In this study, we aimed to standardise the use of DGGE for different group-specific PCR generated 16S rRNA gene fragments, and apply this method to analyse the structure of specific bacterial groups in activated sludge systems of different WWTP. This standardisation was made possible by performing a nested PCR approach. In a first PCR round, specific fragments were amplified by using group specific primers for
methanotrophic members of the alpha-and gamma-Proteobacteria, actinomycetes, alpha-Proteobacteria, ammonia-oxidising bacteria and Acidobacterium, and in parallel a first set of Bacterial primers was used to amplify all members of the domain Bacteria