post-inoculation. The production of NO by B. cinerea in vitro was detected inside the germinating spores and mycelium and in the surrounding medium. In planta production of NO showed a large variation that was dependent on the host plant and developmental stage of the infection. The induced production of NO was detected from 16 h of in vitro incubation in response to externally added NO. The production of NO by B. cinerea is probably modulated to promote fungal colonization of the plant tissue. The production of NO which diffuses outside the fungal cells and the induction of NO production by exogenous NO open up the possibility of NO cross-talk between the fungus and the plant. Finally, the existence of an NO concentration threshold is proposed, which may increase or reduce the plant defence against necrotrophic fungal pathogens.

Structural basis of biological N2O generation by bacterial nitric oxide reductase

Nitric oxide reductase (NOR) is an iron-containing enzyme that catalyzes the reduction of nitric oxide (NO) to generate a major greenhouse gas, nitrous oxide (N(2)O). Here, we report the crystal structure of NOR from Pseudomonas aeruginosa at 2.7 angstrom resolution. The structure reveals details of the catalytic binuclear center. The non-heme iron (Fe(B)) is coordinated by three His and one Glu ligands, but a His-Tyr covalent linkage common in cytochrome oxidases (COX) is absent. This structural characteristic is crucial for NOR reaction. Although the overall structure of NOR is closely related to COX, neither the D- nor K-proton pathway, which connect the COX active center to the intracellular space, was observed. Protons required for the NOR reaction are probably provided from the extracellular side.