Earth's atmosphere contains 78% dinitrogen, which consists of two nitrogen atoms joined by a triple bond. In this form it is completely unavailable to most organisms, however, because large amounts of energy are required to break the triple bond. Most organisms must use sources of "fixed" nitrogen. Nitrogen fixation is the transformation of atmospheric nitrogen to ammonia. Ninety percent of nitrogen fixation is carried out in biological systems by the enzyme nitrogenase, which is unique to prokaryotes. Smaller contributions to the pool of fixed nitrogen come from combustion of fossil fuels, and lightning strikes. After being fixed, nitrogen can be incorporated into mineral and organic compounds by plants and microorganisms, where it is then made available for use by animals.

Nitrogen is found in three major compartments, the air, the soil, and in living organisms. A single atom of nitrogen appears in many different forms as it moves between them. Nitrogen fixing bacteria, such as cyanobacteria, incorporate atmospheric nitrogen into proteins and nucleic acids, so called organic nitrogen. 95-99% of soil nitrogen is in the form of organic nitrogen, mostly present as amine groups of proteins. Non-nitrogen fixing soil microorganisms mineralize organic nitrogen by hydrolyzing proteins from decaying bacterial cells. Mineralization is the conversion of amine and amide nitrogens to ammonia and nitrates. A number of biological processes may cause fixed nitrogen to be released back into the atmosphere as dinitrogen. Known as denitrification, this occurs in the soil simultaneously along with nitrogen fixation and mineralization. Particularly under anaerobic conditions, heterotrophic soil microorganisms extract energy from nitrogen compounds to run their cellular machinery, forming gaseous dinitrogen, which is lost to the atmosphere. Nitrogen is in constant circulation through the ecosystem, being constantly fixed, mineralized and released.

Nitrogen is a key component of plant tissues. Nitrogen containing plant compounds include amino acids, the building blocks of all proteins. These are in turn the basic units of enzymes, which catalyze virtually all biochemical reactions and thereby control most biological processes. Nucleic acids, the components of DNA and RNA, and chlorophyll, the pigment contained in plants which harvests light energy, are also both rich in nitrogen. Plants require more nitrogen than the do any other mineral element. They take up primarily mineral nitrogen, as nitrates (NO3-) and ammonia (NH4+) from the soil. Nitrogen availability is determined by environmental factors including precipitation, soil flora and fauna contributions, carbon/nitrogen ratio in soil, and soil pH.

Nitrogen is in great demand, and is limited in all but a few habitats. In most natural environments nitrogen is taken up by plants and soil organisms as quickly as it becomes available, and the constant flow of nitrogen from atmosphere to soil to living systems is essential to keep up with demand. Plants that form symbiotic relationships with nitrogen fixing bacteria eliminate their dependence on soil nitrogen. Instead they receive a steady supply from the symbiont in exchange for carbohydrates. Nitrogen fixation is an energy intensive process, requiring 25-35 molecules of ATP to convert a single Nitrogen to ammonium ion. This is one of the reasons diazotrophic species are found in symbiosis with plants, which are able to supply the large amounts of carbohydrates needed to support nitrogenase