Bacteria denitrification pathway

Sigman et al. [134] have described a bacterial method for measuring the isotopic composition of seawater nitrate at the natural-abundance level. The method is based on the analysis of nitrous oxide gas (N2O) produced quantitatively from nitrate by denitrifying bacteria. The classical denitrification pathway consists of the stepwise reduction of nitrate (NOp to nitrite (N02), nitric oxide (NO), nitrous oxide (N2O), and dinitrogen (N2) ... 

As will be discussed further in this chapter, there is now much evidence to suggest that NO is an obligatory intermediate in the denitrification pathway. Furthermore, there is evidence that NH3 nitrifiers can synthesize the denitrification apparatus in addition to the nitrification apparatus and that the former system can produce NO and N2O (also N2 in at least one case) from nitrite under low partial pressures of O2. It is possible therefore that NO may be an intermediate in the denitrification activity of nitrifiers and so arise as a secondary consequence of NH3 oxidation. NO can also be ptoduced by nondenitrifying organisms under certain conditions. For example, NO can be slowly produced by the anaerobic reduction of nitrite, but only in absence of nitrate, by a variety of enteric bacteria. Some of the NO can be further reduced to N2O. 

Nitric oxide reductase (Nor) forms part of the denitrification pathway found in Bacteria and Archaea. Denitrification is the five-step conversion of nitrate to dinitrogen according to NOs N02 NO N2O N2. Nor catalyzes the reaction,... 

Many bacterial genera contain denitrifying species Achromobacter, Alcaligenes (Alcaligenes odorans denitrifies nitrite). Bacillus, Chromobacterium, Coryne-bacterium, Halobacterium, Hyphomicrobium, Morax-ella, Paracoccus, Pseudomonas, Spirillum, Thiobacil-lus and Xanthomonas. In some species of Pseudomonas and Corynebacterium, N O is the final denitrification product. All these bacteria are aerobes that are able to respire (denitrify) nitrate under anaerobic conditions. The only true anaerobe able to carry out denitrification is Propionibacterium. There is no evidence for other intermediates in the above denitrification pathway, but in the formation of nitrous oxide (NjO) an NN bond must be formed, and there may exist transient enzyme-bound intermediates that have not yet been identified. The enzymology of denitrification from nitrite is poorly understood. It seems likely that each stage is linked to electron transport via a cytochrome system, but sites of ATP synthesis have not been unequivocally located. 

O-exchange studies of Ye et al. (1991) support, we believe, the catalysis by nitrite reductase of redox reversibility between nitrite and NO as depicted in the first line of Eq. (3). They observed by analyzing the 0 content of product N2O that all eight strains of denitrifying bacteria studied could catalyze the exchange of 0 between water and nitrite or NO by way of an electrophilic (nitrosyl donor) species of NO. The rates and extent of these exchange reactions depended on whether the bacterium made use of a heme- or Cu-type nitrite reductase. Contrary to the conclusions of Ye et al. (1991), we do not believe that this study otherwise informs about the pathway of denitrification or whether NO is an intermediate. 

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. 

Nitrifying bacteria are traditionally considered to be obligate aerobes they require molecular oxygen for reactions in the N oxidation pathways and for respiration. They are reputed to be microaerophiles, however, who thrive best under relatively low oxygen conditions. Microaerophily may be important in interface environments such as the sediment water interface and in the oxygen minimum zones of the ocean. The role of oxygen in sedimentary nitrification and coupled nitrification/ denitrification is discussed above in the section on nitrification in sediments. 

There are two pathways of dissimilatory nitrate reduction, generally thought to be mediated by anaerobic, or facultatively anaerobic bacteria, using NOs" as a terminal electron acceptor in respiration (Fig. 21.ID and F) (see Chapter 6, Devol, this volume). One pathway leads to production of ammonium, and may act as an internal cychng loop within the system (D Elia and Wiebe, 1990). The other pathway, denitrification, ends in production of N2O and/or N2 gas, which can then be lost from the system to the atmosphere. 

Chemoautotrophic denitrification coupled to H2S, S°, or 8203 occurs in some bacteria of the genus Thiobacillus such as T. denitrificans (Hoor, 1981 Section 8.08.7.9). Nitrate reduction by such a pathway increased with FeS additions and followed Michaelis-Menten kinetics in a marine sediment (Garcia-Gil and Golterman, 1993). 

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