DETECTION OF AMMONIUM-OXIDIZING BACTERIA OF THE BETA-SUBCLASS OF THE CLASS PROTEOBACTERIA IN AQUATIC SAMPLES WITH THE PCR

The PCR was used as the basis for the development of a sensitive and s pecific assay for the detection of ammonium-oxidizing bacteria belongi ng to the beta-subclass of the class Proteobacteria. PCR primers were selected on the basis of nucleic acid sequence data available for seve n species of nitrifiers in this subclass. The specificity of the ammon ium oxidizer primers was evaluated by testing known strains of nitrifi ers, several serotyped environmental nitrifier isolates, and other mem bers of the Proteobacteria, including four very closely related, nonni trifying species (as determined by rRNA sequence analysis). DNA extrac ts from 19 bacterio plankton samples collected from Lake Bonney, Antar ctica, and the Southern California Eight were assayed for the presence of ammonium oxidizers. By using a two stage amplification procedure, ammonium oxidizers were detected in samples collected from both sites, Chemical data collected simultaneously support the occurrence of nitr ification and the presence of nitrifiers. This is the first report des cribing PCR primers specific for ammonium-oxidizing bacteria and the s uccessful amplification of nitrifier genes coding for rRNA from DNA ex tracts from natural samples. This application of PCR is of particular importance for the detection and study of microbes, such as autotrophi c nitrifiers, which are difficult or impossible to isolate from indige nous microbial communities.