Nitrification, the conversion of ammonia to nitrate, is an important process in soils: ammonia is less soluble and so less easily lost by leaching, but is also less mobile and so less available to plants.  The group of bacteria responsible for this nitrifying activity in agricultural soils are autotrophic, needing only ammonia and carbon dioxide for growth.  The rate-limiting step in the process of soil nitrification is the initial oxidation of ammonia to nitrite as carried out by autotrophic ammonia oxidising bacteria.  This nitrite is then rapidly oxidised further to nitrate by autotrophic nitrite oxidising bacteria. The autotrophic ammonia oxidizers are difficult to culture, and little is known about their ecology, but they are thought to be a phylogenetically similar (closely related) group and PCR primers that amplify the 16S ribosomal RNA gene (16S) or the gene for the enzyme ammonia monooxygenase (amoA) can be used to investigate their activity, diversity and population dynamics in soil.

Nitrifying bacteria on the Broadbalk long-term fertilizer experiment

We have compared nitrification rates (using a ¹⁵N isotopic pool dilution assay) in Broadbalk soils with different fertilizer inputs before and after adding ammonium nitrate fertilizer, with the population size and diversity using quantitative PCR.  Results showed that nitrification is closely related to ammonia concentrations, responding rapidly (in hours) to ammonia addition.  Fertiliser addition also increases the population size but this takes around six weeks.  However, populations in plots receiving no fertilizer additions were only about 50-fold lower than those receiving ammonium nitrate or farmyard manure (Mendum et al., 1999).  Only group 3 and 4 nitrifiers were detected in Broadbalk soils but the relative abundance of each group varied according to fertilizer regime (Mendum & Hirsch, 2002), indicating differences in population structure.  (Tom Mendum and Penny Hirsch)

Nitrification Rates

Number of amoA and 16S genes as determined by cPCR

Ratio of group 3 to group 4 ammonia oxidising bacteria

References:

Mendum, T.A., Sockett, R.E. & Hirsch, P.R,. (1999) Use of molecular and isotopic techniques to monitor the response of autotrophic ammonia-oxidizing populations of the subdivision of the class Proteobacteria in arable soils to nitrogen fertilizer.  Applied Environmental Microbiology 65: 4155-4162.

Mendum, T.A. & Hirsch, P.R,. (2002). Changes in the population structure of beta-group autotrophic ammonia oxidising bacteria in arable soils in response to agricultural practice. Soil Biology Biochemistry 34, 1479-1485.

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