Nitrogen cycle in microorganisms

Nitrogen is a critically important nutrient for organisms, including microorganisms . This element is one of the most abundant elemental constituents of eukaryotic tissues and prokaryotic cell walls, and is an integral component of amino acids, proteins, and nucleic acids.

Most plants obtain their nitrogen by assimilating it from their environment, mostly as nitrate or ammonium dissolved in soil water that is taken up by roots, or as gaseous nitrogen oxides that are taken up by plant leaves from the atmosphere. However, some plants live in a symbiotic relationship with microorganisms that have the ability to fix atmospheric nitrogen (which can also be called dinitrogen) into ammonia. Such plants benefit from access to an increased supply of nitrogen.

As well, nitrogen-assimilating microorganisms are of benefit to animals. Typically animals obtain their needed nitrogen through the plants they ingest. The plant's organic forms of nitrogen are metabolized and used by the animal as building blocks for their own necessary biochemicals. However, some animals are able to utilize inorganic sources of nitrogen. For example, ruminants, such as the cow, can utilize urea or ammonia as a consequence of the metabolic action of the microorganisms that reside in their forestomachs. These microbes can assimilate nitrogen and urea and use them to synthesize the amino acids and proteins, which are subsequently utilized by the cow.

Nitrogen (N) can occur in many organic and inorganic forms in the environment. Organic nitrogen encompasses a diversity of nitrogen-containing organic molecules, ranging from simple amino acids, proteins, and nucleic acids to large and complex molecules such as the humic substances that are found in soil and water.

In the atmosphere, nitrogen exists as a diatomic gas (N₂). The strong bond between the two nitrogen atoms of this gas make the molecule nonreactive. Almost 80% of the volume of Earth's atmosphere consists of diatomic nitrogen, but because of its almost inert character, few organisms can directly use this gas in their nutrition. Diatomic nitrogen must be "fixed" into other forms by certain microorganisms before it can be assimilated by most organisms.

Another form of nitrogen is called nitrate (chemically displayed as NO₃-). Nitrate is a negatively charged ion (or anion), and as such is highly soluble in water.

Ammonia (NH_3S) usually occurs as a gas, vapor, or liquid. Addition of a hydrogen atom produces ammonium (NH₄+). Like nitrate, ammonium is soluble in water. Ammonium is also electrochemically attracted to negatively charged surfaces associated with clays and organic matter in soil, and is therefore not as mobile as nitrate.

These, and the other forms of nitrogen are capable of being transformed in what is known as the nitrogen cycle.

Nitrogen is both very abundant in the atmosphere and is relatively inert and nonreactive. To be of use to plants, dinitrogen must be "fixed" into inorganic forms that can be taken up by roots or leaves. While dinitrogen fixation can occur non-biologically, biological fixation of dinitrogen is more prevalent.

A bacterial enzyme called nitrogenase is capable of breaking the tenacious bond that holds the two nitrogen atoms together. Examples of nitrogen-fixing bacteria include Azotobacter, Beijerinkia, some species of Klebsiella, Clostridium, Desulfovibrio, purple sulfur bacteria, purple non-sulfur bacteria, and green sulfur bacteria.

Some species of plants live in an intimate and mutually beneficial symbiosis with microbes that have the capability of fixing dinitrogen. The plants benefit from the symbiosis by having access to a dependable source of fixed nitrogen, while the microorganisms benefit from energy and habitat provided by the plant. The best known symbioses involve many species in the legume family (Fabaceae) and strains of a bacterium known as Rhizobium japonicum. Some plants in other families also have dinitrogen-fixing symbioses, for example, red alder (Alnus rubra ) and certain member of Actinomycetes. Bacteria from the genera Frankia and Azospirillum are also able to establish symbiotic relationships with non-leguminous plants. Many species of lichens , which consist of a symbiotic relationship between a fungus and a blue-green bacterium, can also fix dinitrogen.

Ammonification is a term for the process by which the organically bound nitrogen of microbial, plant, and animal biomass is recycled after their death. Ammonification is carried out by a diverse array of microorganisms that perform ecological decay services, and its product is ammonia or ammonium ion. Ammonium is a suitable source of nutrition for many species of plants, especially those living in acidic soils. However, most plants cannot utilize ammonium effectively, and they require nitrate as their essential source of nitrogen nutrition.

Nitrate is synthesized from ammonium by an important bacterial process known as nitrification. The first step in nitrification is the oxidation of ammonium to nitrite (NO₂-), a function carried out by bacteria in the genus Nitrosomonas. Once formed, the nitrite is rapidly oxidized further to nitrate, by bacteria in the genus Nitrobacter. The bacteria responsible for nitrification are very sensitive to acidity, so this process does not occur at significant rates in acidic soil or water.

Denitrification is another bacterial process, carried out by a relatively wide range of species. In denitrification, nitrate is reduced to either nitrous oxide or dinitrogen, which is then emitted to the atmosphere. One of the best studies bacterial examples is Pseudomonas stutzeri. This bacterial species has almost 50 genes that are known to have a direct role in denitrification. The process of denitrification occurs under conditions where oxygen is not present, and its rate is largest when concentrations of nitrate are large. Consequently, fertilized agricultural fields that are wet or flooded can have quite large rates of denitrification. In some respects, denitrification can be considered to be an opposite process to dinitrogen fixation. In fact, the global rates of dinitrogen fixation and denitrification are in an approximate balance, meaning that the total quantity of fixed nitrogen in Earth's ecosystems is neither increasing nor decreasing substantially over time.

See also Biogeochemical cycles; Economic uses and benefits of microorganisms