Nitrification

Nitrification is the biological oxidation of ammonia or ammonium to nitrite followed by the oxidation of the nitrite to nitrate. 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. This process was discovered by the Russian microbiologist Sergei Winogradsky.

The oxidation of ammonia into nitrite is performed by two groups of organisms, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). AOB can be found among the β-proteobacteria and gammaproteobacteria. Currently, two AOA, Nitrosopumilus maritimus and Nitrososphaera viennensis, have been isolated and described. In soils the most studied AOB belong to the genera Nitrosomonas and Nitrosococcus. Although in soils ammonia oxidation occurs by both AOB and AOA, AOA dominate in both soils and marine environments, suggesting that Thaumarchaeota may be greater contributors to ammonia oxidation in these environments.

The second step (oxidation of nitrite into nitrate) is done (mainly) by bacteria of the genus Nitrobacter and Nitrospira. Both steps are producing energy to be coupled to ATP synthesis. Nitrifying organisms are chemoautotrophs, and use carbon dioxide as their carbon source for growth. Some AOB possess the enzyme, urease, which catalyzes the conversion of the urea molecule to two ammonia molecules and one carbon dioxide molecule. Nitrosomonas europaea, as well as populations of soil-dwelling AOB, have been shown to assimilate the carbon dioxide released by the reaction to make biomass via the Calvin Cycle, and harvest energy by oxidizing ammonia (the other product of urease) to nitrite. This feature may explain enhanced growth of AOB in the presence of urea in acidic environments.

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