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Gases (g) occur both free in the soil atmosphere and dissolved in soil water.

Gases (g) occur both free in the soil atmosphere and dissolved in soil water.

or assimilation of inorganic forms of N by microbes and other soil heterotrophs; nitrification, which is the conversion of ammonium (NH4) to nitrite (NO2) and then nitrate (NO33); and denitrification, which is the conversion of nitrate to nitrous oxide (N2O) and then dinitrogen gas (N2). Other N species (Table 13.1) are involved in these conversions primarily as intermediaries, and during conversion can escape to the environment where they can participate in chemical reactions or be transported elsewhere for further reactions.

Lohnis (1913) first formulated the concept of the N cycle, which formalizes the notion that N species are converted from one form to another in an orderly and predictable fashion, and that at global equilibrium as much dinitrogen gas that is fixed each year by N2 fixation must be annually converted back to N2 gas via denitrification (Fig. 13.1).

The fact that N2 fixation—both biological and industrial—now far outpaces historical rates of denitrification is the principal reason N has become a major modern pollutant (Galloway et al., 2003). Making managed ecosystems more N conservative and removing N from waste streams are major environmental challenges that require a fundamental knowledge of soil microbial N transformations (Robertson, 1997).

Although the microbiology, physiology, and biochemistry of N cycle processes have been extensively studied for many decades, it is important to note that much of our understanding of these processes has been derived from molecular and organismal scale studies. In some cases, data from the laboratory have impaired our ability to understand and evaluate these processes in nature. Laboratory studies have characterized the nature and regulation of the processes that we discuss in this chapter, but the reductionist nature of these studies has caused us to overlook sometimes surprising possibilities for activity and regulating factors in the natural environment. The occurrence of denitrification (an anaerobic process) in dry and even desert soils is but one example: theory and years of laboratory work suggested that denitrification ought to occur only in wetland and muck soils, but when new field-based methods became available in the 1970s it became abundantly clear that almost all soils denitrify.

N-Deposition

FIGURE 13.1 Schematic representation of the major elements of the terrestrial nitrogen cycle. Those processes mediated by soil microbes appear in bold. Gases appear in brackets.

N-Deposition

FIGURE 13.1 Schematic representation of the major elements of the terrestrial nitrogen cycle. Those processes mediated by soil microbes appear in bold. Gases appear in brackets.

Key problems have also arisen from evaluating microbial N cycle processes in isolation from other biogeochemical processes in nature (e.g., carbon (C) metabolism and plant nutrient uptake), from underestimating the physiological flexibility of bacteria in nature (e.g., nitrifying denitrifiers, aerobic denitrifiers, anammox bacteria), and from focusing almost exclusively on those microbes that can be cultivated in the laboratory. The disconnect between laboratory-derived knowledge and what actually occurs in the field is a problem throughout soil microbial ecology, but is perhaps most acute in the area of N cycling, which has great practical importance at field, landscape, regional, and global scales. It is when we attempt to scale up information from the microbial scale, to address real questions relating to plant growth, water pollution, and atmospheric chemistry at ecosystem, landscape, and regional scales, that this problem becomes obvious and important.

nitrogen mineralization and immobilization

A critical process in any nutrient cycle is the conversion of organic forms of nutrients in dead biomass (detritus) into simpler, soluble forms that can be taken up again by plants and other microbes. This conversion is carried out by microorganisms that release, or mineralize, nutrients as a by-product of their consumption of detritus. While microorganisms attack detritus primarily as a source of energy and carbon to support their growth, they also have a need for nutrients, especially N, to assemble proteins, nucleic acids, and other cellular components. If plant detritus is rich in N, microbial needs are easily met and N release, or mineralization, proceeds. If plant detritus is low in N, microorganisms must scavenge additional N from their surroundings, taking up or immobilizing N in their biomass.

The key to understanding mineralization-immobilization is to "think like a microbe" that is attempting to make a living by obtaining energy and C from detritus. Sometimes the detritus has all the N that the microbe needs, so as C is consumed, any extra N is released (mineralized) to the soil solution. Sometimes the detritus does not have enough N to meet microbial needs, so as C is consumed N is retained by the microbes and even more N must be immobilized from the soil solution. Indeed, it has been shown that microbes invest energy in the synthesis of enzymes (e.g., amidases to acquire N and phosphatases to acquire P) to acquire nutrients that they need while decomposing substrates of low quality. Microbial N uptake is also affected by organism growth efficiency. For example, fungi have wider C:N ratios in their tissues than bacteria and therefore—because of their lower N needs—can grow more efficiently on low-N substrates.

Mineralization results in an increase, while immobilization results in a decrease, in simple, plant-available forms of N in the soil. Traditionally, ammonium has been viewed as the immediate product of mineralization. In fact in the older literature mineralization is often referred to as ammonification. More recently, recognition of the fact that plants can take up simple, soluble organic forms of nutrients leads us to broaden our definition of mineralization products to include any simple, soluble forms of N that can be taken up by plants (see Schimel and Bennet, 2004). Plants from a variety of habitats have been shown to take up amino acids and other organic N forms; mycorrhizas play a role in this uptake by absorbing amino acids, amino sugars, peptides, proteins, and chitin that are then used by their hosts as an N source.

It is important to recognize that mineralization and immobilization are occurring at the same time within relatively small volumes of soil. While one group of microbes might be consuming a protein-rich and therefore nitrogen-rich piece of organic matter (think seed or leguminous leaf tissue), another group, perhaps 100 |xm away, might be consuming detritus rich in C but low in N (think leaf stalk or wood). The first group is mineralizing N while the second is immobilizing it, perhaps even immobilizing the same N that is being mineralized by the first.

As a result of the simultaneous nature and small scale of these processes, it is also important to make a distinction between gross and net mineralization and immobilization. Gross N mineralization is the total amount of soluble N produced by microorganisms, and gross N immobilization is the total amount of soluble N consumed. Net N mineralization is the balance between the two. When gross mineralization exceeds gross immobilization, inorganic N in the soil is increasing, i.e., there is net mineralization. When gross immobilization exceeds gross mineralization, inorganic N in the soil is decreasing, i.e., there is net immobilization.

Mineralization and immobilization are carried out by a wide array of micro-organisms—aerobes, anaerobes, fungi, and bacteria. Soil fauna also play an important role in mineralization and immobilization processes. They are responsible for much of the preliminary decomposition of detritus, they feed on and can regulate

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