We employ laboratory-scale bioreactors of varying sizes and dimensions to investigate how microbial community structure and function are affected by varying experimental conditions, and to evaluate and apply ecological theory derived from higher organisms in the context of microbial biofilm communities. The highly complex biofilm communities present in activated sludge bioreactors provide a tractable system in which to study the interactions of microorganisms from a community ecology perspective, with the dual advantage of elucidating the hidden ‘universe’ of microbes performing such intricate functions.