Polyphosphate is the key biopolymer in wastewater treatment (WWT) processes applying enhanced biological phosphorus removal (EBPR) by polyphosphate-accumulating organisms (PAO). Alternating anaerobic (no oxygen and no nitrate) and aerobic phases is used to promote a net phosphorus removal from the wastewater as PAO are capable to take up and store phosphate as intracellular polyphosphate during the aerobic growth phase. In the anaerobic phase, PAO replenish their carbon and energy source in form of polyhydroxyalkanoates (PHA) from volatile fatty acids (VFA) present or formed in the wastewater. The energy and reducing equivalents needed to form PHA come from glycogen and polyphosphate, the polymers that are replenished during the aerobic phase. A few PAO have been already identified, among which Candidatus Accumulibacter phosphatis is a major player in WWT microbial communities enriched with VFA. However, depending on the carbon source the microbial community can strongly fluctuate and other PAO might play a major role in phosphorus removal. We are studying the dynamics of microbial communities in lab-scale aerobic granular sludge sequencing batch reactors subjected to changes of carbon source going from simple VFA to a mixture of VFA, glucose and amino acids. Both metagenomic approaches targeting polyphosphate kinase (ppk) genes and functional analysis of PAO using fluorescence techniques staining the polyphosphate polymer allow us to investigate the key metabolic genes in the synthesis of polyphosphate and expand the knowledge on the diversity of PAO in such engineered systems.