Effects of oxygen, pH and nitrate concentration on denitrification by Pseudomonas species

Biopolymer as an additive for effective biochar-based rhizobial inoculant

Biochar is an efficient and inexpensive carrier for bacteria that stimulate plant development and growth. In this study, different biopolymer additives (cellulose, xanthan gum, chitin and tryptone) were tested with different addition ratios (1:0.1, 1:0.5 and 1:1) on further enhancing biochar capacity for supporting the growth and activity of Bradyrhizobium japonicum (CB1809). We utilized pine wood biochar (PWBC) pyrolyzed at 400 °C as the base inoculum carrier. The shelf life and survival rate of CB1809 were counted using the colony-forming unit (CFU) method for up to 120 days. Peat served as a standard reference material against which all treatments were compared. Subsequent experiments evaluated the ability of carrier inoculants to promote Glycine max L. (soybean) plant growth and nodulation under different watering regimes, i.e., 55 % water holding capacity (WHC) (D0), 30 % WHC (D1) and, 15 % WHC (D2) using sandy loam soil. Results revealed that among different additives; xanthan gum with 1:0.5 to PWBC [PWBC-xanthan gum(1:0.5)] was observed as a superior formulation in supporting rhizobial shelf life and survival rate of CB1809. In pot experiments, plants with PWBC-xanthan gum(1:0.5) formulation showed significant increase in various physiological characteristics (nitrogenase activity, chlorophyll pigments, membrane stability index, and relative water content), root architecture (root surface area, root average diameter, root volume, root tips, root forks and root crossings), and plant growth attributes (shoot/root dry biomass, shoot/root length, and number of nodules). Additionally, a reduced enrichment of isotopic signatures (δ13C, δ15N) was observed in plants treated with PWBC-xanthan gum(1:0.5), less enrichment of δ15N indicates an inverse link to nodulation and nitrogenase activity, while lower δ13C values indicates effective water use efficiency by plants during drought stress. These results suggest that biopolymers supplementation of the PWBC is useful in promoting shelf life or survival rate of CB1809.

Community structures and biodeterioration processes of epilithic biofilms imply the significance of micro-environments

Epilithic biofilms colonising outdoor stone monuments can intensify the deterioration processes of the stone materials and pose great challenges to their protection. In this study, biodiversity and community structures of the epilithic biofilms colonising the surfaces of five outdoor stone dog sculptures were characterised by high-throughput sequencing. Although they are exposed to the same envrionment in a small yard, the analysis of their biofilm populations revealed high biodiversity and species richness as well as great differences in community compostions. Interestingly, populations responsible for pigment production (e.g., Pseudomonas, Deinococcus, Sphingomonas and Leptolyngbya) and for nitrogen (e.g., Pseudomonas, Bacillus, and Beijerinckia) and sulfur cycling (e.g., Acidiphilium) were the core common taxa in the epilithic biofilms, suggesting the potential biodeterioration processes. Furthermore, significant positive corrolections of metal elements rich in stone with biofilm communities showed that epilithic biofilms could take in minerals of stone. Importantly, geochemical properties of soluble ions (higher concentration of SO₄^2- than NO₃^-) and slightly acidic micro-environments on the surfaces suggest corrosion of biogenic sulfuric acids as a main mechanism of biodeterioration of the sculptures. Interestingly, relative abundacne of Acidiphilium showed a positive correlation with acidic micro-environments and SO₄^2- concentrations, implying they could be an indicator of sulfuric acid corrosion. Together, our findings support that micro-environments are inportant to community assembly of epilithic biofilms and the biodeterioration processes involved.

Study of a three-dimensional biofilm-electrode reactor (3D-BER) that combined heterotrophic and autotrophic denitrification (HAD) to remove nitrate from water

A three-dimensional biofilm-electrode reactor (3D-BER) that combined heterotrophic and autotrophic denitrification (HAD) was developed to remove nitrate. The denitrification performance of the 3D-BER was evaluated under different experimental conditions, including current intensities (0-80 mA), COD/N ratios (0.5-5), and hydraulic retention times (2-12 h). The results showed that excessive current limited the nitrate removal efficiency. However, a longer hydraulic retention time was not required to achieve a better denitrification effect in the 3D-BER. Moreover, the nitrate could be effectively reduced over a broad range of COD/Ns (1-2.5), and its removal rate peaked at 89% at I = 40 mA, HRT = 8 h, and COD/N = 2. Although the current reduced the diversity of microorganisms in the system, it promoted the growth of dominant species. Nitrification microorganisms were enriched in the reactor, especially Thauera and Hydrogenophaga, which were crucial to the denitrification process. Thus, the combination of autotrophic denitrification and heterotrophic denitrification was promoted by the 3D-BER system to increase the efficiency of nitrogen removal.

Quorum sensing responses of r-/K-strategists Nitrospira in continuous flow and sequencing batch nitrifying biofilm reactors

A better understanding of r-/K-strategists nitrifiers will help to balance the design and operation of bioprocesses for efficient pollution removal from wastewater. The objectives of study were to investigate the nitrite oxidation biokinetics, biofilm property, microbial community and quorum sensing (QS) of nitrifying biofilm in a continuously flow reactor (CFR) and a sequencing batch reactor (SBR). Results showed that nitrite-oxidizing bacteria were estimated to have a nitrite half saturation constant of 76.23 and 224.73 μM in CFR and SBR, respectively. High-throughput and metagenomic sequencing results showed that Nitrospira and Candidatus Nitrospira defluvii were the dominated nitrite-oxidizing taxa performing nitrite oxidation in both reactors. Nitrifying biofilm developed in CFR and SBR showed obviously different properties. Biofilm in SBR had an obviously higher ratio of polysaccharide and protein in extracellular polymeric substances, and higher thickness than in CFR. Metagenomics and chemical analysis revealed various types of acyl-homoserine lactone (AHL) circuit genes (e.g., luxI, lasI, hdtS) and four types of AHL signaling substances (e.g., C₆-HSL, C₈-HSL, C₁₀-HSL and 3-oxo-C₁₀-HSL) in nitrifying biofilm. The concentrations of these AHLs in biomass and water phases were obviously higher in SBR than that in CFR. Together, AHLs-based QS might affect the formation of nitrifying biofilm and thus contribute to the different biokinetics of Nitrospira in CFR and SBR. Our insights may reveal the molecular mechanism of Nitrospira for different biokinetics, and indicate the AHL association with Nitrospira adaptation to various conditions.

Denitrification kinetics during aquifer storage and recovery of drainage water from agricultural land

An aquifer storage transfer and recovery (ASTR) system was studied in which tile drainage water (TDW) was injected with relatively high NO₃ (about 14 mg/L) concentrations originating from fertilizers. Here we present the evolution of denitrification kinetics at 6 different depths in the aquifer before, and during ASTR operation. First-order denitrification rate constants increased over time before and during the first days of ASTR operation, likely due to microbial adaptation of the native bacterial community and/or bioaugmentation of the aquifer by denitrifying bacteria present in injected TDW. Push-pull tests were performed in the native aquifer before ASTR operation. Obtained first-order denitrification rate constants were negligible (0.00-0.03 d^-1) at the start, but increased to 0.17-0.83 d^-1 after a lag-phase of about 6 days. During the first days of ASTR operation in autumn 2019, the arrival of injected TDW was studied at 2.5 m distance from the injection well. First-order denitrification rate constants increased again over time (maximum >1 d^-1). Three storage periods without injection were monitored in winter 2019, fall 2020, and spring 2021 during ASTR operation. First-order rate constants ranged between 0.12 and 0.61 d^-1. Denitrification coupled to pyrite oxidation occurred at all depths, but other oxidation processes were indicated as well. NO₃ concentration trends resembled Monod kinetics but were fitted also to a first-order decay rate model to facilitate comparison. Rate constants during the storage periods were substantially lower than during injection, probably due to a reduction in the exchange rate between aquifer solid phases and injected water during the stagnant conditions. Denitrification rate constants deviated maximally a factor 5 over time and depth for all in-situ measurement approaches after the lag-phase. The combination of these in-situ approaches enabled to obtain more detailed insights in the evolution of denitrification kinetics during AS(T)R.

Bioretention for removal of nitrogen: processes, operational conditions, and strategies for improvement

As one of the low-impact development measures, bioretention plays an important role in reducing the runoff peak flow and minimizing runoff pollutants, such as heavy metals, suspended solids, and nutrients. However, the efficiency of nitrogen removal in the bioretention system is unstable, owing to the different chemical properties of various forms of nitrogen and the limitations of current bioretention system for nitrogen transformation. This review article summarizes the recent advances in bioretention system in treatment of urban stormwater and agricultural runoff for nitrogen removal. The microbial characteristics and main processes of nitrogen transformation in bioretention are reviewed. The operational conditions affecting nitrogen removal, including climatic conditions, pH, wet-dry alternation, influent loads and nitrogen concentration, and hydraulic residence time are discussed. Finally, measures or strategies for increasing nitrogen removal efficiency are proposed from the perspectives of structural improvement of the bioretention system, optimization of medium composition, and enhancement of the nitrogen removal reaction processes.

Transformation and source identification of N in the upper reaches of the Han River basin, China: evaluated by a stable isotope approach

Given the spatial and temporal variability in hydrological conditions and nitrogen (N) processes, it is of great uncertainty to identify the N sources and evaluate N transformation processes in the upper Han River. Investigations were conducted in November 2015 and January, April, and July 2016, using an isotopic method and water quality monitoring. The significant and positive correlation between NO₃^- concentrations and Cl^- (p < 0.01) in most sampling months suggested that the great influence of human activities and sewage or manure was the dominant NO₃^- source. The δ¹⁵NO₃^- values and NO₃^-/Cl^- variations indicated that riverine N mainly came from soil organic N and sewage in November. Fertilizer and sewage were the major N sources in January and April, respectively. In July, water was influenced by various N inputs. The nitrification process played an important role in the low δ¹⁵NO₃^- values in January, while both nitrification and plant uptake resulted in the increase in δ¹⁵NH₄⁺ values in April. The simultaneous effect of N fixation and plant uptake maintained the stabilization of δ¹⁵NH₄⁺ concentrations. Our study provides theoretical basis on N sources and transformations for controlling N pollution and improving water quality in the upper Han River in the near future.

Variations in dissolved inorganic carbon species in effluents from large-scale municipal wastewater treatment plants (Qingdao, China) and their potential impacts on coastal acidification

With rapid development of global wastewater treatment plants (WWTPs), acidification and enhanced CO₂ release in receiving waters caused by high-CO₂ treated wastewater input have raised concerns. Insights into the variations in dissolved inorganic carbon (DIC) species in treated wastewater contribute to understanding the mechanisms of the acidification process. Here, we investigated three large-scale municipal WWTPs that discharged into the coast of Qingdao, China, for variations in effluent DIC species and their control mechanisms. The results showed that the effluent DIC concentrations, with a range of 2554-5718 μmol/L, significantly exceeded the concentration in seawater and mainly increased from winter to spring and decreased from summer to autumn. The effluent DIC and its δ¹³C_DIC showed a good negative correlation. The ratios of effluent DIC to total alkalinity (DIC/TAlk) ranged from 1.00 to 1.24, and the proportions of CO₂ in DIC ranged from 0.9 to 19.7%; both sets of values significantly exceeded those in seawater. The proportions of CO₃^2- in DIC were only ~ 0.4%. These features determined that the CO₂ concentrations in effluents fluctuated from 3 to 80 times the concentration in seawater, whereas the CO₃^2- concentrations were less than 1/15 of those in seawater. Organic matter degradation and nitrogen removal processes made important contributions to the high effluent CO₂ concentrations. The increase in solubility induced by decreased temperature may be the main cause for the higher effluent CO₂ concentrations during winter as well as spring months with low effluent temperatures. Correspondingly, the effluent pH values were significantly lower than the seawater pH values and showed a good negative logarithmic correlation with the DIC/TAlk values, reflecting the control of DIC species on the pH values in treated wastewater. Variations in DIC species in treated wastewater can cause changes in the affected region and the degree of the induced acidification in receiving waters.

Regenerative stormwater conveyance (RSC) for reducing nutrients in urban stormwater runoff depends upon carbon quantity and quality

Regenerative stormwater conveyance (RSC), a relatively new stormwater management approach, is extensively implemented throughout the mid-Atlantic for nutrient control, but little is known of its pollutant reduction capabilities and controlling factors. This study examined effects of organic carbon (C) quantity and quality on stream water quality and nutrient retention at two RSCs near Annapolis, Maryland, USA by comparing longitudinal changes in water quality at paired restored and unrestored stream reaches, and conducting lab experiments simulating RSC processes. Results showed that RSCs consistently had lower dissolved oxygen saturation (DO%) and pH relative to nearby unrestored streams, probably due to release of labile dissolved organic carbon (DOC). At one RSC, with high nitrate (NO₃^-) inputs, retention of N (16-37%) and release of DOC (18-54%) were observed with the highest retention of N during summer, and the rates of N retention and DOC release were larger than that of the adjacent unrestored tributary (N: 5-8%, DOC: <18%). At another RSC site with lower NO₃^- concentrations, N retention and DOC release were not apparent. Mesocosm experiments showed that NO₃^- retention varies with organic C quantity and quality depending on incubating temperature; retention of total N did not increase with organic C due to release of other N species (e.g., organic N). Lab mesocosms showed an increase in the release of soluble reactive phosphorus (SRP) with increasing organic C quantity and quality. However, field measurements did not show any evidence of SRP release at RSCs. The changes in SRP concentrations in streams seemed to be a function of iron levels and leaf litter inputs, but control factors for SRP warrant further investigation. This study suggests that RSC as a restoration approach may be effective for reducing N depending upon C quantity and quality as well as water temperature and N levels.

Denitrification rates in estuarine sediments of Ashtamudi, Kerala, India

Estuarine sediments are important sites for denitrification, which is microbially mediated reduction of nitrate to dinitrogen that also influences global climate change by co-production of nitrous oxide, a potent greenhouse gas. Physicochemical properties and nutrients of sediment samples that influence denitrification rate were studied in Ashtamudi estuarine sediments. They were pH, electrical conductivity (EC), salinity, nitrate-nitrogen (NO₃^--N), exchangeable ammonia (NH₃^--N), total kjeldahl nitrogen (TKN) and organic carbon (Corg). Sediment samples were collected from six stations during summer, monsoon of 2013 and 13 stations from monsoon 2014 and summer 2015. The sedimentary denitrification potential ranged from 0.49 ± 0.05 to 4.85 ± 0.782 mmol N₂O m^-2 h^-1. Maximum denitrification was observed in S4, which is attributed to a local anthropogenic source coupled with intense rainfall episode preceding the sampling season of monsoon 2013. However, this trend was not repeated in the subsequent monsoon samples. This shows that in Ashtamudi, monsoonal effects do not influence sedimentary denitrification. Among the various environmental variables, NO₃^--N, Corg and NH₃-N were the key factors that influence denitrification in the Ashtamudi estuarine sediments. Among these key factors, NO₃^--N was the limiting factor for denitrification, and hence, it is of prime importance to understand the source of NO₃^--N that fuel denitrification in the sediments. In Ashtamudi, the concentration of NO₃^--N in overlying water was very less, which suggests reduced nitrogen yield in the estuary from the fluvial input of Kallada River and agricultural runoff. Sedimentary NO₃^--N correlated with denitrification which reveals that denitrification is coupled with nitrification in the sediments. This is further explained by the fact that NH₃-N positively correlated with denitrification. The anoxic sediments were the source of ammonia for nitrous oxide production by nitrogen mineralisation. Also, the Corg in sediment samples were sufficient to support denitrification and Corg was an important factor favouring but not limiting denitrification. The results of sediment denitrification in Ashtamudi can be a model for tropical estuaries experiencing unpredictable rainfall as well as high temperature than temperate systems.

Evaluation of fly ash pellets for phosphorus removal in a laboratory scale denitrifying bioreactor

Nitrate and orthophosphate from agricultural activities contribute significantly to nutrient loading in surface water bodies around the world. This study evaluated the efficacy of woodchips and fly ash pellets in tandem to remove nitrate and orthophosphate from simulated agricultural runoff in flow-through tests. The fly ash pellets had previously been developed specifically for orthophosphate removal for this type of application, and the sorption bench testing showed a good promise for flow-through testing. The lab-scale horizontal-flow bioreactor used in this study consisted of an upstream column filled with woodchips followed by a downstream column filled with fly ash pellets (3 and 1 m lengths, respectively; both 0.15 m diameter). Using influent concentrations of 12 mg/L nitrate and 5 mg/L orthophosphate, the woodchip bioreactor section was able to remove 49-85% of the nitrate concentration at three hydraulic retention times ranging from 0.67 to 4.0 h. The nitrate removal rate for woodchips ranged from 40 to 49 g N/m³/d. Higher hydraulic retention times (i.e., smaller flow rates) corresponded with greater nitrate load reduction. The fly ash pellets showed relatively stable removal efficiency of 68-75% across all retention times. Total orthophosphate adsorption by the pellets was 0.059-0.114 mg P/g which was far less than the saturated capacity (1.69 mg/g; based on previous work). The fly ash pellets also removed some nitrate and the woodchips also removed some orthophosphate, but these reductions were not significant. Overall, woodchip denitrification followed by fly ash pellet P-sorption can be an effective treatment technology for nitrate and phosphate removal in subsurface drainage.

BTEX biodegradation and its nitrogen removal potential by a newly isolatedPseudomonasthivervalensisMAH1

Benzene, toluene, ethylbenzene, and xylene (BTEX) are of great environmental concern because of their widespread occurrence in groundwater and soil, posing an increasing threat to human health. The aerobic denitrifying BTEX-degrading bacterium Pseudomonas thivervalensis MAH1 was isolated from BTEX-contaminated sediment under nitrate-reducing conditions. The degradation rates of benzene, toluene, ethylbenzene, and xylene by strain MAH1 were 4.71, 6.59, 5.64, and 2.59 mg·L−1·day−1, respectively. The effects of sodium citrate, nitrate, and NaH2PO4on improving BTEX biodegradation were investigated, and their optimum concentrations were 0.5 g·L−1, 100 mg·L−1, and 0.8 mmol·L−1, respectively. Moreover, MAH1, which has nirS and nosZ genes, removed ammonium, nitrate, and nitrite at 2.49 mg NH4+-N·L−1·h−1, 1.50 mg NO3−-N·L−1·h−1, and 0.83 mg NO2−-N·L−1·h−1, respectively. MAH1 could help in mitigating the pollution caused by nitrogen amendments for biostimulation. This study highlighted the feasibility of using MAH1 for the bioremediation of BTEX-contaminated sites.

Heterotrophic nitrification and aerobic denitrification by a novel groundwater origin cold-adapted bacterium at low temperatures

A novel cold-adapted aerobic denitrifyingP. migulaeAN-1 was isolated. Its nitrifying–denitrifying capability was determined. Nitrate removal of the strain was described by Monod kinetics with a non-competitive substrate inhibition and optimized.

N and O isotope fractionation in nitrate during chemolithoautotrophic denitrification by Sulfurimonas gotlandica

Chemolithoautotrophic denitrification is an important mechanism of nitrogen loss in the water column of euxinic basins, but its isotope fractionation factor is not known. Sulfurimonas gotlandica GD1(T), a recently isolated bacterial key player in Baltic Sea pelagic redoxcline processes, was used to determine the isotope fractionation of nitrogen and oxygen in nitrate during denitrification. Under anoxic conditions, nitrate reduction was accompanied by nitrogen and oxygen isotope fractionation of 23.8 ± 2.5‰ and 11.7 ± 1.1‰, respectively. The isotope effect for nitrogen was in the range determined for heterotrophic denitrification, with only the absence of stirring resulting in a significant decrease of the fractionation factor. The relative increase in δ(18)ONO3 to δ(15)NNO3 did not follow the 1:1 relationship characteristic of heterotrophic, marine denitrification. Instead, δ(18)ONO3 increased slower than δ(15)NNO3, with a conserved ratio of 0.5:1. This result suggests that the periplasmic nitrate reductase (Nap) of S. gotlandica strain GD1(T) fractionates the N and O in nitrate differently than the membrane-bound nitrate reductase (Nar), which is generally prevalent among heterotrophic denitrifiers and is considered as the dominant driver for the observed isotope fractionation. Hence in the Baltic Sea redoxcline, other, as yet-unidentified factors likely explain the low apparent fractionation.

Nitrogen sources, transport and processing in peri-urban floodplains

Peri-urban floodplains are an important interface between developed land and the aquatic environment and may act as a source or sink for contaminants moving from urban areas towards surface water courses. With increasing pressure from urban development the functioning of floodplains is coming under greater scrutiny. A number of peri-urban sites have been found to be populated with legacy landfills which could potentially cause pollution of adjacent river bodies. Here, a peri-urban floodplain adjoining the city of Oxford, UK, with the River Thames has been investigated over a period of three years through repeated sampling of groundwaters from existing and specially constructed piezometers. A nearby landfill has been found to have imprinted a strong signal on the groundwater with particularly high concentrations of ammonium and generally low concentrations of nitrate and dissolved oxygen. An intensive study of nitrogen dynamics through the use of N-species chemistry, nitrogen isotopes and dissolved nitrous oxide reveals that there is little or no denitrification in the majority of the main landfill plume, and neither is the ammonium significantly retarded by sorption to the aquifer sediments. A simple model has determined the flux of total nitrogen and ammonium from the landfill, through the floodplain and into the river. Over an 8 km reach of the river, which has a number of other legacy landfills, it is estimated that 27.5 tonnes of ammonium may be delivered to the river annually. Although this is a relatively small contribution to the total river nitrogen, it may represent up to 15% of the ammonium loading at the study site and over the length of the reach could increase in-stream concentrations by nearly 40%. Catchment management plans that encompass floodplains in the peri-urban environment need to take into account the likely risk to groundwater and surface water quality that these environments pose.

Extending the viability of acute brain slices

The lifespan of an acute brain slice is approximately 6–12 hours, limiting potential experimentation time. We have designed a new recovery incubation system capable of extending their lifespan to more than 36 hours. This system controls the temperature of the incubated artificial cerebral spinal fluid (aCSF) while continuously passing the fluid through a UVC filtration system and simultaneously monitoring temperature and pH. The combination of controlled temperature and UVC filtering maintains bacteria levels in the lag phase and leads to the dramatic extension of the brain slice lifespan. Brain slice viability was validated through electrophysiological recordings as well as live/dead cell assays. This system benefits researchers by monitoring incubation conditions and standardizing this artificial environment. It further provides viable tissue for two experimental days, reducing the time spent preparing brain slices and the number of animals required for research.

Encystment in Acanthamoeba castellanii: a review

Differentiation of Acanthamoeba castellanii trophozoites involves massive turnover of cellular components and remodelling of organelle structure and function so as to produce a cryptobiotic cell, resistant to desiccation, heat, freezing, and chemical treatments. This review presents a summary of a decade of research on the most studied aspects of the biochemistry of this process, with emphasis on problems of biocide and drug resistances, putative new targets, molecular and cell biology of the process of encystment, and the characteristics of the encysted state. As well as the intrinsic pathogenicity of the organism towards the cornea, and the ability of related species to invade the human brain, its propensity for harbouring and transmitting pathogenic bacteria and viruses is considerable and leads to increasing concerns. The long-term survival and resistance of cysts to drugs and biocides adds another layer of complexity to the problem of their elimination.

Nitrous oxide production in sputum from cystic fibrosis patients with chronic Pseudomonas aeruginosa lung infection

Chronic lung infection by Pseudomonas aeruginosa is the major severe complication in cystic fibrosis (CF) patients, where P. aeruginosa persists and grows in biofilms in the endobronchial mucus under hypoxic conditions. Numerous polymorphonuclear leukocytes (PMNs) surround the biofilms and create local anoxia by consuming the majority of O₂ for production of reactive oxygen species (ROS). We hypothesized that P. aeruginosa acquires energy for growth in anaerobic endobronchial mucus by denitrification, which can be demonstrated by production of nitrous oxide (N₂O), an intermediate in the denitrification pathway. We measured N₂O and O₂ with electrochemical microsensors in 8 freshly expectorated sputum samples from 7 CF patients with chronic P. aeruginosa infection. The concentrations of NO₃⁻ and NO₂⁻ in sputum were estimated by the Griess reagent. We found a maximum median concentration of 41.8 µM N₂O (range 1.4–157.9 µM N₂O). The concentration of N₂O in the sputum was higher below the oxygenated layers. In 4 samples the N₂O concentration increased during the initial 6 h of measurements before decreasing for approximately 6 h. Concomitantly, the concentration of NO₃⁻ decreased in sputum during 24 hours of incubation. We demonstrate for the first time production of N₂O in clinical material from infected human airways indicating pathogenic metabolism based on denitrification. Therefore, P. aeruginosa may acquire energy for growth by denitrification in anoxic endobronchial mucus in CF patients. Such ability for anaerobic growth may be a hitherto ignored key aspect of chronic P. aeruginosa infections that can inform new strategies for treatment and prevention.

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.

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.

The effect of nitrate concentration on sulfide-driven autotrophic denitrification in marine sediment

The effect of nitrate concentration on denitrification rate, microbial community and byproduct accumulation in sulfide-driven autotrophic denitrification, one of the dominant processes during anoxic marine sediment remediation, was investigated in this study. Microorganisms which were phylogenetically closely related with Sulfurimonas denitrificans of ε-Proteobacteria and Thiohalomonas denitrificans of γ-Proteobacteria were the major autotrophic denitrifiers in this study. Nitrate concentration was demonstrated to have selective effect on denitrifying microbial community as revealed by denaturing gradient gel electrophoresis. Denitrifiers enriched at 30 mM NO(3)(-) have higher diversity than other two groups (10, and 80 mM NO(3)(-)) according to Shannon index. Denitrification showed zero-order reaction kinetics when nitrate concentration was higher than 4mM. Neither absolute nitrate concentration nor overall nitrate/sulfide ratio acted as the determinant for denitrification byproduct (i.e. N(2)O and NO(2)(-)) accumulation. The limitation of sulfide due to low mass transfer might be the reason for the byproduct accumulation.

A simple and rapid GC/MS method for the simultaneous determination of gaseous metabolites

We modified and tuned a commercial model of a gas chromatography/mass spectrometry (GC/MS) instrument to develop a simple and rapid method for the simultaneous quantification of a variety of gas species. Using the developed method with the newly modified instrument, gas species such as H(2), N(2), O(2), CO, NO, CH(4), CO(2), and N(2)O, which are common components of microbial metabolism, were accurately identified based on their retention times and/or mass-to-charge ratios (m/z) in less than 2.5 min. By examining the sensitivities and dynamic ranges for the detection of H(2), N(2), O(2), CH(4), CO(2), and N(2)O, it was demonstrated that the method developed in this study was sufficient for accurately monitoring the production and the consumption of these gaseous species during microbial metabolism. The utility of the new method was demonstrated by a denitrification study with Pseudomonas aureofaciens ATCC 13985(T). This method will be suitable for a variety of applications requiring the identification of gaseous metabolites in microorganisms, microbial communities, and natural ecosystems.

Association of novel and highly diverse acid-tolerant denitrifiers with N2O fluxes of an acidic fen

Wetlands are sources of denitrification-derived nitrous oxide (N2O). Thus, the denitrifier community of an N2O-emitting fen (pH 4.7 to 5.2) was investigated. N2O was produced and consumed to subatmospheric concentrations in unsupplemented anoxic soil microcosms. Total cell counts and most probable numbers of denitrifiers approximated 10(11) cells x g(DW)(-1) (where DW is dry weight) and 10(8) cells x g(DW)(-1), respectively, in both 0- to 10-cm and 30- to 40-cm depths. Despite this uniformity, depth-related maximum reaction rate (v(max)) values for denitrification in anoxic microcosms ranged from 1 to 24 and -19 to -105 nmol N2O h(-1) x g(DW)(-1), with maximal values occurring in the upper soil layers. Denitrification was enhanced by substrates that might be formed via fermentation in anoxic microzones of soil. N2O approximated 40% of total nitrogenous gases produced at in situ pH, which was likewise the optimal pH for denitrification. Gene libraries of narG and nosZ (encoding nitrate reductase and nitrous oxide reductase, respectively) from fen soil DNA yielded 15 and 18 species-level operational taxonomic units, respectively, many of which displayed phylogenetic novelty and were not closely related to cultured organisms. Although statistical analyses of narG and nosZ sequences indicated that the upper 20 cm of soil contained the highest denitrifier diversity and species richness, terminal restriction fragment length polymorphism analyses of narG and nosZ revealed only minor differences in denitrifier community composition from a soil depth of 0 to 40 cm. The collective data indicate that the regional fen harbors novel, highly diverse, acid-tolerant denitrifier communities capable of complete denitrification and consumption of atmospheric N2O at in situ pH.

Effect of nitrate and acetylene on nirS, cnorB, and nosZ expression and denitrification activity in Pseudomonas mandelii

Nitrate acts as an electron acceptor in the denitrification process. The effect of nitrate in the range of 0 to 1,000 mg/liter on Pseudomonas mandelii nirS, cnorB, and nosZ gene expression was studied, using quantitative reverse transcription-quantitative PCR. Denitrification activity was measured by using the acetylene blockage method and gas chromatography. The effect of acetylene on gene expression was assessed by comparing denitrification gene expression in P. mandelii culture grown in the presence or absence of acetylene. The higher the amount of NO(3)(-) present, the greater the induction and the longer the denitrification genes remained expressed. nirS gene expression reached a maximum at 2, 4, 4, and 6 h in cultures grown in the presence of 0, 10, 100, and 1,000 mg of KNO(3)/liter, respectively, while induction of nirS gene ranged from 12- to 225-fold compared to time zero. cnorB gene expression also followed a similar trend. nosZ gene expression did not respond to NO(3)(-) treatment under the conditions tested. Acetylene decreased nosZ gene expression but did not affect nirS or cnorB gene expression. These results showed that nirS and cnorB responded to nitrate concentrations; however, significant denitrification activity was only observed in culture with 1,000 mg of KNO(3)/liter, indicating that there was no relationship between gene expression and denitrification activity under the conditions tested.

Effect of pH and temperature on denitrification gene expression and activity in Pseudomonas mandelii

Pseudomonas mandelii liquid cultures were studied to determine the effect of pH and temperature on denitrification gene expression, which was quantified by quantitative reverse transcription-PCR. Denitrification was measured by the accumulation of nitrous oxide (N(2)O) in the headspace in the presence of acetylene. Levels of gene expression of nirS and cnorB at pH 5 were 539-fold and 6,190-fold lower, respectively, than the levels of gene expression for cells grown at pH 6, 7, and 8 between 4 h and 8 h. Cumulative denitrification levels were 28 micromol, 63 micromol, and 22 micromol at pH 6, 7, and 8, respectively, at 8 h, whereas negligible denitrification was measured at pH 5. P. mandelii cells grown at 20 degrees C and 30 degrees C exhibited 9-fold and 94-fold increases in levels of cnorB expression between 0 h and 2 h, respectively, and an average 17-fold increase in levels of nirS gene expression. In contrast, induction of cnorB and nirS gene expression for P. mandelii cells grown at 10 degrees C did not occur in the first 4 h. Levels of cumulative denitrification at 10 h were 6.6 micromol for P. mandelii cells grown at 10 degrees C and 20 degrees C and 30 micromol for cells grown at 30 degrees C. Overall, levels of cnorB and nirS expression were relatively insensitive to pH values over the range of pH 6 to 8 but were substantially reduced at pH 5, whereas gene expression was sensitive to temperature, with induction and time to achieve maximum gene expression delayed as the temperature decreased from 30 degrees C. Low pH and temperature negatively affected denitrification activity.

Influence of the Pseudomonas quinolone signal on denitrification in Pseudomonas aeruginosa

Denitrification is a well-studied respiratory system that is also important in the biogeochemical nitrogen cycle. Environmental signals such as oxygen and N-oxides have been demonstrated to regulate denitrification, though how denitrification is regulated in a bacterial community remains obscure. Pseudomonas aeruginosa is a ubiquitous bacterium that controls numerous genes through cell-to-cell signals. The bacterium possesses at least two N-acyl-L-homoserine lactone (AHL) signals. In our previous study, these quorum-sensing signals controlled denitrification in P. aeruginosa. In addition to the AHL signals, a third cell-to-cell communication signal, 2-heptyl-3-hydroxy-4-quinolone, referred to as the Pseudomonas quinolone signal (PQS), has been characterized. In this study, we examined the effect of PQS on denitrification to obtain more insight into the respiratory regulation in a bacterial community. Denitrification in P. aeruginosa was repressed by PQS, which was partially mediated by PqsR and PqsE. Measuring the denitrifying enzyme activities indicated that nitrite reductase activity was increased by PQS, whereas PQS inhibited nitric oxide reductase and the nitrate-respiratory chain activities. This is the first report to demonstrate that PQS influences enzyme activities, suggesting this effect is not specific to P. aeruginosa. Furthermore, when iron was supplied to the PQS-added medium, denitrifying activity was almost restored, indicating that the iron chelating property of PQS affected denitrification. Thus, our data indicate that PQS regulates denitrification primarily through iron chelation. The PQS effect on denitrification was relevant in a condition where oxygen was limited and denitrification was induced, suggesting its role in controlling denitrification where oxygen is present.

Nitric oxide reductase gene expression and nitrous oxide production in nitrate-grown Pseudomonas mandelii

Pure cultures of Pseudomonas mandelii were incubated with or without nitrate, which acts as a substrate and an electron acceptor for denitrification. Nitric oxide reductase (cnorB) gene expression was measured using a quantitative reverse transcription-PCR, and nitrous oxide emissions were measured by gas chromatography. P. mandelii cells in either the presence or absence of nitrate demonstrated an increase in cnorB gene expression during the first 3 h of growth. The level of expression of cnorB in nitrate-amended cells remained high (average, 2.06 x 10(8) transcripts/microg of RNA), while in untreated cells it decreased to an average of 3.63 x 10(6) transcripts/microg of RNA from 4 to 6 h. Nitrous oxide accumulation in the headspace was detected at 2 h, and cumulative emissions continued to increase over a 24-h period to 101 mumol in nitrate-amended cells. P. mandelii cnorB gene expression was not detected under aerobic conditions. These results demonstrate that P. mandelii cnorB gene expression was induced 203-fold at 4 h when nitrate was present in the medium. Accumulations of N(2)O indicated that the cNorB enzyme was synthesized and active.

Effect of pH on anoxic sulfide oxidizing reactor performance

The effects of pH on the performance of anoxic sulfide oxidizing (ASO) reactor were evaluated. Performance was investigated under various operational conditions at influent pH range of 4-11. At the influent pH of 7-7.5 during loading tests and HRT tests, the sulfide oxidation was partial. In general, the amount of sulfate formed decreased with the increasing sulfide and nitrite loadings. The bacterial communities in ASO reactors were more sensitive to acidic pH compared with alkaline pH, as nitrite and sulfide removal rates dropped significantly when exposed to acidic pH 3. High dissolved bisulfide ions, nitrite and excess of sulfate (>300 mg/L) might have inhibited the sulfide oxidation under highly acidic and alkaline conditions in the ASO reactor. Based on sulfide and nitrite removal efficiencies, the ASO reactor can be operated in a wide range of pH, i.e. 5-11.

Influence of mixed liquor recycle ratio and dissolved oxygen on performance of pre-denitrification submerged membrane bioreactors

The conflicting influence of mixed liquor recycle ratio and dissolved oxygen on nitrogen removal and membrane fouling of a pre-denitrification submerged MBR was investigated in this study. It was found that a high aeration rate of 10 L air/min was able to minimize membrane fouling as compared with lower aeration rates of 5 and 2.5L air/min in this study. Faster fouling at lower aeration rate was due to the decrease in cross-flow velocity across the membrane surface. However, high DO concentration (average of 5.1+/-0.5mg O2/L) present in the recycle mixed liquor at an aeration rate of 10 L air/min deteriorated the TN removal efficiency when operating at a recycle ratio of more than 3. A lower aeration rate of 5L air/min, resulting in an average DO concentration of 3.4+/-0.7 mg O2/L in the recycle mixed liquor, led to an improvement in TN removal efficiency: 63%, 80%, 84% and 89% for mixed liquor recycle ratio of 1, 3, 5 and 10, respectively. Further decrease in aeration rate to 2.5L air/min, resulting in an average DO concentration of 1.9+/-0.8 mg O2/L, did not improve the TN removal efficiency. Using a newly developed simplified nitrification-denitrification model, it was calculated that the COD/NO3(-)-N required for denitrification at 10 L air/min aeration rate was higher than those associated with 5 and 2.5L air/min aeration rates. The model also revealed that denitrification at an aeration rate of 10 L air/min was limited by COD concentration present in the wastewater when operating at a mixed liquor recycle ratio of 3 and higher.

Stimulating hydrogenotrophic denitrification in simulated groundwater containing high dissolved oxygen and nitrate concentrations

In agricultural areas, nitrate (NO3-) is a common groundwater pollutant as a result of extensive fertilizer application. At elevated concentrations, NO3- consumption causes methemoglobinemia in infants and has been linked to several cancers; therefore, its removal from groundwater is important. The addition of hydrogen gas (H2) via gas-permeable membranes has been shown to stimulate denitrification in a laboratory-scale reactor. This research, using large columns packed with aquifer material to which a simulated groundwater was fed, was conducted to further identify the conditions required for the use of membrane-delivered H2 in situ. In this study, we show that this novel technology was capable of treating highly contaminated (25 mg/L NO3- -N) and oxygenated (5.5mg/L dissolved oxygen) water, but that nutrient addition and gas pressure adjustment was required. Complete NO3- reduction was possible without the accumulation of either NO2- or N2O when the H2 lumen pressure was increased to 17 psi and phosphate was added to the groundwater. The total organic carbon content of the effluent, 110 cm downgradient of H2 addition, did not increase. The results from these experiments demonstrate that this technology can be optimized to provide effective NO3- removal in even challenging field applications.

Screening and characterization of bacteria that can utilize ammonium and nitrate ions simultaneously under controlled cultural conditions

Eighteen bacterial stock cultures were examined for their ability to utilize NH(4)(+) and NO(3)(-) simultaneously in a medium containing NH(4)NO(3) with shaking using a test tube capped with a cotton stopper. Pseudomonas aeruginosa NBRC 12689 utilized 1 mg/ml of NH(4)NO(3) most rapidly of the cultures tested. The bacterium could completely utilize 5 mg/ml of NH(4)NO(3) within 3 d, 6 mg/ml of NH(4)Cl within 3 d, and 20 mg/ml of NaNO(3) within 2 d under optimum conditions. The addition of Fe(2+) to the NH(4)NO(3) medium markedly promoted the utilization of the two ions. When the Pseudomonas strain utilized 5 mg/ml of NH(4)NO(3) completely, the total nitrogen in the culture including its cells decreased to 41% of that of the NH(4)NO(3) originally provided. GC-MS analysis showed that the removed nitrogen was probably denitrified. When the bacterium was incubated in the NH(4)NO(3) medium with shaking in a vial sealed with a rubber stopper, N(2) accumulated, but not N(2)O at the final phase of cultivation. On the other hand, both N(2) and N(2)O were detected in the NaNO(3) medium. We concluded that the bacterium removed NH(4)(+) from NH(4)NO(3) as a nitrogen source for its cell components, together with the denitrification of NO(3)(-) under controlled shaking conditions. In addition, NH(4)(+) promoted the cell growth of the bacterium and denitrification to N(2), preventing the accumulation of N(2)O.

N fertilization effects on denitrification and N cycling in an aggrading forest

We investigated N cycling and denitrification rates following five years of N and dolomite amendments to whole-tree harvested forest plots at the long-term soil productivity experiment in the Fernow Experimental Forest in West Virginia, USA. We hypothesized that changes in soil chemistry and nutrient cycling induced by N fertilization would increase denitrification rates and the N2O:N2 ratio. Soils from the fertilized plots had a lower pH (2.96) than control plots (3.22) and plots that received fertilizer and dolomite (3.41). There were no significant differences in soil %C or %N between treatments. Chloroform-labile microbial biomass carbon was lower in fertilized plots compared to control plots, though this trend was not significant. Extractable soil NO3- was elevated in fertilized plots on each sample date. Soil-extractable NH4+, NO3-, pH, microbial biomass carbon, and %C varied significantly by sample date suggesting important seasonal patterns in soil chemistry and N cycling. In particular, the steep decline in extractable NH4+ during the growing season is consistent with the high N demands of a regenerating forest. Net N mineralization and nitrification also varied by date but were not affected by the fertilization and dolomite treatments. In a laboratory experiment, denitrification was stimulated by NO3- additions in soils collected from all field plots, but this effect was stronger in soils from the unfertilized control plots, suggesting that chronic N fertilization has partially alleviated a NO3- limitation on denitrification rates. Dextrose stimulated denitrification only in the whole-tree-harvest soils. Denitrification enzyme activity varied by sample date and was elevated in fertilized plots for soil collected in July 2000 and June 2001. There were no detectable treatment effects on N2O or N2 flux from soils under anaerobic conditions, though there was strong temporal variation. These results suggest that whole-tree harvesting has altered the N status of these soils so they are less prone to N saturation than more mature forests. It is likely that N losses associated with the initial harvest and high N demand by aggrading vegetation is minimizing, at least temporarily, the amount of inorganic N available for nitrification and denitrification, even in the fertilized plots in this experiment.

Environmental controls on denitrifying communities and denitrification rates: insights from molecular methods

The advent of molecular techniques has improved our understanding of the microbial communities responsible for denitrification and is beginning to address their role in controlling denitrification processes. There is a large diversity of bacteria, archaea, and fungi capable of denitrification, and their community composition is structured by long-term environmental drivers. The range of temperature and moisture conditions, substrate availability, competition, and disturbances have long-lasting legacies on denitrifier community structure. These communities may differ in physiology, environmental tolerances to pH and O2, growth rate, and enzyme kinetics. Although factors such as O2, pH, C availability, and NO3- pools affect instantaneous rates, these drivers act through the biotic community. This review summarizes the results of molecular investigations of denitrifier communities in natural environments and provides a framework for developing future research for addressing connections between denitrifier community structure and function.

The effect of phosphogypsum on greenhouse gas emissions during cattle manure composting

Phosphogypsum (PG), a by-product of the phosphate fertilizer industry, reduces N losses when added to composting livestock manure, but its impact on greenhouse gas emissions is unclear. The objective of this research was to assess the effects of PG addition on greenhouse gas emissions during cattle feedlot manure composting. Sand was used as a filler material for comparison. The seven treatments were PG10, PG20, PG30, S10, S20, and S30, representing the rate of PG or sand addition at 10, 20, or 30% of manure dry weight and a check treatment (no PG or sand) with three replications. The manure treatments were composted in open windrows and turned five times during a 134-d period. Addition of PG significantly increased electrical conductivity (EC) and decreased pH in the final compost. Total carbon (TC), total nitrogen (TN), and mineral nitrogen contents in the final composted product were not affected by the addition of PG or sand. From 40 to 54% of initial TC was lost during composting, mostly as CO(2), with CH(4) accounting for <14%. The addition of PG significantly reduced CH(4) emissions, which decreased exponentially with the compost total sulfur (TS) content. The emission of N(2)O accounted for <0.2% of initial TN in the manure, increasing as compost pH decreased from alkaline to near neutral. Based on the total greenhouse gas budget, PG addition reduced greenhouse gas emissions (CO(2)-C equivalent) during composting of livestock manure by at least 58%, primarily due to reduced CH(4) emission.

Immunological method for direct assessment of the functionality of a denitrifying strain of Pseudomonas fluorescens in soil

This work describes an immunological method for detection and quantification in complex environments of the dissimilative nitrate reductase (NRA) responsible for the reduction of nitrate to nitrite, which plays an important role in ecosystem functioning. The alpha-catalytic subunit of the enzyme was purified from the denitrifying strain Pseudomonas fluorescens YT101 and used for the production of polyclonal antibodies. These antibodies were used to detect and quantify the NRA by a chemifluorescence technique on Western blots after separation of total proteins from pure cultures and soil samples. The specificity, detection threshold and reproducibility of the proposed method were evaluated. A soil experiment showed that our method can be applied to complex environmental samples.

Effects of pH and precipitation on autohydrogenotrophic denitrification using the hollow-fiber membrane-biofilm reactor

Experiments carried out in a hollow-fiber, membrane-biofilm reactor (HFMBR) showed that the optimum pH for autotrophic denitrification was in the range 7.7-8.6, with the maximum efficiency at 8.4. Increasing the pH above 8.6 caused a significant decrease in nitrate removal rate and a dramatic increase in nitrite accumulation. The pH rose by 1.2 units when a large buffer was not added, suggesting that some field applications may require pH control. Precipitation of Ca(2+) occurred in every experiment. Precipitation was the largest sink for carbonate, and it also offset alkalinity production by denitrification. Although the alkalinity increased in most cases, systems with a high carbonate buffer and high pH accentuated precipitation, and the net change in alkalinity was negative. The long-term success of field applications of the HFMBR may depend upon the interactions among calcium concentration, total carbonate concentration, pH, and alkalinity changes.

Cell biology and molecular basis of denitrification

Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.

Soil and sediment bacteria capable of aerobic nitrate respiration

Several laboratory strains of gram-negative bacteria are known to be able to respire nitrate in the presence of oxygen, although the physiological advantage gained from this process is not entirely clear. The contribution that aerobic nitrate respiration makes to the environmental nitrogen cycle has not been studied. As a first step in addressing this question, a strategy which allows for the isolation of organisms capable of reducing nitrate to nitrite following aerobic growth has been developed. Twenty-nine such strains have been isolated from three soils and a freshwater sediment and shown to comprise members of three genera (Pseudomonas, Aeromonas, and Moraxella). All of these strains expressed a nitrate reductase with an active site located in the periplasmic compartment. Twenty-two of the strains showed significant rates of nitrate respiration in the presence of oxygen when assayed with physiological electron donors. Also isolated was one member of the gram-positive genus Arthrobacter, which was likewise able to respire nitrate in the presence of oxygen but appeared to express a different type of nitrate reductase. In the four environments studied, culturable bacteria capable of aerobic nitrate respiration were isolated in significant numbers (10(4) to 10(7) per g of soil or sediment) and in three cases were as abundant as, or more abundant than, culturable bacteria capable of denitrification. Thus, it seems likely that the corespiration of nitrate and oxygen may indeed make a significant contribution to the flux of nitrate to nitrite in the environment.

Isolation and characterisation of a strain of Pseudomonas putida that can express a periplasmic nitrate reductase

A strain of Pseudomonas putida that can express a nitrate reductase that is located in the periplasmic compartment was isolated from freshwater. The enzyme was active in vivo during arginine fermentation and at the onset of oxygen limitation in batch cultures. The activity of the enzyme increased the yield of bacteria following fermentative growth under anoxic conditions with arginine, but nitrate reduction did not support growth on non-fermentable carbon substrates under anoxic conditions. Cells expressing the periplasmic nitrate reductase were capable of reducing nitrate in the presence of oxygen. Nitrate reduction under oxic conditions was clearly coupled to a respiratory electron transport chain because: (1) the process was sensitive to the respiratory inhibitors rote-none and 2-n-heptyl-4-hydroxyquinoline N-oxide, and (2) membrane-bound and periplasmic cytochromes were involved. This is the first report of the presence of a periplasmic nitrate reductase in a member of the gamma proteobacteria.

Denitrification and its control

Denitrification in bacteria comprises a series of four reduction reactions; for nitrate, nitrite, nitric oxide and nitrous oxide. Nitrogen gas is the final product. The nature of the enzymes catalysing these reactions is described along with the the properties of the underlying electron transport systems. The factors influencing the expression of the reductases for the four reactions are reviewed along with the effect of oxygen on the activities of the enzymes of denitrification. The main emphasis is on observations made with Paracoccus denitrificans and Pseudomonas stutzeri.