Nitrogen is a very important element for life because it is a major constituent of proteins and nucleic acids. It is a macronutrient, and in nature, it is recycled from organic compounds and stored in the form of ammonia, ammonium ions, nitrate, nitrite, or nitrogen gas by many metabolic processes. Many of these metabolic processes are carried out only by prokaryotes.

The largest pool of nitrogen available in the terrestrial ecosystem is gaseous nitrogen (N₂) from the air, but this nitrogen is not usable by plants, which are the primary producers of the ecosystem. Gaseous nitrogen is transformed, or "fixed"into more readily available forms, such as ammonia (NH₃), through the process of nitrogen fixation. Nitrogen-fixing bacteria include Azotobacter in soil and the ubiquitous photosynthetic cyanobacteria. Some nitrogen fixing bacteria, like Rhizobium, live in symbiotic relationships in the roots of legumes. Another source of ammonia is ammonification, the process by which ammonia is released during the decomposition of nitrogen-containing organic compounds. The ammonium ion is progressively oxidized by different species of bacteria in a process called nitrification. The nitrification process begins with the conversion of ammonium to nitrite (NO₂^-), and continues with the conversion of nitrite to nitrate. Nitrification in soils is carried out by bacteria belonging to the genera Nitrosomas, Nitrobacter, and Nitrospira. Most nitrogen in soil is in the form of ammonium (NH₄⁺) or nitrate (NO₃^-). Ammonia and nitrate can be used by plants or converted to other forms.

Inside the plant cells, ammonia combines with glutamate to produce glutamine. The glutamine is then further converted into other amino acids and nucleotides. Later, animals consume these plants and use the amino acids to synthesize their own proteins and nucleotides. Since animals cannot store a large pool of amino acids, the ingested amino acids are regularly broken down inside the cells. But free ammonia released during amino acid catabolism is highly toxic to cells. So, excess ammonia is converted into a non-toxic form - urea – using a series of reactions called the urea cycle. Urea is then excreted out of the body through urine and eventually goes back into the soil. Later, soil bacteria use the enzyme urease to degrade the excreted urea into ammonia, which can again be taken up by the plants. In fact, when plants and animals die, their protein content is also degraded by the microbes to produce amino acids. The nitrifying microbes present in the soil convert these amino acids into nitrite and then into nitrate. Finally, the denitrifying bacteria, certain archaea, and some classes of fungi convert these nitrates back to gaseous nitrogen, thus returning nitrogen to the atmosphere.

This text is adapted from Openstax, Biology 2e, Section 22.5: Beneficial Prokaryotes