The expression of redox proteins of denitrification inThiosphaera pantotropha grown with oxygen,nitrate, and nitrous oxide as electron acceptors

The redox proteins and enzymes involved in denitrification inThiosphaera pantotropha exhibited a differential expression in response to oxygen. Pseudoazurin was completely repressed during batch or continuous culture under oxic conditions. Cytochromecd ₁ nitrite reductase was also heavily repressed after aerobic growth. Nitrite, nitric oxide, and nitrous oxide reductase activities were detected in intact cells under some conditions of aerobic growth, indicating that aerobic denitrification might occur in some circumstances. However, the rates of denitrification were much lower after aerobic growth than after anaerobic growth. Growth with nitrous oxide as sole electron acceptor mimicked aerobic growth in some respects, implying that expression of parts of the denitrification apparatus might be controlled by the redox state of a component of the electron transport chain rather than by oxygen itself. Nevertheless, the regulation of expression of nitrous oxide reductase was linked to the oxygen concentration.     

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.     

Heterotrophic nitrification and denitrification are the main sources of nitrous oxide in two paddy soils

Plant and Soil - Fusarium wilt (FW) is the major constraint on cape gooseberry (Physalis peruviana L.) production. Fungicides have been ineffective in disease control and alternative tools are not...     

High rates of denitrification and nitrous oxide emission in arid biological soil crusts from the Sultanate of Oman

Using a combination of process rate determination, microsensor profiling and molecular techniques, we demonstrated that denitrification, and not anaerobic ammonium oxidation (anammox), is the major nitrogen loss process in biological soil crusts from Oman. Potential denitrification rates were 584±101 and 58±20 μmol N m⁻² h⁻¹ for cyanobacterial and lichen crust, respectively. Complete denitrification to N₂ was further confirmed by an ¹⁵NO₃⁻ tracer experiment with intact crust pieces that proceeded at rates of 103±19 and 27±8 μmol N m⁻² h⁻¹ for cyanobacterial and lichen crust, respectively. Strikingly, N₂O gas was emitted at very high potential rates of 387±143 and 31±6 μmol N m⁻² h⁻¹ from the cyanobacterial and lichen crust, respectively, with N₂O accounting for 53–66% of the total emission of nitrogenous gases. Microsensor measurements revealed that N₂O was produced in the anoxic layer and thus apparently originated from incomplete denitrification. Using quantitative PCR, denitrification genes were detected in both the crusts and were expressed either in comparable (nirS) or slightly higher (narG) numbers in the cyanobacterial crusts. Although 99% of the nirS sequences in the cyanobacterial crust were affiliated to an uncultured denitrifying bacterium, 94% of these sequences were most closely affiliated to Paracoccus denitrificans in the lichen crust. Sequences of nosZ gene formed a distinct cluster that did not branch with known denitrifying bacteria. Our results demonstrate that nitrogen loss via denitrification is a dominant process in crusts from Oman, which leads to N₂O gas emission and potentially reduces desert soil fertility.     

Dinitrogen and nitrous oxide produced by denitrification and nitrification in soil with and without barley plants

Summary To examine the effect of barley roots on denitrification, a pot experiment was designed to compare N₂O production and denitrification in soils with and without barley plants. Denitrification, N₂O resulting from denitrification and nitrification, and respiration were estimated by incubating pots with soil with and without intact plants in plastic bags at high moisture levels. C₂H₂-inhibition of nitrous oxide reductase (partial pressure of 10 kPa C₂H₂) was used to determine total denitrification rates while incubations with ambient air and with C₂H₂ at partial pressures of 2.5–5 Pa were used to estimate the amounts of N₂O released from autotrophic nitrification and from denitrification processes. Other sources of N₂O were presumed to be negligible. Potential denitrification, nitrification and root biomass were measured in subsamples collected from four soil depths. A positive correlation was found between denitrification rates and root biomass. N₂ was the predominant denitrification product found close to roots; N₂O formed by non autotrophic nitrifiers, assumed to be denitrifiers originated in soil not affected by growing roots. Apparently, roots promote denitrification because they consumed oxygen, thereby increasing the anaerobic volume of the soil. The ratio of actual to potential denitrification rates increased over time, especially in the presence of roots.     

Studies on the differential inhibition by azide on the nitrite/nitrous oxide level of denitrification.

A gas chromatographic method was used to demonstrate that nitrite can counteract the inhibition by azide of nitrous oxide reductase activity in denitrifiers. This effect explains why azide (and cyanide) can inhibit nitrogen production from nitrous oxide in these organisms but have little effect on nitrogen production from nitrite. Although the physiological basis by which nitrite opposes the action of azide remains unknown, extensive destruction of azide by nitrite can be ruled out as an explanation.     

Studies on the differential inhibition by azide on the nitrite/nitrous oxide level of denitrification.

A gas chromatographic method was used to demonstrate that nitrite can counteract the inhibition by azide of nitrous oxide reductase activity in denitrifiers. This effect explains why azide (and cyanide) can inhibit nitrogen production from nitrous oxide in these organisms but have little effect on nitrogen production from nitrite. Although the physiological basis by which nitrite opposes the action of azide remains unknown, extensive destruction of azide by nitrite can be ruled out as an explanation.     

Distinguishing nitrous oxide production from nitrification and denitrification on the basis of isotopomer abundances

The intramolecular distribution of nitrogen isotopes in N2O is an emerging tool for defining the relative importance of microbial sources of this greenhouse gas. The application of intramolecular isotopic distributions to evaluate the origins of N2O, however, requires a foundation in laboratory experiments in which individual production pathways can be isolated. Here we evaluate the site preferences of N2O produced during hydroxylamine oxidation by ammonia oxidizers and by a methanotroph, ammonia oxidation by a nitrifier, nitrite reduction during nitrifier denitrification, and nitrate and nitrite reduction by denitrifiers. The site preferences produced during hydroxylamine oxidation were 33.5 +/- 1.2 per thousand, 32.5 +/- 0.6 per thousand, and 35.6 +/- 1.4 per thousand for Nitrosomonas europaea, Nitrosospira multiformis, and Methylosinus trichosporium, respectively, indicating similar site preferences for methane and ammonia oxidizers. The site preference of N2O from ammonia oxidation by N. europaea (31.4 +/- 4.2 per thousand) was similar to that produced during hydroxylamine oxidation (33.5 +/- 1.2 per thousand) and distinct from that produced during nitrifier denitrification by N. multiformis (0.1 +/- 1.7 per thousand), indicating that isotopomers differentiate between nitrification and nitrifier denitrification. The site preferences of N2O produced during nitrite reduction by the denitrifiers Pseudomonas chlororaphis and Pseudomonas aureofaciens (-0.6 +/- 1.9 per thousand and -0.5 +/- 1.9 per thousand, respectively) were similar to those during nitrate reduction (-0.5 +/- 1.9 per thousand and -0.5 +/- 0.6 per thousand, respectively), indicating no influence of either substrate on site preference. Site preferences of approximately 33 per thousand and approximately 0 per thousand are characteristic of nitrification and denitrification, respectively, and provide a basis to quantitatively apportion N2O.     

Nitrate respiration,denitrification, and utilization of nitrogen sources by aerobic carbon monoxide-oxidizing bacteria

We describe the ability of carboxydotrophic bacteria for nitrate respiration or denitrification. Four out of fourteen strains examined could denitrify heterotrophically forming N₂ (Pseudomonas carboxydoflava) or N₂O (Pseudomonas carboxydohydrogena, Pseudomonas compransoris, and Pseudomonas gazotropha). Three carried out a heterotrophic nitrate respiration (Arthrobacter 11/x, Azomonas B1, and Azomonas C2). P. carboxydohydrogena could use H₂ as electron donor for nitrate respiration under chemolithoautotrophic growth conditions. CO did not support denitrification or nitrate respiration of carboxydotrophic bacteria, although the free energy changes of the reactions would be sufficiently negative to allow growth. CO at 50 kPa was a weak inhibitor of N₂O-reduction in carboxydotrophic and non-carboxydotrophic bacteria and decelerated denitrifying growth. Carboxydotrophic bacteria could utilize a wide range of N-sources. Results obtained with a plasmid-cured mutant of Pseudomonas carboxydovorans OM5 showed, that genes involved in nitrogen assimilation entirely reside on the chromosome. In the presence of an suitable electron donor, most carboxydotrophic bacteria could carry out a reduction of nitrate to nitrite that did not support growth and did not lead to the formation of ammonia.This article is dedicated to Professor Hans G. Schlegel on the occasion of his 65th birthday and in admiration for his élan and eternal idealism     

Shell biofilm nitrification and gut denitrification contribute to emission of nitrous oxide by the invasive freshwater mussel Dreissena polymorpha (zebra mussel)

Nitrification in shell biofilms and denitrification in the gut of the animal accounted for N(2)O emission by Dreissena polymorpha (Bivalvia), as shown by gas chromatography and gene expression analysis. The mussel's ammonium excretion was sufficient to sustain N(2)O production and thus potentially uncouples invertebrate N(2)O production from environmental N concentrations.     

Suppression of nitrification and nitrous oxide emission by the tropical grass Brachiaria humidicola

Nitrification by soil nitrifiers may result in substantial losses of applied nitrogen through NO₃ ^– leaching and N₂O emission. The biological inhibition of nitrification by crop plants or pasture species is not well known. This study was conducted to evaluate the ability of three pasture species, Brachiaria humidicola, B. decumbens and Melinis minutiflora to inhibit nitrification. Plants were grown in a growth chamber for sixty days, fertilized with (NH₄)₂SO₄. After harvesting, the soil was incubated with (NH₄)₂SO₄ for 24 days. Ammonium oxidizing bacteria (AOB), NH₄-N levels, and N₂O emission were monitored at 4 d intervals. Among the species studied, B. humidicola inhibited nitrification and maintained NH₄-N in soil to a much greater extent than the other two species. This nitrification inhibition lasted for 12 days after initiation of soil incubation study (i.e. from 60 DAS when the plants were harvested). The AOB populations and N₂O emission from the soil were significantly lower in the soils where B. humidicola has been grown compared to the other two species. Root exudates and soil extracts of B. humidicola suppressed AOB populations, whereas those of B. decumbens and M. minutiflora did not. The results are in consistence with the hypothesis that B. humidicola suppressed nitrification and N₂O emissions through an inhibitory effect on the AOB population.     

Effects of oxygen concentration and moisture content of refuse on nitrification,denitrification and nitrous oxide production

The purposes of this study were to evaluate the potential production of nitrous oxide (N₂O), which is known as a greenhouse gas, to identify the reaction responsible for it and to examine the effects of oxygen and moisture content on nitrification, denitrification and N₂O production. Applying a tracer method using a ¹⁵N-isotope into an oxygen controllable reactor with artificial refuse proved that biological denitrification was a main source of released N₂O even when the oxygen of the bulk atmosphere was as high as 15%. Calculating the mass balance for nitrogenous compounds showed that only denitrification occurred as the sole microbial process when the bulk oxygen was 0–5%. With increasing oxygen above 5% nitrification also began to occur simultaneously with denitrification. As the bulk space of the refuse became aerobic, the total amount of N₂ produced from denitrification decreased but the proportion of N₂O in the (N₂ + N₂O) increased. Denitrification was the main source of released N₂O when the moisture content was between 40–60% and oxygen 10%. The amounts of nitrification, denitrification and N₂ production increased as the moisture content increased.     

Losses of inorganic carbon and nitrous oxide from a temperate freshwater wetland in relation to nitrate loading

We studied the export of inorganic carbon and nitrous oxide (N₂O) from a Danish freshwater wetland. The wetland is situated in an agricultural catchment area and is recharged by groundwater enriched with nitrate (NO₃ ^–) (1000 M). NO₃ ^– in recharging groundwater was reduced (57.5 mol NO₃ ^– m^–2 yr^–) within a narrow zone of the wetland. Congruently, the annual efflux of carbon dioxide (CO₂) from the sediment was 19.1 mol C m^–2 when estimated from monthly in situ measurements. In comparison the CO₂ efflux was 4.8 mol C m^–2 yr^–1 further out in the wetland, where no NO₃ ^– reduction occurred. Annual exports of inorganic carbon in groundwater and surface water was 78.4 mol C m^–2 and 6.1 mol C m^–2 at the two sites, respectively. N₂O efflux from the sedimenst was detectable on five out of twelve sampling dates and was significantly (P < 0.0001) higher in the NO₃ ^– reduction zone (0.35–9.40 mol m^–2 h^–1, range of monthly means) than in the zone without NO₃ ^– reduction (0.21–0.41 mol m^–2 h^–1). No loss of dissolved N₂O could be measured. Total annual export of N₂O was not estimated. The reduction of oxygen (O₂) in groundwater was minor throughout the wetland and did not exceed 0.2 mol 0₂ m^–2yr^–1. Sulfate (SO₄ ^––) was reduced in groundwater (2.1 mol SO₄ ^–– m^–2 yr^–1) in the zone without NO₃ ^– reduction. Although the NO₃ ^– in our wetland can be reduced along several pathways our results strongly suggest that NO₃ ^– loading of freshwater wetlands disturb the carbon balance of such areas, resulting in an accelerated loss of inorganic carbon in gaseous and dissolved forms.     

The tetranuclear copper active site of nitrous oxide reductase: the CuZ center

This review focuses on the novel CuZ center of nitrous oxide reductase, an important enzyme owing to the environmental significance of the reaction it catalyzes, reduction of nitrous oxide, and the unusual nature of its catalytic center, named CuZ. The structure of the CuZ center, the unique tetranuclear copper center found in this enzyme, opened a novel area of research in metallobiochemistry. In the last decade, there has been progress in defining the structure of the CuZ center, characterizing the mechanism of nitrous oxide reduction, and identifying intermediates of this reaction. In addition, the determination of the structure of the CuZ center allowed a structural interpretation of the spectroscopic data, which was supported by theoretical calculations. The current knowledge of the structure, function, and spectroscopic characterization of the CuZ center is described here. We would like to stress that although many questions have been answered, the CuZ center remains a scientific challenge, with many hypotheses still being formed.     

Mesaconyl-coenzyme A hydratase, a new enzyme of two central carbon metabolic pathways in bacteria

The coenzyme A (CoA)-activated C5-dicarboxylic acids mesaconyl-CoA and beta-methylmalyl-CoA play roles in two as yet not completely resolved central carbon metabolic pathways in bacteria. First, these compounds are intermediates in the 3-hydroxypropionate cycle for autotrophic CO2 fixation in Chloroflexus aurantiacus, a phototrophic green nonsulfur bacterium. Second, mesaconyl-CoA and beta-methylmalyl-CoA are intermediates in the ethylmalonyl-CoA pathway for acetate assimilation in various bacteria, e.g., in Rhodobacter sphaeroides, Methylobacterium extorquens, and Streptomyces species. In both cases, mesaconyl-CoA hydratase was postulated to catalyze the interconversion of mesaconyl-CoA and beta-methylmalyl-CoA. The putative genes coding for this enzyme in C. aurantiacus and R. sphaeroides were cloned and heterologously expressed in Escherichia coli, and the proteins were purified and studied. The recombinant homodimeric 80-kDa proteins catalyzed the reversible dehydration of erythro-beta-methylmalyl-CoA to mesaconyl-CoA with rates of 1,300 micromol min(-1) mg protein(-1). Genes coding for similar enzymes with two (R)-enoyl-CoA hydratase domains are present in the genomes of Roseiflexus, Methylobacterium, Hyphomonas, Rhodospirillum, Xanthobacter, Caulobacter, Magnetospirillum, Jannaschia, Sagittula, Parvibaculum, Stappia, Oceanicola, Loktanella, Silicibacter, Roseobacter, Roseovarius, Dinoroseobacter, Sulfitobacter, Paracoccus, and Ralstonia species. A similar yet distinct class of enzymes containing only one hydratase domain was found in various other bacteria, such as Streptomyces species. The role of this widely distributed new enzyme is discussed.     

Diurnal patterns of denitrification, oxygen consumption and nitrous oxide production in rivers measured at the whole-reach scale

1. Denitrification, net oxygen consumption and net nitrous oxide flux to the atmosphere were measured in three small rivers (discharge approximately 2–27 m³ s^?1) at the whole reach scale during Spring and Summer, 2002. Two of these rivers (Iroquois River and Sugar Creek in north‐west Indiana – north‐east Illinois, U.S.A.) drained agricultural catchments and the other (Millstone River in central New Jersey, U.S.A.) drained a mixed suburban–agricultural catchment. 2. Denitrification, oxygen consumption and N₂O flux were measured based on net changes in dissolved gas concentrations (N₂, O₂, and N₂O) during riverine transport, correcting for atmospheric exchange. On each date, measurements were made during both light and dark periods. 3. Denitrification rates in these rivers ranged from 0.31 to 15.91 mmol N m^?2 h^?1, and rates within each river reach were consistently higher during the day than during the night. This diurnal pattern could be related to cyclic patterns of nitrification driven by diurnal variations in water column pH and temperature. 4. Oxygen consumption ranged from 2.56 to 241 mmol O₂ m^?2 h^?1. In contrast to denitrification, net oxygen consumption was generally higher during the night than during the day. 5. River water was consistently supersaturated with N₂O, ranging from 102 to 209% saturated. Net flux of N₂O to the atmosphere ranged from 0.4 to 60 μmol N m^?2 h^?1. Net flux of N₂O was generally higher at night than during the day. The high flux of N₂O from these rivers strengthens the argument that rivers are an important contributor to anthropogenic emissions of this greenhouse gas.     

Inability of Pseudomonas stutzeri denitrification mutants with the phenotype of Pseudomonas aeruginosa to grow in nitrous oxide

Pseudomonas aeruginosa PAO1 reduced nitrous oxide to dinitrogen but did not grow anaerobically in nitrous oxide. Two transposon insertion Nos- mutants of Pseudomonas stutzeri exhibited the P. aeruginosa phenotype. Growth yield studies demonstrated that nitrous oxide produced in vivo was productively respired, but nitrous oxide supplied exogenously was not. The defect may be in electron transport or in nitrous oxide uptake.