Rapid quantification and analysis of genetic diversity among Gordonia populations in foaming activated sludge plants

Activated sludge plants, sporadically suffers malfunction due to the proliferation of filamentous bacteria mainly Gordonia and Microthrix species. Nested Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (nested PCR-RFLP) in combination with quantitative real-time PCR (q PCR) was applied to study the distribution of Gordonia in foaming samples. Samples of mixed liquor were collected from three full-scale activated sludge plants that were experiencing filamentous biological foaming. Partial sequencing of 16S rRNA genes revealed the dominance of Gordonia amarae (60-80%), Gordonia terrae (10%), Gordonia polyisoprenivorans (30-40%) and an unidentified Gordonia species (20-50%). Restriction enzyme analysis of the amplicons exhibited 87.14 to 99.6% similarity at interspecies level. The q PCR results showed that there was an average of 15.6% Gordonia 16S rRNA copies with respect to the total bacterial 16S rRNA gene in foaming sludge samples with the highest being 23.51% and lowest being 10.28%. The presence of Gordonia spp. in the foaming samples was observed throughout the year but was lower during winter and its presence was significantly higher in foaming samples, compared to Microthrix parvicella (r = 0.007, P < 5%). This approach could help to quantify and confirm the existence of genetically diverse indigenous Gordonia spp. in foaming samples and can be used as an indicator of forthcoming foaming incidents.