Moving bed biofilm reactor (MBBR) systems are increasingly used for municipal and industrial wastewater treatment, yet in contrast to activated sludge (AS) systems, little is known about their constituent microbial communities. This study investigated the community composition of two municipal MBBR wastewater treatment plants (WWTPs) in Wellington, New Zealand. Monthly samples comprising biofilm and suspended biomass were collected over a 12-month period. Bacterial and archaeal community composition was determined using a full-cycle community approach, including analysis of 16S rRNA gene libraries, fluorescence in situ hybridization (FISH) and automated ribosomal intergenic spacer analysis (ARISA). Differences in microbial community structure and abundance were observed between the two WWTPs and between biofilm and suspended biomass. Biofilms from both plants were dominated by Clostridia and sulfate-reducing members of the Deltaproteobacteria (SRBs). FISH analyses indicated morphological differences in the Deltaproteobacteria detected at the two plants and also revealed distinctive clustering between SRBs and members of the Methanosarcinales, which were the only Archaea detected and were present in low abundance (<5%). Biovolume estimates of the SRBs were higher in biofilm samples from one of the WWTPs which receives both domestic and industrial waste and is influenced by seawater infiltration. The suspended communities from both plants were diverse and dominated by aerobic members of the Gammaproteobacteria and Betaproteobacteria. This study represents the first detailed analysis of microbial communities in full-scale MBBR systems and indicates that this process selects for distinctive biofilm and planktonic communities, both of which differ from those found in conventional AS systems.T he moving bed biofilm reactor (MBBR) system was developed in the late 1980s for the treatment of domestic and industrial wastewaters. These systems are now operating in more than 22 countries (including New Zealand) and range from large-to small-scale wastewater treatment plants (WWTPs) (35). The MBBR process combines features of both fixed-growth and activated sludge (AS) systems in that the microbial community is largely retained within the reactor as a biofilm on suspended carriers, with a smaller planktonic fraction being present in suspension as free-floating cells or small flocs. MBBR technology offers a number of advantages over conventional technologies for treating waste, including a high effluent quality, no bulking problems, and lower cost. Other advantages of fixed biofilm growth include the decoupling of biomass retention from hydraulic retention time leading to longer sludge ages and low waste sludge volumes (5, 37).Studies on the microbial community composition of conventional activated sludge systems indicate that the community is typically dominated by aerobic or facultatively anaerobic heterotrophic bacteria belonging to the Betaproteobacteria (41). It is unclear whether similar communities are found in MBBR pr...