Ammonification

Nitrogen is one of the most abundant elements in the tissues of all organisms and is a component of many biochemicals, particularly amino acids, proteins, and nucleic acids. Consequently, nitrogen is one of the critically important nutrients and is required in relatively large quantities by all organisms. Animals receive their supply of nitrogen through the foods they eat, but plants must assimilate inorganic forms of this nutrient from their environment.

However, the rate at which the environment can supply inorganic nitrogen is limited and usually small in relation to the metabolic demands of plants. Therefore, the availability of inorganic forms of nitrogen is frequently a limiting factor for the productivity of plants. This is a particularly common occurrence for plants growing in terrestrial and marine environments, and to a lesser degree, in fresh waters (where phosphate supply is usually the primary limiting nutrient, followed by nitrate).

The dead biomass of plants, animals, and microorganisms contains large concentrations of organically bound nitrogen in various forms, such as proteins and amino acids. The process of decomposition is responsible for recycling the inorganic constituents of the dead biomass and preventing it from accumulating in large unusable quantities. Decomposition is, of course, mostly carried out through the metabolic functions of a diverse array of bacteria, fungi, actinomycetes, other microorganisms, and some animals. Ammonification is a particular aspect of the more complex process of organic decay, specifically referring to the microbial conversion of organic-nitrogen into ammonia (NH₃) or ammonium (NH ⁺ 4 ).

Ammonification occurs under oxidizing conditions in virtually all ecosystems and is carried out by virtually all microorganisms that are involved in the decay of dead organic matter. In situations where oxygen is not present, a condition referred to as anaerobic, different microbial decay reactions occur, and these produce nitrogen compounds known as amines.

The microbes derive some metabolically useful energy from the oxidation of organic-nitrogen to ammonium. In addition, much of the ammonium is assimilated and used as a nutrient for the metabolic purposes of the microbes. However, if the microbes produce ammonium in quantities that exceed their own requirements, as is usually the case, the surplus is excreted into the ambient environment (such as the soil), and is available for use as a nutrient by plants, or as a substrate for another microbial process, known as nitrification (see below). Animals, in contrast, mostly excrete urea or uric acid in their nitrogen-containing liquid wastes (such as urine), along with diverse organic-nitrogen compounds in their feces. The urea, uric acid, and organic nitrogen of feces are all substrates for microbial ammonification.

One of the most elementary of the ammonification reactions is the oxidation of the simple organic compound, urea (CO(NH₂)₂), to ammonia through the action of a microbial enzyme known as urease. (Note that two units of ammonia are produced for every unit of urea that is oxidized.) Urea is a commonly utilized agricultural fertilizer, used to supply ammonia or ammonium for direct uptake by plants, or as a substrate for the microbial production of nitrate through nitrification (see below).

Ammonium is a suitable source of nitrogen uptake for many species of plants, particularly those that live in acidic soils and waters. However, most plants that occur in non-acidic soils cannot utilize ammonium very efficiently, and they require the anion nitrate (NO ⁺ 3 ) as their source of nitrogen uptake. The nitrate is generally derived by the bacterial oxidation of ammonium to nitrite, and then to nitrate, in an important ecological process known as nitrification. Because the species of bacteria that carry out nitrification are extremely intolerant of acidity, this process does not occur at significant rates in acidic soils or waters. This is the reason why plants growing in acidic habitats can only rely on ammonium as their source of nitrogen nutrition.

Because ammonium is a positively charged cation, it is held relatively strongly by ion-exchange reactions occurring at the surfaces of clay minerals and organic matter in soils. Consequently, ammonium is not leached very effectively by water as it percolates downward through the soil. This is in contrast to nitrate, which is highly soluble in soil water and is leached readily. As a result, nitrate pollution can be an important problem in agricultural areas that have been heavily fertilized with nitrogen-containing fertilizers.