In denitrification, bacteria use NO- as electron acceptor, usually in the absence of oxygen. As such, denitrification could be considered as a way of breathing under low oxygen conditions. The bacteria involved first reduce NO3- to nitrite (NO2-), and then to NO, N2O and/or N2 (Fig. 15.1). Denitrification is the largest natural source of atmospheric N2O. Most N2O formed during denitrifica-tion will, however, never reach the atmosphere, because bacteria reduce it to N2 in the last step.
Denitrification is an anaerobic, micro-bially mediated process that, in most aquatic and sedimentary environments, is coupled to the oxidation of organic matter. Only in groundwater systems, pyrite (FeS2) and other Fe2+-containing minerals may also act as an important electron donor (Appelo and Postma, 1993). If NO- is low or absent, denitrifying organisms are able to use only N2O as an electron acceptor (Butterbach-Bahl et al., 1998).
The capacity to denitrify with reactive organic carbon as an electron donor is widespread among different types of facultative anaerobic bacteria. However, only a few genera are abundantly present in soils, sediments, marine water and freshwater such as the Pseudomonas and Alcaligenes species (Tiedje, 1988). The organisms responsible for denitrification coupled to pyrite oxidation may involve species of Thiobacillus and Gallionella (e.g. Appelo and Postma, 1993). Generally, it can be assumed that if sufficient electron donors - either as organic carbon or pyrite - and nitrogen oxides are present in a low-oxygen environment, bacteria with the appropriate metabolic capability will occupy the denitrification niche. All denitri-fiers in natural environments are assumed to be capable of the complete denitrification sequence resulting in N2 as the final product (Firestone and Davidson, 1989).
The key factors limiting rates of denitrifi-cation vary from environment to environment. Most surface soils, particularly fertilized soils, contain sufficient organic carbon and NO-, and the presence of oxygen most commonly limits denitrification. The same generally holds true for the water column of lakes and the oceans. In aquatic sediments, oxygen penetration is strongly diffusion-limited and the availability of NO3-, NO and N2O is generally the limiting factor (Firestone and Davidson, 1989). In contrast, electron donor availability often controls denitrification rates in many groundwater systems. As a consequence, plumes of NO3- and/ or N2O-containing groundwater may persist in an oxygen-depleted environment (DeSimone and Howes, 1998; Groffman et al., 1998). Riparian zones are an exception because of the relatively large input of organic matter. This often allows for efficient removal of NO3- from groundwater, prior to discharge to surface waters (Vidon and Hill, 2004). This removal of NO3- may be accompanied by significant N2O production (Hefting et al., 2003).
In soils, denitrification is extremely variable in space and time. This makes it difficult to accurately measure rates of denitrification (Hofstra and Bouwman, in press; Parkin, 1990) and N2O exchange (Lapitan et al., 1999) in the field. This variability is related to the microscale (millimetre to centimetre) inhomogeneity of well-drained soils caused by the presence of, for example, earthworm castings, particles of decomposing organic matter and soil aggregates. The outside of organic carbon-rich particles and aggregates is oxic and can support high rates of nitrification while denitrification occurs in the suboxic interior (Parkin, 1987). These microsites explain why denitrification can occur even in well-drained soils.
NO3- production in soils (nitrification) occurs only under aerobic conditions. The oxygen status and thus coupled nitrification-denitrification in soils can change rapidly depending upon soil moisture and the consequent rate of oxygen diffusion through soils (Tiedje, 1988). An example of the rapid changes in denitrification with changing oxygen status is the pulse of soil denitrification often seen after episodic rainfall or irrigation events (Rolston et al., 1982; Ryden, 1983; Sexstone et al., 1985; Van Kessel et al., 1993). If anoxic conditions persist until NO3- is depleted, soil denitrifiers may become limited by NO3-.
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