Physiology and kinetics of autotrophic denitrification by Thiobacillus denitrificans

Summary A strain of Thiobacillus denitrificans was isolated after enrichment under anaerobic conditions by the continuous culture technique using thiosulfate as energy source and nitrate as electron acceptor and nitrogen source. The isolate was an active denitrifyer, the optimal conditions being 30°C and pH 7.5–8.0. Denitrification was inhibited by sulfate (the reaction product) above 5 g SO ₄ ⁼ /l, whereas high concentrations of the substrates nitrate and thiosulfate were less harmful; nitrite affected denitrification above 0.2 g NO ₂ ^– /l. During the time course of denitrification in a batch culture growth and substrate consumption slowed down already after only half the substrate was utilized due to product inhibition. The following parameters were determined in continuous culture under nitrate limitation: _max=0.11 h^–1, K _S=0.2 mg NO ₃ ^– /l, maximum denitrification rate=0.78 g NO ₃ ^– /g cells·h, g cells/g NO ₃ ^– , g cells/g S₂O ₃ ⁼ . Nitrite did not accumulate during steady state denitrification; the denitrification gas was almost pure N₂. The concentrations of N₂O and NO were below 1 ppm.     

Aerobic denitrification in various heterotrophic nitrifiers

Various heterotrophic nitrifiers have been tested and found to also be aerobic denitrifiers. The simultaneous use of two electron acceptors (oxygen and nitrate) permits these organisms to grow more rapidly than on either single electron acceptor, but generally results in a lower yield than is obtained on oxygen, alone. One strain, formerly known as Pseudomonas denitrificans, was grown in the chemostat and shown to achieve nitrification rates of up to 44 nmol NH₃ min^–1 mg protein^–1 and denitrification rates up to 69 nmol NO _inf3 ^sup–1 min^–1 mg protein^–1.Unlike Thiosphaera pantotropha, this strain needed to induce its nitrate reductase. However, the remainder of the denitrifying pathway was constitutive and, like T. pantotropha, Ps. denitrificans probably possesses the copper nitrite reductase.     

Biological denitrification of water in a two-chambered immobilized-cell bioreactor

Summary A double-chambered bioreactor based on a composite immobilized-cell gel layer/microporous membrane structure was applied to the continuous denitrification of high-nitrate water. Immobilized denitrifying bacteria (Pseudomonas denitrificans) were provided with separate flows of nitrate and carbon (C) nutrient, with no contamination of the treated water by cell leakage from the gel. Using acetate (7.5 mm) as a C source and a C/N ratio of 3 (mol/mol), specific denitrification rates ranging from 15 to 25 g NO _inf3 ^sup– · h^–1 · – cm^–2 membrane surface (50–85 g NO _inf3 ^sup– · h^–1 · cm^–3 gel) were obtained. The denitrifying activity remained stable for several months. At the flow rate used (10 cm³ · h^–1), the effluents contained noticeable amounts of NO _inf2 ^sup– ions but the treated water remained uncontaminated by the carbon nutrient. Most NO _inf2 ^sup– ions disappeared from the treated water in a second reactor connected in series. When fed with an unchlorinated sludge supernatant as C nutrient, immobilized bacteria performed efficient denitrification of water for only 3 weeks. Diffusion experiments showed that acetate ions diffused much less rapidly than NO _inf3 ^sup– or NO _inf2 ^sup– ions through the composite structure. Further developments of the system are considered.     

Kinetics of a fluidized-bed reactor for ground-water denitrification

A fluidized-bed reactor, with sand as the carrier and ethanol as the carbon and electron source, was investigated for the biological denitrification of ground water. The paper concentrates on the reactor's kinetics, with special emphasis on nitrite as the intermediate product. Intrinsic zero-order kinetic parameters for both nitrate and nitrite were determined by batch and continuous experiments. Values for the maximum specific nitrate and nitrite removal rates of 11 g and 6 g NO _inf3 ^sup– (g volatile suspended solids)^–1 day^–1, respectively, were obtained. These values were used to interpret nitrate and nitrate concentration profiles in an experimental fluidized-bed reactor operating at different conditions of hydraulic loading and retention time.     

Nitrification and denitrification in a system of reciprocating jet bioreactor

Concept of separation of stages coupled with novel design of reciprocating jet bioreactor have been incorporated in this research for the development of high efficiency treatment system for contaminated wastewaters.Evaluation of pilot plant data reveals that a three stage reciprocating jet bioreactor system could be effectively employed for nitrification and denitrification of highly polluted wastewater obtained from Berlin wastewater treatment plant. Such a system with COD destruction stage (residence time 1–3 hours) followed by nitrification stage (residence time 3–4.5 hours) and denitrification stage (residence time 0.3 hours) gives COD destruction rate upto 58 kg COD/(m³ day), nitrification rate upto 3.2 NH ₄ ⁺ -N/(m³ day) and denitrification rate upto 28 kg NO ₃ ^– -N/(m³ day) while providing COD, NH ₄ ⁺ -N and NO ₃ ^– -N conversion of more than 90%.Nitrification and denitrification of wastewater at such a short residence time is possible mainly due to the employment of reciprocating jet bioreactor system.Paper presented at the Third Joint Schlesinger Seminar on Transport phenomena and processes in biological systems, Technion — Israel Institute of Technology, Haifa, Israel, May 8–9, 1990     

Artifacts associated with the use of thiocyanate and valinomycin/K+ as permeant ions in oxidant pulse experiments on denitrifying bacteria

By means of¹⁵N-tracer and oxidant pulse methods and with nitrate-grownParacoccus denitrificans it was found that KSCN completely inhibited reduction of N₂O and nitrate in the 1 to 10 mM range, but had little or no effect on reduction of O₂ or nitrite at 150 mM. These observations confirm a previous report. Potassium thiocyanate was insufficiently permeant across the cytoplasmic membrane ofParacoccus denitrificans andPseudomonas denitrificans even at 150 mM to prevent membrane polarization when oxidant pulses were large. Polarization and inhibition artifacts due to KSCN have created some confusion in the literature. Whereas valinomycin had little direct effect on reduction of nitrite, N₂O, and O₂ individually byPa. denitrificans, it caused a temporary nitrite-dependent inhibition of N₂O reduction. Under nonpolarizing conditions the H⁺/2e^– ratios for O₂, N₂O, and nitrite (8.0, 4.3, and 4.5, respectively) confirmed those reported previously from this laboratory. The present results largely but not entirely agree with data from another laboratory.     

Denitrification with methanol in the presence of high salt concentrations and at high pH levels

Summary In the combined ion exchange/biological denitrification process for nitrate removal from ground water, in which nitrate is removed by ion exchange, the resins are regenerated in a closed circuit by a biological denitrification reactor. This denitrification reactor eliminates nitrate from the regenerant. Methanol is used as electron donor for biological denitrification. To obtain sufficient regeneration of the resins within a reasonable time, high NaCl or NaHCO₃ concentrations (10–30 g/l) in the regenerant are necessary. High NaHCO₃ concentrations affected the biological denitrification in three ways: a) a slight decrease in denitrification capacity (30%) was observed; b) the yield coefficient and CH₃OH/NO₃ ^-–N ratio decreased. When high NaHCO₃ concentrations (above 10g NaHCO₃/l) were used, the yield coefficient was 0.10–0.13 g VSS/g NO₃ ^-–N and the CH₃OH/NO₃ ^-–N ratio was 2.00–2.03 g/g; c) high NaHCO₃ concentrations influenced nitrite production. Nitrite is an intermediate product of biological denitrification and with rising NaHCO₃ concentrations nitrite accumulation was suppressed. This was explained by the effect of high NaHCO₃ concentrations on the pH in the microenvironment of the denitrifying organisms. High NaCl concentrations also resulted in a slight decrease in denitrification capacity, but the second and third effects were not observed in the presence of high NaCl concentrations.Although the pH in the regenerant will rise as a result of biological denitrification, the capacity of a denitrification reactor did not decrease significantly when a pH of 8.8–9.2 was reached.     

Intermediates of denitrification in the chemoautotroph Thiobacillus denitrificans

Summary Intact cells obtained from Thiobacillus denitrificans grown autotrophically with thiosulfate as the oxidizable substrate and nitrate as the final electron acceptor catalyzed the reduction of nitrate, nitrite and nitric oxide stoichiometrically to nitrogen gas with the concomitant oxidation of thiosulfate. In addition, nitrous oxide was also capable of acting as the terminal oxidant of the respiratory chain with thiosulfate as the reductant. The anaerobic oxidation of thiosulfate by NO₃ ^-, NO, and N₂O was sensitive to the flavoprotein inhibitors, antimycin A or NHQNO, and cyanide or azide thus, implicating the participation of flavins, and cytochromes of b-, c-, and a-types in the denitrification process. The nitrite reductase system, however, was not markedly affected by the electron transport chain inhibitors. The experimental observations suggest that the dissimilatory nitrate reduction in the chemoautotroph T. denitrificans involves nitrite, nitric oxide, and nitrous oxide as theintermediates with nitrogen gas as the final reduction product.Non-Standard Abbreviations TTFA Thenoyltrifluoroacetone - NHQNO 2-n-nonyl-4-hydroxyquinoline N-oxide     

Denitrification in a South Louisiana wetland forest receiving treated sewage effluent

Although denitrification has the potential to reduce nitrate (NO ₃ ^– ) pollution of surface waters, the quantification of denitrification rates is complex because it requires differentiation from other mechanisms and is highly variable in both space and time. This study first measured potential denitrification rates at a wetland forest site in south Louisiana before receipt of secondary wastewater effluent, and then, following 30 months of effluent application, landscape gradients of dissolved nitrate (NO ₃ ^– ) and nitrous oxide (N₂O) were measured. A computer model was developed to quantify N transformations. Floodwater NO ₃ ^– and N₂O concentrations were higher in the forest receiving effluent than in the adjacent control forest. Denitrification rates of NO ₃ ^– -amended soil cores ranged from 0.03–0.45 g N m^–2 d^–1 with an overall mean of 0.10 g N m^–2 d^–1. Effluent N is being applied at a rate of approximately 0.034 g N m^–2 d^–1, with approximately 95% disappearing along a 1 km transect. In the treatment forest, floodwater NO ₃ ^– concentrations decreased from 1000 M at the inflow point to 50 M along the 1 km transect. Nitrous oxide concentrations increased from 0.25 M to 1.2 M within the first 100 m, but decreased to 0.1 M over the next 900 m. The initial increase in N₂O was presumably a result ofin situ denitrification. Model analyses indicated that denitrification was directly associated with nitrification and was limited by the availability of NO ₃ ^– produced by nitrification. Due to different redox potential optima, coupling of nitrification and denitrification was a function of a balance of environmental conditions that was moderately favorable to both processes. N removal efficiency was largely dependent on the proportion of effluent NH ₄ ⁺ to NO ₃ ^– . When NH ₄ ⁺ /NO ₃ ^– was 1, average N removal efficiency ranged from 95–100%, but ratios that were >1 reduced average efficiencies to as low as 57%. Actual effluent NH ₄ ⁺ /NO ₃ ^– loading ratios at this site are approximately 0.2 and are consistently <1.     

Heterotrophic nitrification and aerobic denitrification inAlcaligenes faecalis strain TUD

Heterotrophic nitrification and aerobic and anaerobic denitrification byAlcaligenes faecalis strain TUD were studied in continuous cultures under various environmental conditions. Both nitrification and denitrification activities increased with the dilution rate. At dissolved oxygen concentrations above 46% air saturation, hydroxylamine, nitrite and nitrate accumulated, indicating that both the nitrification and denitrification were less efficient. The overall nitrification activity was, however, essentially unaffected by the oxygen concentration. The nitrification rate increased with increasing ammonia concentration, but was lower in the presence of nitrate or nitrite. When present, hydroxylamine, was nitrified preferentially. Relatively low concentrations of acetate caused substrate inhibition (K_I=109 M acetate). Denitrifying or assimilatory nitrate reductases were not detected, and the copper nitrite reductase, rather than cytochrome cd, was present. Thiosulphate (a potential inhibitor of heterotrophic nitrification) was oxidized byA. faecalis strain TUD, with a maximum oxygen uptake rate of 140–170nmol O₂·min^-1·mg prot^-1. Comparison of the behaviour ofA. faecalis TUD with that of other bacteria capable of heterotrophic nitrification and aerobic denitrification established that the response of these organisms to environmental parameters is not uniform. Similarities were found in their responses to dissolved oxygen concentrations, growth rate and ammonia concentration. However, they differed in their responses to externally supplied nitrite and nitrate.     

Nitrite reduction by a mixed culture under conditions relevant to shortcut biological nitrogen removal

Dissimilative reduction of nitrite by nitrite-acclimated cellswas investigated in a batch reactor under various environmental conditions that can beencountered in shortcut biological nitrogen removal (SBNR: ammonia to nitrite andnitrite to nitrogen gas). The maximum specific nitrite reduction rate was as much as 4.3 times faster than the rate of nitrate reduction when individually tested, but the reaction was inhibited in the presence of nitrate when the initial nitrate concentration was greater than approximately 25 mg-N/l or the initialNO ₃ ^- N/NO ₂ ^- N ratio was larger than 0.5. Nitrite reduction was also inhibited by nitrite itself when theconcentration was higher than that to which the cells had been acclimated. Therefore, it was desirable to avoid excessively high nitrite and nitrate concentrations in a denitrification reactor. Nitrite reduction, however, was not affected by an alkaline pH (in the range of 7–9) or a high concentration of FA (in the range of 16–39 mg/l), which can be common in SBNR processes. The chemical oxygen demand (COD) requirement for nitrite reduction was approximately 22–38% lower than that for nitrate reduction, demonstrating that the SBNR process can be economical. The specific consumption,measured as the ratio of COD consumed to nitrogen removed, was affected by the availability of COD and the physiological state of the cells. The ratio increased when the cells grew rapidly and were storing carbon and electrons.     

Reduction of nitrate byPseudomonas putrefaciens entrapped in composite agar layer/microporous membrane structures

Summary Composite structures consisting of aPseudomonas putrefaciens immobilized-cell agar layer bounded by a microporous membrane filter were used for water denitrification. With methanol as the C-source, one litre of high nitrate water (3 mM) was completely freed from NO ₃ ^– and NO ₂ ^– ions in 11 days at a rate of 90 mol N–NO ₃ ^– /day/g of agar gel, while no production of ammonium ions could be detected. When acetic acid was substituted for methanol, the denitrifying activity was lower. No noticeable contamination of the treated water due to cell leakage from the biocatalytic structures occurred during the incubation periods.     

Metabolic regulation including anaerobic metabolism inParacoccus denitrificans

Under anaerobic circumstances in the presence of nitrateParacoccus denitrificans is able to denitrify. The properties of the reductases involved in nitrate reductase, nitrite reductase, nitric oxide reductase, and nitrous oxide reductase are described. For that purpose not only the properties of the enzymes ofP. denitrificans are considered but also those fromEscherichia coli, Pseudomonas aeruginosa, andPseudomonas stutzeri. Nitrate reductase consists of three subunits: the subunit contains the molybdenum cofactor, the subunit contains the iron sulfur clusters, and the subunit is a special cytochromeb. Nitrate is reduced at the cytoplasmic side of the membrane and evidence for the presence of a nitrate-nitrite antiporter is presented. Electron flow is from ubiquinol via the specific cytochromeb to the nitrate reductase. Nitrite reductase (which is identical to cytochromecd ₁) and nitrous oxide reductase are periplasmic proteins. Nitric oxide reductase is a membrane-bound enzyme. Thebc ₁ complex is involved in electron flow to these reductases and the whole reaction takes place at the periplasmic side of the membrane. It is now firmly established that NO is an obligatory intermediate between nitrite and nitrous oxide. Nitrous oxide reductase is a multi-copper protein. A large number of genes is involved in the acquisition of molybdenum and copper, the formation of the molybdenum cofactor, and the insertion of the metals. It is estimated that at least 40 genes are involved in the process of denitrification. The control of the expression of these genes inP. denitrificans is totally unknown. As an example of such complex regulatory systems the function of thefnr, narX, andnarL gene products in the expression of nitrate reductase inE. coli is described. The control of the effects of oxygen on the reduction of nitrate, nitrite, and nitrous oxide are discussed. Oxygen inhibits reduction of nitrate by prevention of nitrate uptake in the cell. In the case of nitrite and nitrous oxide a competition between reductases and oxidases for a limited supply of electrons from primary dehydrogenases seems to play an important role. Under some circumstances NO formed from nitrite may inhibit oxidases, resulting in a redistribution of electron flow from oxygen to nitrite.P. denitrificans contains three main oxidases: cytochromeaa ₃, cytochromeo, and cytochromeco. Cytochromeo is proton translocating and receives its electrons from ubiquinol. Some properties of cytochromeco, which receives its electrons from cytochromec, are reported. The control of the formation of these various oxidases is unknown, as well as the control of electron flow in the branched respiratory chain. Schemes for aerobic and anaerobic electron transport are given. Proton translocation and charge separation during electron transport from various electron donors and by various electron transfer pathways to oxygen and nitrogenous oxide are given. The extent of energy conservation during denitrification is about 70% of that during aerobic respiration. In sulfate-limited cultures (in which proton translocation in the NADH-ubiquinone segment of the respiratory chain is lost) the extent of energy conservation is about 60% of that under substrate-limited conditions. These conclusions are in accordance with measurements of molar growth yields.     

Anaerobic expression of nitric oxide reductase from denitrifying Pseudomonas stutzeri

NO reductase synthesis was investigated immunochemically and by activity assays in cells of Pseudomonas stutzeri ZoBell grown in continuous culture at discrete aeration levels, or in O₂-limited batch cultures supplemented with N oxides as respiratory substrate. Under aerobic conditions, NO reductase was not expressed in P. stutzeri. Oxygen limitation in combination with the presence of nitrate or nitrite derepressed NO reductase synthesis. On transition from aerobic to anaerobic conditions in continuous culture, NO reductase was synthesized below 3% air saturation and reached maximum expression under anaerobic conditions. By use of mutant strains defective in nitrate respiration or nitrite respiration, the inducing effect of individual N oxides on NO reductase synthesis could be discriminated. Nitrite caused definite, concentration-dependent induction, while nitrate promoted moderate enzyme synthesis or amplified effects of nitrite. Exogenous nitric oxide (NO) in concentrations 25 M induced trace amounts of NO reductase; in higher concentrations it arrested cell growth. Nitrite reductase or NO reductase were not detected immunochemically under these conditions. NO generated as an intermediate appeared not to induce NO reductase significantly. Antiserum raised against the P. stutzeri NO reductase showed crossreaction with cell extracts from P. stutzeri JM300, but not with several other denitrifying pseudomonads or Paracoccus denitrificans.     

Mutation of the regulatory phosphorylation site of tobacco nitrate reductase results in high nitrite excretion and NO emission from leaf and root tissue

In wild-type Nicotiana plumbaginifolia Viv. and other higher plants, nitrate reductase (NR) is regulated at the post-translational level and is rapidly inactivated in response to, for example, a light-to-dark transition. This inactivation is caused by phosphorylation of a conserved regulatory serine residue, Ser 521 in tobacco, and interaction with divalent cations or polyamines, and 14-3-3 proteins. The physiological importance of the post-translational NR modulation is presently under investigation using a transgenic N. plumbaginifolia line. This line expresses a mutated tobacco NR where Ser 521 has been changed into aspartic acid (Asp) by site-directed mutagenesis, resulting in a permanently active NR enzyme [C. Lillo et al. (2003) Plant J 35:566–573]. When cut leaves or roots of this line (S₅₂₁) were placed in darkness in a buffer containing 50 mM KNO₃, nitrite was excreted from the tissue at rates of 0.08–0.2 mol (g FW)^–1 h^–1 for at least 5 h. For the control transgenic plant (C1), which had the regulatory serine of NR intact, nitrite excretion was low and halted completely after 1–3 h. Without nitrate in the buffer in which the tissue was immersed, nitrite excretion was also low for S₅₂₁, although 20–40 mol (g FW)^–1 nitrate was present inside the tissue. Apparently, stored nitrate was not readily available for reduction in darkness. Leaf tissue and root segments of S₅₂₁ also emitted much more nitric oxide (NO) than the control. Importantly, NO emission from leaf tissue of S₅₂₁ was higher in the dark than in the light, opposite to what was usually observed when post-translational NR modulation was operating.Abbreviations NR Nitrate reductase - NO Nitric oxide - Ser Serine - WT Wild type     

Denitrification by Alcaligenes denitrificans in a closed rotating biological contactor

Biological denitrification using a pure culture of Alcaligenes denitrificans was investigated in a closed rotating biological contactor, which operated with a hydraulic retention time of 2 h, a carbon/nitrogen ratio of 2:1, with a dissolved O₂ concentration below 6 mg l^–1 and under three different phosphate concentrations. Alcaligenes denitrificans was not repressed by O₂ limitation and the removal of nitrate was about 30% more efficient at the intermediate phosphate concentration (20 mg P l^–1).     

Chemical oxygen demand reduction in a whey fermentation

Summary Preparations of living Pseudomonas denitrificans cells immobilized in alginate gel were used in the denitrification of water. In the presence of an exogenous carbon source the entrapped microorganisms reduced nitrate and nitrite to gaseous products and to achieve complete reduction, carbon to nitrogen ratios of over two were required. The effects on denitrification of particle size and the number of bacteria in the gel were investigated. Apparent K_m values for nitrate and nitrite reduction were calculated for free and immobilized cells. When the immobilized cells were incubated in nutrient media, an increase in reduction rate was observed and this was shown to be caused by the growth of cells within the gel particles. Immobilized P. denitrificans cells retained 75% of their initial nitrate reduction capacity after 21 days of storage at +4°C. The operational stability of the alginate-immobilized cells was studied both in batch and in a column which was operated continuously. A column (45 g of alginate-cell fibers in 80 ml) denitrified a high nitrate drinking water (100 mg NO₃/l) with a rate of 300 ml of nitrate and nitrite free water/day/g of gel. The half life for nitrate reduction was estimated to be 30 days.     

Ancient hemes for ancient catalysts

Tetrapyrroles are essential molecules in living organisms and perform a multitude of functions in all kingdoms. Their synthesis is achieved in cells via a complex biosynthetic machinery which is unlikely to be maintained, if unnecessary. Here we propose that ancient hemes, such as the d₁-heme of cd₁ nitrite reductase or the siroheme of bacterial and plant nitrite and sulphite reductases, are molecular fossils which have survived the evolutionary pressure because their role is strategic for the organism where they are found today. The peculiar NO-releasing propensity of the d₁-heme of P. aeruginosa NIR, recently shown by our group is, in our opinion, an example of this strategy. The hypothesis is that the d₁-heme structure might be a pre-requisite for the fast rate of NO dissociation from the ferrous form, a property which is crucial to enzymatic activity and cannot be achieved with a more common b-type heme.Key words: d1-heme, porphyrin, siroheme, nitrite reductase, sulphite reductase, nitric oxide, evolutionPseudomonas aeruginosa is a Gram-negative bacterium commonly found in soil and water, well known for its metabolic versatility; under anaerobic conditions it can use nitrate and nitrite to produce energy via the denitrification pathway. In natural environments, denitrification is the part of the biological nitrogen cycle in which nitrate is transformed into nitrogen gas; reduction of nitrate occurs in four stages each catalyzed by a specific metalloenzyme.^1,2 P. aeruginosa is also an opportunistic pathogen, capable of causing serious infections in several hosts, such as humans and plants^3,4; pathogenesis, NO metabolism and denitrification are strictly related.^5,6The conversion of nitrite (NO₂^-) to nitric oxide (NO) is catalyzed in denitrifying bacteria by the periplasmic nitrite reductases (NIR).⁷ In P. aeruginosa NIR is a heme-containing enzyme (cd₁NIR) which produces NO in the active site where the unique d₁-heme cofactor (Fig. 1) is bound. This peculiar heme is synthesized from iron-protoporphyrin IX and belongs to the isobacteriochlorines subgroup;¹ it is exclusively found in this type of bacterial NIR.Open in a separate windowFigure 1Chemical structure of the d₁-heme.Reduction of nitrite involves binding of this molecule to the reduced d₁-heme, followed by dehydration to yield NO; release of NO and re-reduction of the enzyme close the cycle. An high affinity for nitrite (and anions) of the ferrous d₁-heme is a peculiar feature of cd₁NIR.⁷ However since the product NO is a powerful inhibitor of ferrous hemeproteins, enzymatic turnover demands the quick release of NO. In our recent paper⁸ we have shown that NO dissociates rapidly from the reduced form of the specialized d₁-heme of P. aeruginosa cd₁NIR. This unexpected result indicates that cd₁NIR behaves differently from other hemeproteins, since the rate of NO dissociation is by far faster (more than 100-fold) than that measured for any other heme in the ferrous state.^8–11Our hypothesis is that the d₁-heme structure might be a prerequisite for the fast rate of NO dissociation from the ferrous form, a property which cannot be achieved with a standard b-type heme.A major consequence of our finding is that this property of the d₁-heme is essential to avoid quasi-irreversible binding of NO to the reduced heme, which would jeopardize the physiological function of the enzyme evolved to scavenge nitrite, the toxic product of nitrate reduction. From the bioenergetic view-point, the main energy-generating step in denitrification is nitrate reduction (with a net H⁺ traslocation of 2H⁺/2e^-); thus, although a complex electron transfer chain is often present, the major biological role of the reductive steps downstream of nitrate reduction is likely to be nitrite scavenging.² If the complex of NO with reduced cd₁NIR was very long lived it would hamper further reaction cycles thus resulting in the accumulation of nitrite which is toxic for the bacterium. In line with this interpretation, we have also shown very recently¹² that nitrite is able to displace NO from the ferrous enzyme; thus substrate availability is the key factor that controls the enzyme turnover.From the standpoint of molecular evolution it is accepted that bacterial denitrification is an ancient metabolic pathway which existed even before oxygen became abundant in the athmosphere. Several reports pointed out that the enzymes involved in aerobic respiration derive from those involved in the denitrification pathway. Primitive denitrifying bacteria (similar to the extant Paracoccus denitrificans) can be considered as a common ancestral symbiotic prototype of the eukaryotic mitochondrion. Indeed there is compelling evidence that modern eukaryotic oxidases evolved from bacterial NO-reductase once oxygen became available as a major oxidant.^13,14In microrganisms, other “ancient” metabolisms are represented by sulphite and nitrite reduction pathways, which were well suited for a prebiotic photoreducing environment.¹⁵ Also in these pathways several enzymes are heme-containing proteins in which modified hemes, such as siroheme, are used as cofactors.¹⁶ Interestingly also in plants siroheme is a relevant porphyrin group,¹⁷ being the cofactor of plant nitrite and sulphite reductases, required for the assimilation of inorganic nitrogen and sulphur from the environment.Tetrapyrroles are essential molecules in living organisms and perform a multitude of functions in all kingdoms. Their biosynthesis is achieved in cells via branched pathways which are expensive in terms of energy consumption.^16–18 The single pathways are tightly regulated and often activated only “on demand” when the specific heme group is required. Therefore, parsimony suggests that a complex biosynthetic machinery is unlikely to be maintained, if unnecessary.We thus propose that these ancient hemes (such as the d₁-heme or the siroheme) are molecular fossils which have survived the evolutionary pressure because their role is strategic only for the organism where they are found today. The peculiar NO-releasing propensity of the d₁-heme of P. aeruginosa NIR shown by our group could be, in our opinion, an example of this strategy. A major challenge for the future is to unveil other uncommon features of these hemes.     

Nitrite oxidation in the Namibian oxygen minimum zone

Nitrite oxidation is the second step of nitrification. It is the primary source of oceanic nitrate, the predominant form of bioavailable nitrogen in the ocean. Despite its obvious importance, nitrite oxidation has rarely been investigated in marine settings. We determined nitrite oxidation rates directly in ¹⁵N-incubation experiments and compared the rates with those of nitrate reduction to nitrite, ammonia oxidation, anammox, denitrification, as well as dissimilatory nitrate/nitrite reduction to ammonium in the Namibian oxygen minimum zone (OMZ). Nitrite oxidation (⩽372 nM NO₂⁻ d⁻¹) was detected throughout the OMZ even when in situ oxygen concentrations were low to non-detectable. Nitrite oxidation rates often exceeded ammonia oxidation rates, whereas nitrate reduction served as an alternative and significant source of nitrite. Nitrite oxidation and anammox co-occurred in these oxygen-deficient waters, suggesting that nitrite-oxidizing bacteria (NOB) likely compete with anammox bacteria for nitrite when substrate availability became low. Among all of the known NOB genera targeted via catalyzed reporter deposition fluorescence in situ hybridization, only Nitrospina and Nitrococcus were detectable in the Namibian OMZ samples investigated. These NOB were abundant throughout the OMZ and contributed up to ∼9% of total microbial community. Our combined results reveal that a considerable fraction of the recently recycled nitrogen or reduced NO₃⁻ was re-oxidized back to NO₃⁻ via nitrite oxidation, instead of being lost from the system through the anammox or denitrification pathways.     

Mixed culture hydrogenotrophic nitrate reduction in drinking water

Isolation and identification of the bacteria from a hydrogenotrophic reactor for the denitrification of drinking water revealed that several microorganisms are involved. Acinetobacter sp., Aeromonas sp., Pseudomonas sp. and Shewanella putrefaciens were repeatedly isolated from the hydrogenotrophic sludge and postulated to be of primary importance in the process. Nitrate reduction to nitrite appears to be a property of a diverse group of organisms. Nitrite reduction was found to be stimulated by the presence of organic growth factors. Thus, in a mixed culture, hydrogenotrophic denitrification reactor, NO _inf2 ^sup– formed by NO _inf3 ^sup– -reducers can be converted by true denitrifiers thriving on organic growth factors either present in the raw water, or excreted by the microbial community. Mixotrophic growth also contributes to NO _inf2 ^sup– reduction. Finally, chemolithotrophic bacteria participate in the nitrite to nitrogen gas conversion.Offprint requests to: W. Verstraete.