Dissimilatory nitrogen oxide reduction denitrification

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. 

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. 

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. 

Figure 12 Major reduction-oxidation reactions involving nitrogen. The reactions are numbered as follows (1) mineralization, (2) ammonium assimilation, (3) nitrification, (4) assimilatory or dissimilatory nitrate reduction, (5) ammonium oxidation, (6) nitrite oxidation, (7) assimilatory or dissimilatory nitrate reduction, (8) assimilatory or dissimilatory nitrite reduction, (9) denitrification, (10) chemodenitrification, (11) anaerobic ammonium oxidation, and (12) dinitrogen fixation (after Capone, 1991) (reproduced by permission of ASM Press from Microbial Production and Consumption of Greenhouse Gases Methane, Nitrogen Oxides, and Halomethanes, 1991).

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. 

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.)...

Figure 21.1 Microbial nitrogen cycling processes in sedimentary environments on a coral reef (A) nitrogen fixation (B) ammonification (C) nitrification (D) dissimilatory nitrate reduction and denitrification (E) assimilatory nitrite/nitrate reduction (F) ammonium immobilization and assimilation. Adapted from D Elia and Wiebe (1990). Anammox (the anaerobic oxidation of NH4" with NO2 yielding N2 ) is not represented, as it has not yet been shown to occur on coral reefs, but may be found to be important in reef sediments.

In contrast, many gram-negative bacteria contain a nitrate reductase (EC 1.7.99.4 and/or 1.9.6.1) that also reduces nitrate to nitrite although under anaerobic conditions. The dissimilatory nitrite reduction leading to denitrification encompasses then the reduction of nitrite to nitric oxide by dissimilatory nitrite reductases (NiR, EC 1.7.2.1) that, in combination with nitric oxide reductases (NOR) and nitrous oxide reductases (N2OR), transform nitrite into nitrogen ... 

Denitrification in the strict sense involves the dissimilatory reduction, by essentially aerobic bacteria, of nitrate or nitrite to the gaseous oxides (nitric oxide, NO, and nitrous oxide, N2O), which may themselves be further reduced to nitrogen (Nj). Denitrification does not include assimilation of these ions by plants or microorganisms or loss by leaching. The products of denitrification are not assimilable by higher plants and most microorganisms, and thus this process is deleterious to soil fertility [1, 27]. 

FIGURE 8.5 Oxidation and reduction reactions of nitrogen in wetlands. Numbers 1-7 refer to pathways of nitrogen reactions. 1 = ammonification 2 = immobilization 3 = nitrification 4 = denitrification 5 = dissimilatory nitrate reduction to ammonia 6 = dinitrogen fixation and 7 = ammonia volatilization. 

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