Nitrification
Nitrification is executed by specialized groups of micro-organisms that transform ammonium to nitrate in two steps. In the first step, ammonium is converted to nitrite. In the second step, nitrite is transformed to nitrate. Each step is carried out by a different set of micro-organisms capable of producing enzymes that catalyse the oxidation reactions required for the conversion of ammonium to nitrate. Both steps only occur in aerated soils. Specialized groups of ammonium-oxidising and nitrite-oxidising bacteria and archaea can carry out nitrification and in certain cases fungi as well.
In the Nutrient Cycling model, nitrification is considered under Nitrogen transformation. The conversion of ammonium to nitrate makes nitrogen available for plant uptake but also more prone to leaching. Nitrate available in soil is also at risk of being further denitrified when local conditions are anaerobic. Plants take up ammonium, nitrite and nitrate to satisfy their nitrogen demand. Nitrification is included in the Carbon and Climate Regulation model because – in addition to nitrite and nitrate – this process can generate N2O, a potent greenhouse gas (300 times more potent than CO2). Whether nitrification contributes to N2O emissions depends on the oxygen levels and pressure in the soil. Overall, the process of denitrification taking place under anaerobic conditions is a more significant contributor to N2O emissions.
Nitrification rates can be measured in the field or can be measured on soil samples in the lab by means of incubations potentially using stable isotopes (15N) or nitrification inhibitors[1]. Another approach is to measure the activity of enzymes involved in the nitrification reactions or the associated functional genes[2],[3],[4].
[1] Norton JM, Stark JM. 2011. Chapter Fifteen - Regulation and Measurement of Nitrification in Terrestrial Systems. In: Klotz MG, ed. Research on Nitrification and Related Processes, Part A. Methods in Enzymology. Academic Press, 343–368.
[2] Groffman PM. 1987. Nitrification and denitrification in soil: A comparison of enzyme assay, incubation and enumeration methods. Plant and Soil 97: 445–450.
[3] Junier P, Molina V, Dorador C, Hadas O, Kim O-S, Junier T, Witzel K-P, Imhoff JF. 2010. Phylogenetic and functional marker genes to study ammonia-oxidizing microorganisms (AOM) in the environment. Applied Microbiology and Biotechnology 85: 425–440.
[4] Poly F, Wertz S, Brothier E, Degrange V. 2008. First exploration of Nitrobacter diversity in soils by a PCR cloning-sequencing approach targeting functional gene nxrA. FEMS Microbiology Ecology 63: 132–140.