Environmental Controls Of Denitrification

For decades after its discovery as an important microbial process, denitrifica-tion was assumed to be important only in aquatic and wetland ecosystems. It was not until the advent of whole-ecosystem N budgets and the use of 15N to trace the fate of fertilizer N in the 1950s that denitrification was found to be important in unsaturated soils. These studies suggested the importance of denitrification in fertilized agricultural soils, and with the development of the acetylene block technique in the 1970s the importance of denitrification in even forest and grassland soils was confirmed. Acetylene selectively inhibits nitrous oxide reductase (nos; see Fig. 13.7), allowing the assessment of N2 production by following N2O accumulation in a soil core or monolith treated with acetylene. Unlike N2, small changes in N2O concentration are easily detected in air.

Today, denitrification is known to be an important N cycle process wherever O2 is limiting. In unsaturated soils, this frequently occurs within soil aggregates, in decomposing plant litter, and in rhizospheres. Soil aggregates vary widely in size but in general are composed of small mineral particles and pieces of organic matter <2 mm diameter that are glued to one another with biologically derived polysaccharides. Like most particles in soil, aggregates are surrounded by a thin water film that impedes gas exchange. Modeling efforts in the 1970s and 1980s suggested that the centers of these aggregates ought to be anaerobic owing to a higher respiratory demand in the aggregate center than could be satisfied by O2 diffusion from the bulk soil atmosphere. This was confirmed experimentally in 1985 (Sexstone et al., 1985), providing a logical explanation for active denitrification in soils that appeared otherwise to be aerobic, and an explanation for the almost universal presence of denitrifiers and denitrification enzymes in soils worldwide.

In addition to O2, denitrification is also regulated by soil C and NO—. C is important because most denitrifiers are heterotrophs and require reduced C as the electron donor, although as noted earlier, denitrifiers can also be chemo- and photo-lithotrophs. Nitrate serves as the electron acceptor and must be provided via nitrification, rainfall, or fertilizer. However, O2 is the preferred electron acceptor because of its high energy yield, and thus must be depleted before denitrification occurs. In most soils the majority of denitrifiers are facultative anaerobes that will simply avoid synthesizing denitrification enzymes until O2 drops below some critical threshold.

In the field O2 is by far the dominant control on denitrification rates. Denitrification can be easily stimulated in an otherwise aerobic soil by removing O2 and can be inhibited in saturated soil by drying or otherwise aerating it. The relative importance of C and NO-, the other major controls, will vary by ecosystem. Under saturated conditions, such as those found in wetlands and lowland rice paddies, NO- limits denitrification because the nitrifiers that provide NO- are inhibited at low O2 concentrations. Consequently, denitrification occurs only in the slightly oxygenated rhizosphere and at the sediment-water interface, places where there is sufficient O2 for nitrifiers to oxidize NH4 to NO-, which can then diffuse to deni-trifiers in the increasingly anaerobic zones away from the root surface or sediment-water interface. It is often difficult to find NO- in persistently saturated soils, not only because of low nitrification, but also because of the tight coupling between nitrifiers and denitrifiers. In wetlands with fluctuating water tables or with significant inputs of NO- from groundwater, NO- may be more available.

In unsaturated soils, on the other hand, the availability of soil C more often limits denitrification. In these soils C supports denitrification both directly by providing donor electrons to denitrifiers and indirectly by stimulating O2 consumption by heterotrophs. It can be difficult to distinguish between these two effects experimentally; from a management perspective, there probably is no need to. It is well recognized that exogenous C stimulates denitrification, although the C added must be in an available form and must not lead to N immobilization sufficient to deplete NO- availability.

other nitrogen transformations in soil

Several additional microbial processes transform N in soil, although none are thought to be as quantitatively important as mineralization, immobilization, nitrification, and denitrification. Dissimilatory nitrate reduction to ammonium (DNRA) refers to the anaerobic transformation of nitrate to nitrite and then to ammonium. Like denitrification, this process allows for respiration to go on in the absence of O2, but the ecology of DNRA is much less well understood than that of denitrifi-cation. A capacity for DNRA has been found in facultative and obligately fermentative bacteria and has long been thought to be restricted to highly anaerobic environments such as anaerobic sewage sludge bioreactors, anoxic sediments, and the bovine rumen. More recently, however, DNRA has been found to be common and important in some tropical forest soils (Silver et al., 2001). In these soils the flow of inorganic N through DNRA is as large as or larger than the flow through denitrification and nitrification and may help to conserve N in these ecosystems by shunting nitrate into ammonium rather than to N2O or N2. The importance of DNRA in other soils is not clear because few measurements have been made due to the difficulty of measuring DNRA in the presence of other active N-cycle transformations.

Nonrespiratory denitrification, like respiratory denitrification, also results in the production of N gas (mainly N2O), but the reduction does not enhance growth and can occur in aerobic environments. A variety of nitrate-assimilating bacteria, fungi, and yeast can carry out nonrespiratory denitrification, which may be responsible for some of the N2O now attributed to nitrifiers in well-aerated soils (Robertson and Tiedje, 1987).

Anaerobic ammonium oxidation (anammox), in which ammonium and nitrite are converted to N2, has been only recently discovered (Mulder et al., 1995; Jetten, 2001) and thus its environmental significance is not fully known except in oceanic systems (Kuypers et al., 2005). Anammox bacteria grow very slowly in enrichment culture and only under strict anaerobic conditions; anammox thus is likely to be a significant soil process only in periodically or permanently submerged soils. One pathway, involving the combination of ammonia with nitrite, has been shown to occur in three or four obligate anaerobes, including Brocadia anammoxidans and Scalindua spp. A second pathway involves the nitrifier Nitrosomonas spp., in a nitrogen tetraoxide (N2O4)-dependent reaction that also produces significant amounts of NO and N2O (Schmidt et al., 2002).

Chemodenitrification occurs when NO 2 in soil reacts to form N2 or NOX. This can occur by several aerobic pathways. In the Van Slyke reaction, amino groups in the a position to carboxyls yield N2:

In a similar reaction, NO- reacts with NH+, urea, methylamine, purines, and pyrimidines to yield N2:

HNO2 + NH+ ^ N2 + 2H2O. Chemical decomposition of HNO2 may also occur spontaneously: 3HNO2 ^ HNO3 + H2O + 2NO.

In general chemodenitrification is thought to be a minor pathway for N loss in most ecosystems. It is not easily evaluated in situ, however, and in the lab requires a sterilization procedure that does not itself significantly disrupt soil nitrogen chemistry.

nitrogen movement in the landscape

Microbial transformations of reactive N (Table 13.3) have great importance for soil fertility, water quality, and atmospheric chemistry at ecosystem, landscape, and regional scales. It is at these scales that the disconnect between what we have learned in the laboratory and what we observe in the environment (see Introduction) becomes most obvious.

One approach to thinking about microbial N cycle processes at large scales is to ask a series of questions that attempt to determine if a particular ecosystem is a source or a sink of particular N species of environmental concern (Table 13.4).

TABLE 13.3 Forms of N of Concern in the Environment

N form


Dominant transport vectors

Environmental effects

Nitrate (NO-)



Pollution of drinking

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