The application of modern molecular techniques has led to the identification, in situ quantification, and partial ecophysiological characterisation of bacteria responsible for bulking and foaming or for nutrient removal in sewage treatment systems. Unexpectedly, previously unrecognised, yet uncultured bacteria were demonstrated to catalyse nitrogen and phosphorous removal in activated-sludge and biofilm reactors. These findings provide the basis for the development of novel concepts for improving the efficiency and functional stability of waste water treatment systems.