Dissimilatory denitrification

Figure 2 The dissimilatory denitrification pathway. NO3 is reduced to NO2 by a membrane-bound or periplasmic nitrate reductase(NaR). N02 is reduced to NO by either a cytochrome cdi or copper nitrite reductase (NiR). NO is reduced to N2O by nitric oxide reductase (NOR). N2O is reduced to N2 by nitrous oxide reductase (N2OR). Electron transport from uhiquinol (UQH2) at NaR and the cyt hcj complex is coupled to generation of a proton gradient...

There are two types of dissimilatory denitrification that are considered here. The first is denitrification that takes place during the chemoautotrophic process of nitrification. Nitrification is the sequential oxidation of to N02, which is... 

Figure 3. The general nitrogen model for illustrating the bio geochemical cycling in Forest ecosystems. Explanations for the fluxes 1, ammonia volatilization 2, forest fertilization 3, N2-fixation 4, denitrification 5, nitrate respiration 6, nitrification 7, immobilization 8, mineralization 9, assimilatory and dissimilatory nitrate reduction to ammonium 10, leaching 11, plant uptake 12, deposition N input 13, residue composition, exudation 14, soil erosion 15, ammonium fixation and release by clay minerals 16, biomass combustion 17, forest harvesting 18, litterfall (Bashkin, 2002).

Denitrification, a dissimilatory pathway of nitrate reduction (see Section 3.3 also) into nitrogen oxides, N2O, and dinitrogen, N2, is performed by a wide variety of microorganisms in the forest ecosystems. Measurable rates of N20 production have been observed in many forest soils. The values from 2.1 to 4.0 kg/ha/yr are typical for forest soils in various places of Boreal and Sub-Boreal Forest ecosystems. All in situ studies (field monitoring) of denitrification in forest soils have shown large spatial and temporal variability in response to varying soils characteristics such as acidity, temperature, moisture, oxygen, ambient nitrate and available carbon. 

At this site in the eastern tropical North Pacific, denitrification is responsible fiar the midwater loss of nitrate and production of nitrite. The size of the secondary nitrite maximum is dependent on the relative rates of its production from NO3 and its loss via dissimilatory reduction to N2. The amount of nitrate lost to denitrification is shown as the difference between the measured nitrate and the calculated nitrate. The latter was estimated by multiplying the observed phosphate concentrations by the average nitrate-to-phosphate ratio in the three deepest samples (11.9 1.6pmolN/L). Note that the zone of denitrification is restricted to mid-depths, i.e., the depths of the OMZ at this site. 

Figure 4.1 shows that NOs" is the stable form of nitrogen over the usual range of pe + pH in aerobic environments. The fact that most of the N2 in the atmosphere has not been converted to NO3 therefore indicates that the biological mediation of this conversion in both directions is inefficient. Hence NO3 reduction to N2 occurs by indirect mechanisms involving intermediaries. Dissimilatory reduction of N03 (i.e. where the nitrogen oxide serves as an electron acceptor for the cell s metabolism but the N reduced is not used by the microbes involved) potentially occurs by two processes denitrification. 

As discussed in Chapter 5, in submerged soils nitrification occurs in aerobic sites at the iloodwater-soil and root-soil interfaces. Denitrification occurs upon diffusion of the NO, to the anaerobic bulk soil. Denitrification is favoured over dissimilatory reduction to NH4+(NO, -> NO2 NH4+) because of the large ratio of available carbon to electron acceptors in submerged soils. Denitrification is likely to proceed completely to N2 with little accumulation of N2O because of the very large sink and therefore steep concentration gradient of O2, and because carbon is less likely to be limiting (Section 5.1). 

Tiedje, ]. M. (1988). Ecology of denitrification and dissimilatory nitrate reduction to ammonia. In Biology of Anaerobic Microorganisms (A. J. B. Zehnder, ed.). pp. 179-244. Wiley, New York. 

Bacterial assimilatory nitrate reductases have similar properties.86/86a In addition, many bacteria, including E. coli, are able to use nitrate ions as an oxidant for nitrate respiration under anaerobic conditions (Chapter 18). Tire dissimilatory nitrate reductases involved also contain molybdenum as well as Fe-S centers.85 Tire E. coli enzyme receives electrons from reduced quinones in the plasma membrane, passing them through cytochrome b, Fe-S centers, and molybdopterin to nitrate. The three-subunit aPy enzyme contains cytochrome b in one subunit, an Fe3S4 center as well as three Fe4S4 clusters in another, and the molybdenum cofactor in the third.87 Nitrate reduction to nitrite is also on the pathway of denitrification, which can lead to release of nitrogen as NO, NzO, and N2 by the action of dissimi-latory nitrite reductases. These enzymes873 have been discussed in Chapters 16 and 18. 

Ammonia is oxidized in nature to nitrate via several intermediates in the process of nitrification. Nitrate may be reduced to nitrite by either a dissimilatory or an assimilatory process. Nitrite may be assimilated into the cell via reduction to ammonia, or it may be reduced by microorganisms to N20 and N2 in denitrification. A major part of the total nitrogen in this pathway is lost to the atmosphere. However, in turn, atmospheric dinitrogen is converted to ammonia by various bacteria in nitrogen fixation. 

As noted in Section 62.1.9.6, reduction of nitrate may occur by assimilatory or dissimilatory pathways. In the former case, the nitrate produced is reduced further to ammonia, which is incorporated into the cell. In the latter case, nitrate is reduced anaerobically to nitrite, serving as an electron acceptor in the respiration of facultative or a few obligate anaerobic bacteria. The example of Escherichia coli has been considered in Section 62.1.13.4.3. This process is usually terminated at nitrite, which accumulates around the cells, but may proceed further1511 as nitrite-linked respiration in the process of denitrification. 

Figure 10.5 Major processes involved in the biogeochemical cycling of N in estuaries and the coastal ocean (1) biological N2 fixation (2) ammonia assimilation (3) nitrification (4) assimilatory NC>3 reduction (5) ammonification or N remineralization (6) ammonium oxidation (speculative at this time) (7) denitrification and dissimilatory NO3 reduction to NH4+ and (8) assimilation of dissolved organic nitrogen (DON). (Modified from Libes, 1992.)...

Dissimilatory NO3- reduction to NH4+ pathway similar to denitrification only with more N being retained in a system. 

An, S., and Gardner, W.S. (2002) Dissimilatory nitrate reduction to ammonium (DNRA) as a nitrogen link, versus denitrification as a sink in a shallow estuary (Laguna Madre/Baffin Bay, Texas). Mar. Ecol. Prog. Ser. 237, 41-50. 

This chapter focuses on the chemistry ofbiomimetic copper nitrosyl complexes relevant to the NO-copper interactions in proteins that are central players in dissimilatory nitrogen oxide reduction (denitrification). The current state of knowledge of NO-copper interactions in nitrite reductase, a key denitrifying enzyme, is briefly surveyed the syntheses, structures, and reactivity of copper nitrosyl model complexes prepared to date are presented and the insight these model studies provide into the mechanisms of denitrification and the structures of other copper protein nitrosyl intermediates are discussed. Emphasis is placed on analysis of the geometric features, electronic structures, and biomimetic reactivity with NO or NOf of the only structurally characterized copper nitrosyls, a dicopper(II) complex bridged by NO and a mononuclear tris(pyrazolyl)hydroborate complex having a Cu(I)-NO formulation. 

Two types of dissimilatory nitrate reductases, localized in either the cytoplasmic membrane or the periplasm, are widespread among bacteria. The cytoplasmic membrane-bound nitrate reductase (Nar) catalyzes the first steps of denitrification (NOs" N02 NO N2O... 

Binnerup, S.J., Jensen, K., Revsbech, N. P., Jensen, M. H., and Sorensen, J. (1992). Denitrification, dissimilatory reduction of nitrate to ammonium, and nitrification in a bioturbated estuarine sediment as measured with N-15 and microsensor techniques. Applied and Environmental Microbiology 58, 303-313. 

Christensen, P. B., Rysgaard, S., Sloth, N. P., Dalsgaard, T., and Schwaerter, S. (2000). Sediment mineralization, nutrient fluxes, denitrification and dissimilatory nitrate reduction to ammonium in an estuarine ord with sea cage trout farms. Aquat. Microb. Ecol. 21(1), 73—84. 

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