In the biosphere, the metabolic processes of different species function interdependently to salvage and reuse biologically available nitrogen in a vast nitrogen cycle.

The first step in the cycle is fixation (reduction) of atmospheric nitrogen by nitrogen-fixing bacteria to yield ammonia (NH 3 or NH 4 + ). Although ammonia can be used by most living organisms, soil bacteria that derive their energy by oxidizing ammonia to nitrite (NO 2 ˉ ) and ultimately nitrate ( NO 3 ˉ) are so abundant and active that nearly all ammonia reaching the soil is oxidized to nitrate. This process is known as nitrification.

Plants and many bacteria can take up and readily reduce nitrate and nitrite to ammonia through the action of nitrate and nitrite reductases. This ammonia is incorporated into amino acids by plants. Animals then use plants as a source of amino acids to build their proteins. When organisms die, microbial degradation of their proteins returns ammonia to the soil, where nitrifying bacteria again convert it to nitrite and nitrate.

A balance is maintained between fixed nitrogen and atmospheric nitrogen by bacteria that reduce nitrate and nitrite to N 2 under anaerobic conditions, a process called denitrification. These soil bacteria use NO 3 ˉ or NO 2 ˉ rather than O 2 as the ultimate electron acceptor in a series of reactions that (like oxidative phosphorylation) generates a transmembrane proton gradient, which is used to synthesize ATP.