What Is Nitrification?

Nitrification is the biological oxidation of ammonia to nitrite and then to nitrate, carried out by specialized microorganisms that derive energy from the reaction. It is one of the central transformations of the nitrogen cycle, converting reduced nitrogen that plants and microbes have released into the oxidized form that most crops take up and that leaches readily into groundwater. The organisms responsible are chemolithoautotrophs: they obtain energy by oxidizing an inorganic substrate and fix carbon dioxide for biomass rather than consuming organic carbon. Because the process consumes oxygen and alkalinity while producing acid, it exerts strong control over pH and dissolved oxygen in soils, sediments, aquifers, and engineered water systems.

The reaction was identified in the 1890s by Sergei Winogradsky, whose isolation of nitrifying bacteria established chemolithotrophy as a mode of life. For most of the following century nitrification was understood as an obligate two-organism relay, and only recently has that picture been revised.

The Two Oxidation Steps

The first step, ammonia oxidation, converts ammonia to hydroxylamine and then to nitrite. It is catalyzed by ammonia monooxygenase and hydroxylamine oxidoreductase in ammonia-oxidizing bacteria such as Nitrosomonas, and by ammonia-oxidizing archaea, which dominate in many soils and in the open ocean. The second step, nitrite oxidation, is performed by nitrite-oxidizing bacteria including Nitrobacter, Nitrospira, Nitrococcus, and the marine genus Nitrospina, using nitrite oxidoreductase with oxygen as the terminal electron acceptor. A study of the two guilds in an anammox-inoculated treatment system illustrates how the relative abundance of ammonia oxidizers and nitrite oxidizers governs which nitrogen species accumulate.

Complete ammonia oxidation, or comammox, was described in 2015 in certain Nitrospira strains that carry the enzymes for both steps and run the full conversion from ammonia to nitrate in a single cell. These organisms have high substrate affinity and are now recognized as significant in low-ammonia environments, including drinking water systems.

Stoichiometry sets the engineering constraints. Full oxidation of one mole of ammonium consumes about two moles of oxygen and destroys roughly 7.1 milligrams of alkalinity as calcium carbonate per milligram of nitrogen oxidized. Nitrifiers also grow slowly, with generation times measured in days rather than hours, which makes solids retention time the controlling design variable in any reactor meant to sustain them.

Nitrification in Engineered Systems

Municipal wastewater treatment relies on nitrification to remove ammonia, usually paired with anoxic denitrification that reduces the resulting nitrate to nitrogen gas. Activated sludge plants, moving bed biofilm reactors, and membrane bioreactors are all sized to retain the slow-growing nitrifier population, and they must supply aeration and sometimes supplemental alkalinity. Shortcut processes such as nitritation-denitritation and anammox stop the oxidation at nitrite to reduce aeration and carbon demand.

Nitrification is a nuisance rather than a goal in drinking water. Utilities that use chloramine as a secondary disinfectant release free ammonia into the distribution network, where nitrifiers can colonize pipe biofilms and storage tanks. The result is loss of disinfectant residual, falling pH and dissolved oxygen, and rising nitrite and heterotrophic plate counts. EPA guidance in its drinking water distribution system tools and resources covers monitoring and control, and agency research on the factors affecting nitrification occurrence in chloraminated systems identifies temperature, water age, and chloramine residual as the dominant variables. Temporary conversion to free chlorine is the common corrective measure.

Applications

Nitrification has applications and consequences in a range of fields, including:

• Municipal and industrial wastewater treatment for ammonia removal
• Drinking water distribution system management in chloraminated networks
• Agricultural soil fertility management and nitrification inhibitor use
• Aquaculture and aquarium biofiltration
• Groundwater nitrate contamination assessment and remediation
• Greenhouse gas accounting, since nitrification is a source of nitrous oxide