Nitrification

Nitrification is the biological oxidation of ammonia to nitrite followed by the oxidation of the nitrite to nitrate occurring through separate organisms or direct ammonia oxidation to nitrate in comammox bacteria. The transformation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an important step in the nitrogen cycle in soil. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea. The oxidation of ammonia into nitrite (also known as nitritation) is performed by two groups of organisms, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). AOB can be found among the Betaproteobacteria and Gammaproteobacteria. In soils the most studied AOB belong to the genera Nitrosomonas and Nitrococcus. Since discovery of AOA in 2005, two isolates have been cultivated: Nitrosopumilus maritimus and Nitrososphaera viennensis. When comparing AOB and AOA, AOA dominate in both soils and marine environments, suggesting that Nitrososphaerota (formerly Thaumarchaeota) may be greater contributors to ammonia oxidation in these environments. Crenarchaeol, which is generally thought to be produced exclusively by AOA (specifically Nitrososphaerota), has been proposed as a biomarker for AOA and ammonia oxidation. Crenarchaeol abundance has been found to track with seasonal blooms of AOA, suggesting that it may be appropriate to use crenarchaeol abundances as a proxy for AOA populations and thus ammonia oxidation more broadly. However the discovery of Nitrososphaerota that are not obligate ammonia-oxidizers complicates this conclusion, as does one study that suggests that crenarchaeol may be produced by Marine Group II Euryarchaeota. The second step, known as nitratation, – oxidation of nitrite into nitrate – is done by bacteria (nitrite-oxidizing bacteria, NOB) from the taxa Nitrospirota, Nitrospinota, Pseudomonadota and Chloroflexota. They are present in soil, geothermal springs, freshwater and marine ecosystems.