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The nitrogen cycle describes how the ammonia created by the nitrogenase activity and converted into amino acids is ultimately recycled in the biosphere.

A process known as nitrification occurs when specific bacteria oxidize${\text{NH}}_{\text{3}}$ to (${\mathrm{NO}}_2^{−}$) and (${\mathrm{NO}}_3^{−}$) subsequently to produce nitrate. Denitrification is the process by which some organisms turn nitrate back into dinitrogen ${\mathrm{N}}_2$.

Plants, fungi, and several bacteria reduce nitrate to${\text{NH}}_{\text{3}}$ by a process known as ammonification, where nitrate reductase catalyzes the two-electron reduction of nitrate to nitrite (${\mathrm{NO}}_2^{−}$).

${\mathrm{NO}}_3^{−}+2{\mathrm{H}}^{+}+2{\mathrm{e}}^{−}→{\mathrm{NO}}_2^{−}+{\mathrm{H}}_2\mathrm{O}$

Nitrite is converted to ammonia by nitrite reductase.

${\mathrm{NO}}_2^{−}+7{\mathrm{H}}^{+}+6{\mathrm{e}}^{−}→{\mathrm{NH}}_3+2{\mathrm{H}}_2\mathrm{O}$

Certain bacteria perform the opposite of nitrogen fixation, the direct anaerobic oxidation of${\text{NH}}_{\text{3}}$ back to${\text{N}}_{\text{2}}$without the use of nitrate as an intermediary.