Dissimilatory nitrate reduction to nitrate, nitrous oxide, and ammonium by Pseudomonas putrefaciens

The influence of redox potential on dissimilatory nitrate reduction to ammonium was investigated on a marine bacterium, Pseudomonas putrefaciens. Nitrate was consumed (3.1 mmol liter-1), and ammonium was produced in cultures with glucose and without sodium thioglycolate. When sodium thioglycolate was added, nitrate was consumed at a lower rate (1.1 mmol liter-1), and no significant amounts of nitrite or ammonium were produced. No growth was detected in glucose media either with or without sodium thioglycolate. When grown on tryptic soy broth, the production of nitrous oxide paralleled growth. In the same medium, but with sodium thioglycolate, nitrous oxide was first produced during growth and then consumed. Acetylene caused the nitrous oxide to accumulate. These results and the mass balance calculations for different nitrogen components indicate that P. putrefaciens has the capacity to dissimilate nitrate to ammonium as well as to dinitrogen gas and nitrous oxide (denitrification). The dissimilatory pathway to ammonium dominates except when sodium thioglycolate is added to the medium.     

Dissimilatory nitrate reduction to nitrate, nitrous oxide, and ammonium by Pseudomonas putrefaciens.

The influence of redox potential on dissimilatory nitrate reduction to ammonium was investigated on a marine bacterium, Pseudomonas putrefaciens. Nitrate was consumed (3.1 mmol liter-1), and ammonium was produced in cultures with glucose and without sodium thioglycolate. When sodium thioglycolate was added, nitrate was consumed at a lower rate (1.1 mmol liter-1), and no significant amounts of nitrite or ammonium were produced. No growth was detected in glucose media either with or without sodium thioglycolate. When grown on tryptic soy broth, the production of nitrous oxide paralleled growth. In the same medium, but with sodium thioglycolate, nitrous oxide was first produced during growth and then consumed. Acetylene caused the nitrous oxide to accumulate. These results and the mass balance calculations for different nitrogen components indicate that P. putrefaciens has the capacity to dissimilate nitrate to ammonium as well as to dinitrogen gas and nitrous oxide (denitrification). The dissimilatory pathway to ammonium dominates except when sodium thioglycolate is added to the medium.     

Comparison of denitrification by Pseudomonas stutzeri, Pseudomonas aeruginosa, and Paracoccus denitrificans

A comparison was made of denitrification by Pseudomonas stutzeri, Pseudomonas aeruginosa, and Paracoccus denitrificans. Although all three organisms reduced nitrate to dinitrogen gas, they did so at different rates and accumulated different kinds and amounts of intermediates. Their rates of anaerobic growth on nitrate varied about 1.5-fold; concomitant gas production varied more than 8-fold. Cell yields from nitrate varied threefold. Rates of gas production by resting cells incubated with nitrate, nitrite, or nitrous oxide varied 2-, 6-, and 15-fold, respectively, among the three species. The composition of the gas produced also varied markedly: Pseudomonas stutzeri produced only dinitrogen; Pseudomonas aeruginosa and Paracoccus denitrificans produced nitrous oxide as well; and under certain conditions Pseudomonas aeruginosa produced even more nitrous oxide than dinitrogen. Pseudomonas stutzeri and Paracoccus denitrificans rapidly reduced nitrate, nitrite, and nitrous oxide and were able to grow anaerobically when any of these nitrogen oxides were present in the medium. Pseudomonas aeruginosa reduced these oxides slowly and was unable to grow anaerobically at the expense of nitrous oxide. Furthermore, nitric and nitrous oxide reduction by Pseudomonas aeruginosa were exceptionally sensitive to inhibition by nitrite. Thus, although it has been well studied physiologically and genetically, Pseudomonas aeruginosa may not be the best species for studying the later steps of the denitrification pathway.     

Comparison of denitrification by Pseudomonas stutzeri, Pseudomonas aeruginosa, and Paracoccus denitrificans.

A comparison was made of denitrification by Pseudomonas stutzeri, Pseudomonas aeruginosa, and Paracoccus denitrificans. Although all three organisms reduced nitrate to dinitrogen gas, they did so at different rates and accumulated different kinds and amounts of intermediates. Their rates of anaerobic growth on nitrate varied about 1.5-fold; concomitant gas production varied more than 8-fold. Cell yields from nitrate varied threefold. Rates of gas production by resting cells incubated with nitrate, nitrite, or nitrous oxide varied 2-, 6-, and 15-fold, respectively, among the three species. The composition of the gas produced also varied markedly: Pseudomonas stutzeri produced only dinitrogen; Pseudomonas aeruginosa and Paracoccus denitrificans produced nitrous oxide as well; and under certain conditions Pseudomonas aeruginosa produced even more nitrous oxide than dinitrogen. Pseudomonas stutzeri and Paracoccus denitrificans rapidly reduced nitrate, nitrite, and nitrous oxide and were able to grow anaerobically when any of these nitrogen oxides were present in the medium. Pseudomonas aeruginosa reduced these oxides slowly and was unable to grow anaerobically at the expense of nitrous oxide. Furthermore, nitric and nitrous oxide reduction by Pseudomonas aeruginosa were exceptionally sensitive to inhibition by nitrite. Thus, although it has been well studied physiologically and genetically, Pseudomonas aeruginosa may not be the best species for studying the later steps of the denitrification pathway.     

Energy yield of denitrification: an estimate from growth yield in continuous cultures of Pseudomonas denitrificans under nitrate-, nitrite- and oxide-limited conditions.

The molar growth yields of Pseudomonas denitrificans, for nitrate, nitrite and nitrous oxide, were determined in chemostat culture under electron acceptor-limited conditions. Glutamate was used as the source of energy, carbon and nitrogen. The catabolic pattern was identical, irrespective of the terminal electron acceptors. The molar growth yields, corrected for maintenance energy, were 28-6 g/mol nitrate, 16-9 g/mol nitrite and 8-8 g/mol nitrous oxide. The energy yield, expressed on an electron basis, was proportional to the oxidation number of the nitrogen: nitrate (plus 5), nitrite (plus 3) and nitrous oxide (plus 1). It was concluded that oxidative phosphorylation occurs to a similar extent in each of the electron transport chains associated with the reduction of nitrate to nitrite, nitrite to nitrous oxide and nitrous oxide to nitrogen.     

Characterization of Tn5 mutants deficient in dissimilatory nitrite reduction in Pseudomonas sp. strain G-179, which contains a copper nitrite reductase.

Tn5 was used to generate mutants that were deficient in the dissimilatory reduction of nitrite for Pseudomonas sp. strain G-179, which contains a copper nitrite reductase. Three types of mutants were isolated. The first type showed a lack of growth on nitrate, nitrite, and nitrous oxide. The second type grew on nitrate and nitrous oxide but not on nitrite (Nir-). The two mutants of this type accumulated nitrite, showed no nitrite reductase activity, and had no detectable nitrite reductase protein bands in a Western blot (immunoblot). Tn5 insertions in these two mutants were clustered in the same region and were within the structural gene for nitrite reductase. The third type of mutant grew on nitrate but not on nitrite or nitrous oxide (N2O). The mutant of this type accumulated significant amounts of nitrite, NO, and N2O during anaerobic growth on nitrate and showed a slower growth rate than the wild type. Diethyldithiocarbamic acid, which inhibited nitrite reductase activity in the wild type, did not affect NO reductase activity, indicating that nitrite reductase did not participate in NO reduction. NO reductase activity in Nir- mutants was lower than that in the wild type when the strains were grown on nitrate but was the same as that in the wild type when the strains were grown on nitrous oxide. These results suggest that the reduction of NO and N2O was carried out by two distinct processes and that mutations affecting nitrite reduction resulted in reduced NO reductase activity following anaerobic growth with nitrate.     

Kinetic Explanation for Accumulation of Nitrite, Nitric Oxide, and Nitrous Oxide During Bacterial Denitrification

The kinetics of denitrification and the causes of nitrite and nitrous oxide accumulation were examined in resting cell suspensions of three denitrifiers. An Alcaligenes species and a Pseudomonas fluorescens isolate characteristically accumulated nitrite when reducing nitrate; a Flavobacterium isolate did not. Nitrate did not inhibit nitrite reduction in cultures grown with tungstate to prevent formation of an active nitrate reductase; rather, accumulation of nitrite seemed to depend on the relative rates of nitrate and nitrite reduction. Each isolate rapidly reduced nitrous oxide even when nitrate or nitrite had been included in the incubation mixture. Nitrate also did not inhibit nitrous oxide reduction in Alcaligenes odorans, an organism incapable of nitrate reduction. Thus, added nitrate or nitrite does not always cause nitrous oxide accumulation, as has often been reported for denitrifying soils. All strains produced small amounts of nitric oxide during denitrification in a pattern suggesting that nitric oxide was also under kinetic control similar to that of nitrite and nitrous oxide. Apparent K_m values for nitrate and nitrite reduction were 15 μM or less for each isolate. The K_m value for nitrous oxide reduction by Flavobacterium sp. was 0.5 μM. Numerical solutions to a mathematical model of denitrification based on Michaelis-Menten kinetics showed that differences in reduction rates of the nitrogenous compounds were sufficient to account for the observed patterns of nitrite, nitric oxide, and nitrous oxide accumulation. Addition of oxygen inhibited gas production from ¹³NO₃⁻ by Alcaligenes sp. and P. fluorescens, but it did not reduce gas production by Flavobacterium sp. However, all three isolates produced higher ratios of nitrous oxide to dinitrogen as the oxygen tension increased. Inclusion of oxygen in the model as a nonspecific inhibitor of each step in denitrification resulted in decreased gas production but increased ratios of nitrous oxide to dinitrogen, as observed experimentally. The simplicity of this kinetic model of denitrification and its ability to unify disparate observations should make the model a useful guide in research on the physiology of denitrifier response to environmental effectors.     

Anaerobic energy metabolism of the sulfur-reducing bacterium “Spirillum” 5175 during dissimilatory nitrate reduction to ammonia

In a batch culture experiment the microaerophilic Campylobacter-like bacterium “Spirillum” 5175 derived its energy for growth from the reduction of nitrate to nitrite and nitrite to ammonia. Hereby, formate served as electron donor, acetate as carbon source, and l-cysteine as sulfur source. Nitrite was quantitatively accumulated in the medium during the reduction of nitrate; reduction of nitrite began only after nitrate was exhausted from the medium. The molar growth yield per mol formate consumed, Y_m, was 2.4g/mol for the reduction of nitrate to nitrite and 2.0 g/mol for the conversion of nitrite to ammonia. The gain of ATP per mol of oxidized formate was 20% higher for the reduction of nitrate to nitrite, compared to the reduction of nitrite to ammonia. With succinate as carbon source and nitrite as electron acceptor, Y_m was 3.2g/mol formate, i.e. 60% higher than with acetate as carbon source. No significant amount of nitrous oxide or dinitrogen was produced during growth with nitrate or nitrite both in the presence or absence of acetylene. No growth on nitrous oxide was found. The hexaheme c nitrite reductase of “Spirillum” 5175 was an inducible enzyme. It was present in cells cultivated with nitrate or nitrite as electron acceptor. It was absent in cells grown with fumarate, but appeared in high concentration in “Spirillum” 5175 grown on elemental sulfur. Furthermore, the dissimilatory enzymes nitrate reductase and hexaheme c nitrite reductase were localized in the periplasmic part of the cytoplasmic membrane.     

Denitrifying potential of methanogenic sludge

Summary A methanogenic sludge showed denitrifying activity for acetate, glucose and effluents from methanogenic treatments as substrates; denitrifiers were present in a relatively high number. When glucose was used as substrate dissimilatory reduction of nitrate to ammonium occurred. Methane production from acetate was inhibited by denitrification and resumed after nitrite and nitrous oxide depletion.     

Separate Nitrite, Nitric Oxide, and Nitrous Oxide Reducing Fractions from Pseudomonas perfectomarinus

Pseudomonas perfectomarinus was found to grow anaerobically at the expense of nitrate, nitrite, or nitrous oxide but not chlorate or nitric oxide. In several repetitive experiments, anaerobic incubation in culture media containing nitrate revealed that an average of 82% of the cells in aerobically grown populations were converted to the capacity for respiration of nitrate. Although they did not form colonies under these conditions, the bacteria synthesized the denitrifying enzymes within 3 hr in the absence of oxygen or another acceptable inorganic oxidant. This was demonstrated by the ability, after anaerobic incubation, of cells and of extracts to reduce nitrite, nitric oxide, and nitrous oxide to nitrogen. From crude extracts of cells grown on nitrate, nitrite, or nitrous oxide, separate complex fractions were obtained that utilized reduced nicotinamide adenine dinucleotide as the source of electrons for the reduction of (i) nitrite to nitric oxide, (ii) nitric oxide to nitrous oxide, and (iii) nitrous oxide to nitrogen. Gas chromatographic analyses revealed that each of these fractions reduced only one of the nitrogenous oxides.     

Modulation by copper of the products of nitrite respiration in Pseudomonas perfectomarinus.

A synthetic growth medium was purified with the chelator 1,5-diphenylthiocarbazone to study the effects of copper on partial reactions and product formation of nitrite respiration in Pseudomonas perfectomarinus. This organism grew anaerobically in a copper-deficient medium with nitrate or nitrite as the terminal electron acceptor. Copper-deficient cells had high activity for reduction of nitrate, nitrite, and nitric oxide, but little activity for nitrous oxide reduction. High rates of nitrous oxide reduction were observed only in cells grown on a copper-sufficient (1 micro M) medium. Copper-deficient cells converted nitrate or nitrite initially to nitrous oxide instead of dinitrogen, the normal end product of nitrite respiration in this organism. In agreement with this was the finding that anaerobic growth of P. perfectomarinus with nitrous oxide as the terminal electron acceptor required copper. This requirement was not satisfied by substitution of molybdenum, zinc, nickel, cobalt, or manganese for copper. Reconstitution of nitrous oxide reduction in copper-deficient cells was rapid on addition of a small amount of copper, even though protein synthesis was inhibited. The results indicate an involvement of copper protein(s) in the last step of nitrite respiration in P. perfectomarinus. In addition we found that nitric oxide, a presumed intermediate of nitrite respiration, inhibited nitrous oxide reduction.     

Blockage by acetylene of nitrous oxide reduction in Pseudomonas perfectomarinus.

Suspensions of denitrifying cells of Pseudomonas perfectomarinus reduced nitrate and nitrate as expected to dinitrogen; but, in the presence of acetylene, nitrous oxide accumulated when nitrate or nitrate was reduced. When supplied at the outset in place of nitrate and nitrate, nitrous oxide was rapidly reduced to dinitrogen by cells incubated in anaerobic vessels in the absence of acetylene. In the presence of 0.01 atmospheres of acetylene, however, nitrous oxide was not reduced. Ethylene was not produced, nor did it influence the rate of nitrous oxide reduction when provided instead of acetylene. Cells exposed to 0.01 atmospheres of acetylene for as long as 400 min were able to reduce nitrous oxide after removal of acetylene at a rate comparable to that of cells not exposed to acetylene. Acetylene did not affect the production or functioning of assimilatory nitrate or nitrite reductase in axenic cultures of Enterobacter aerogenes or Trichoderma uride. While exposed to acetylene, bacteria in marine sediment slurries produced measurable quantities of nitrous oxide from glucose- or acetate-dependent reduction of added nitrate. Possible use of acetylene blockage for measurement of denitrification in unamended marine sediments is discussed.     

Blockage by acetylene of nitrous oxide reduction in Pseudomonas perfectomarinus.

Suspensions of denitrifying cells of Pseudomonas perfectomarinus reduced nitrate and nitrate as expected to dinitrogen; but, in the presence of acetylene, nitrous oxide accumulated when nitrate or nitrate was reduced. When supplied at the outset in place of nitrate and nitrate, nitrous oxide was rapidly reduced to dinitrogen by cells incubated in anaerobic vessels in the absence of acetylene. In the presence of 0.01 atmospheres of acetylene, however, nitrous oxide was not reduced. Ethylene was not produced, nor did it influence the rate of nitrous oxide reduction when provided instead of acetylene. Cells exposed to 0.01 atmospheres of acetylene for as long as 400 min were able to reduce nitrous oxide after removal of acetylene at a rate comparable to that of cells not exposed to acetylene. Acetylene did not affect the production or functioning of assimilatory nitrate or nitrite reductase in axenic cultures of Enterobacter aerogenes or Trichoderma uride. While exposed to acetylene, bacteria in marine sediment slurries produced measurable quantities of nitrous oxide from glucose- or acetate-dependent reduction of added nitrate. Possible use of acetylene blockage for measurement of denitrification in unamended marine sediments is discussed.     

Fundamental denitrification kinetic studies with Pseudomonas denitrificans

Fundamental kinetic studies on the reduction of nitrate, nitrite, and their mixtures were performed with a strain of Pseudomonas denitrificans (ATCC 13867). Methanol served as the carbon source and was supplied in excess (2:1 mole ratio relative to nitrate and/or nitrite). Nitrate and nitrite served as terminal electron acceptors as well as sources of nitrogen for biomass synthesis. The results were explained under the assumption that respiration is a growth-associated process. It was found that the sequence of complete reduction of nitrate to nitrogen gas is via nitrite and nitrous oxide.It was found that the specific growth rate of the biomass on either nitrate or nitrite follows Andrews inhibitory kinetics and nitrite is more inhibitory than nitrate. It was also found that the culture has severe maintenance requirements which can be described by Herbert's model, i.e., by self-oxidation of portions of the biomass. The specific maintenance rates at 30 degrees C and pH 7.1 were found to be equal to about 28% of the maximum specific growth rate on nitrate and 23% of the maximum specific growth rate on nitrite. Nitrate and nitrite were found to be involved in a cross-inhibitory noncompetitive kinetic interaction. The extent of this interaction is negligible when the presence of nitrite is low but is considerable when nitrite is present at levels above 15 mg/L.Studies on the effect of temperature have shown that the culture cannot grow at temperatures above 40 degrees C. The optimal temperature for nitrate or nitrite reduction was found to be about 38 degrees C. Using an Arrhenius expression to describe the effect of temperature on the specific growth rates, it was found that the activation energy for the use of nitrate by the culture is 8.6 kcal/mol and 7.21 kcal/mol for nitrite. Arrhenius-type expressions were also used in describing the effect of temperature on each of the parameters appearing in the specific growth rate expressions. Studies on the effect of pH at 30 degrees C have shown that the culture reduces nitrate optimally at a pH between 7.4 and 7.6, and nitrite at a pH between 7.2 and 7.3. (c) 1995 John Wiley & Sons, Inc.     

Induction of a dissimilatory reduction pathway of nitrate in Halobacterium of the Dead Sea. A possible role for the 2 Fe-ferredoxin isolated from this organism

The processes involved in nitrate metabolism in Halobacterium of the Dead Sea are part of a dissimilatory pathway operating in these bacteria. The induction of both nitrate and nitrite reductases is shown to depend on the presence of nitrate and of anaerobic conditions. The gas products of the denitrification process were identified as nitrous oxide and nitrogen. Some properties of two of the enzymes involved in this process, nitrate and nitrite reductases, are reported. It is shown that the 2 Feferredoxin, which is present in large quantities in Halobacterium of the Dead Sea, can serve as an electron donor for nitrite reduction by nitrite reductase. It is suggested that the presence of a dissimilatory pathway for the reduction of nitrate in Halobacterium of the Dead Sea can be used as a tool for its classification.     

Dissimilatory nitrate reduction by Propionibacterium acnes

Propionibacterium acnes P13 was isolated from human feces. The bacterium produced a particulate nitrate reductase and a soluble nitrite reductase when grown with nitrate or nitrite. Reduced viologen dyes were the preferred electron donors for both enzymes. Nitrous oxide reductase was never detected. Specific growth rates were increased by nitrate during growth in batch culture. Culture pH strongly influenced the products of dissimilatory nitrate reduction. Nitrate was principally converted to nitrite at alkaline pH, whereas nitrous oxide was the major product of nitrate reduction when the bacteria were grown at pH 6.0. Growth yields were increased by nitrate in electron acceptor-limited chemostats, where nitrate was reduced to nitrite, showing that dissimilatory nitrate reduction was an energetically favorable process in P. acnes. Nitrate had little effect on the amounts of fermentation products formed, but molar ratios of acetate to propionate were higher in the nitrate chemostats. Low concentrations of nitrite (ca. 0.2 mM) inhibited growth of P. acnes in batch culture. The nitrite was slowly reduced to nitrous oxide, enabling growth to occur, suggesting that denitrification functions as a detoxification mechanism.     

Dissimilatory nitrate reduction by Propionibacterium acnes.

Propionibacterium acnes P13 was isolated from human feces. The bacterium produced a particulate nitrate reductase and a soluble nitrite reductase when grown with nitrate or nitrite. Reduced viologen dyes were the preferred electron donors for both enzymes. Nitrous oxide reductase was never detected. Specific growth rates were increased by nitrate during growth in batch culture. Culture pH strongly influenced the products of dissimilatory nitrate reduction. Nitrate was principally converted to nitrite at alkaline pH, whereas nitrous oxide was the major product of nitrate reduction when the bacteria were grown at pH 6.0. Growth yields were increased by nitrate in electron acceptor-limited chemostats, where nitrate was reduced to nitrite, showing that dissimilatory nitrate reduction was an energetically favorable process in P. acnes. Nitrate had little effect on the amounts of fermentation products formed, but molar ratios of acetate to propionate were higher in the nitrate chemostats. Low concentrations of nitrite (ca. 0.2 mM) inhibited growth of P. acnes in batch culture. The nitrite was slowly reduced to nitrous oxide, enabling growth to occur, suggesting that denitrification functions as a detoxification mechanism.     

Dissimilatory reduction of nitrate and nitrite in the bovine rumen: nitrous oxide production and effect of acetylene.

15N tracer methods and gas chromatography coupled to an electron capture detector were used to investigate dissimilatory reduction of nitrate and nitrite by the rumen microbiota of a fistulated cow. Ammonium was the only 15N-labeled end product of quantitative significance. Only traces of nitrous oxide were detected as a product of nitrate reduction; but in experiments with nitrite, up to 0.3% of the added nitrogen accumulated as nitrous oxide, but it was not further reduced. Furthermore, when 13NO3- was incubated with rumen microbiota virtually no [13N]N2 was produced. Acetylene partially inhibited the reduction of nitrite to ammonium as well as the formation of nitrous oxide. It is suggested that in the rumen ecosystem nitrous oxide is a byproduct of dissimilatory nitrite reduction to ammonium rather than a product of denitrification and that the latter process is absent from the rumen habitat.     

Denitrification by Actinomycetes and Purification of Dissimilatory Nitrite Reductase and Azurin from Streptomyces thioluteus

Many actinomycete strains are able to convert nitrate or nitrite to nitrous oxide (N₂O). As a representative of actinomycete denitrification systems, the system of Streptomyces thioluteus was investigated in detail. S. thioluteus attained distinct cell growth upon anaerobic incubation with nitrate or nitrite with concomitant and stoichiometric conversion of nitrate or nitrite to N₂O, suggesting that the denitrification acts as anaerobic respiration. Furthermore, a copper-containing, dissimilatory nitrite reductase (CuNir) and its physiological electron donor, azurin, were isolated. This is the first report to show that denitrification generally occurs among actinomycetes.     

The bioenergetics of denitrification

In anaerobically grown Paracoccus denitrificans the dissimilatory nitrate reductase is linked to the respiratory chain at the level of cytochromes b. Electron transport to nitrite and nitrous oxide involves c-type cytochromes. During electron transport from NADH to nitrate one phosphorylation site is passed, whereas two sites are passed during electron transport from NADH to oxygen, nitrite and nitrous oxide. The presentation of a respiratory chain as a linear array of electron carriers gives a misleading picture of the efficiency of energy conservation since the location of the reductases is not taken into account. For the reduction of nitrite and nitrous oxide, protons are utilized from the periplasmic space, whereas for the reduction of oxygen and nitrate, protons are utilized from the cytoplasmic side of the inner membrane. Evidence for two transport systems for nitrate was obtained. One is driven by the proton motive force; this system is used to initiate nitrate reduction. The second system is a nitrate-nitrite antiport system. A scheme for proton translocation and electron transport to nitrate, nitrite, nitrous oxide and oxygen is presented. The number of charges translocated across the membrane during flow of two electrons from NADH is the same for all nitrogenous oxides and is 67-71% of that during electron transfer to oxygen via cytochrome o. These findings are in accordance with growth yield studies. YMAX electron values determined in chemostat cultures for growth with various substrates and hydrogen acceptors are proportional to the number of charges translocated to these hydrogen acceptors during electron transport.