In situ detection of rhodococci associated with activated sludge foams

Genus-specific 16S rRNA targeted oligonucleotide probes, Rco1 and Rco2, were designed and used to detect rhodococci in activated sludge foam samples by confocal laser scanning microscopy. Pure cultures were used to find the optimal hybridisation conditions which were determined by comparing the mean fluorescent intensities of target and non-target cells from images captured using a confocal laser scanning microscope (CLSM). The combination of fluorescent in situ hybridisation with rRNA-targeted oligonucleotide probes and confocal laser scanning microscopy provides an effective way of detecting rhodococci in environmental samples.