Enumerating ammonia-oxidizing bacteria in environmental samples using competitive PCR.

Primers targeting part of the ammonia-monooxygenase gene (amoA) have been used to detect and characterize ammonia-oxidizing bacteria (AOB) in different environments. In this study, a quantitative polymerase chain reaction (PCR) technique using a competitive template for the amoA primer pair is described and evaluated. The method is based on addition of an internal standard to the PCR, a competitive template, which is amplified together with the template in the environmental sample. By adding different amounts of competitive template to the sample and observing the relative intensity of environmental amplificate and competitive amplificate, the number of amoA gene copies can be determined. Different tests were made to evaluate the competitive PCR method (cPCR) with respect to equal amplification efficiency of the two templates, degeneracy of the priming site and the importance of flanking regions surrounding the competitive template. Calibration curves made by addition of known amounts of Nitrosomonas europaea to soil samples revealed a detection limit for this technique of less than 1000 cells g(-1) soil and a linear response over a wide range of cell additions. Cloning and sequencing of amoA amplificates have confirmed the specificity of the primers, as we have not detected any false positives among the more than 200 clones investigated. The vertical distribution of ammonia-oxidizers in the upper cm of a waterlogged rice paddy soil was compared to nitrate and oxygen concentration profiles determined with microsensors and to net process rates derived from these profiles.