Industrial-scale bioreactors treat wastewater of temporally variable composition under different weather conditions, while the microbial populations of wastewater treatment plants are often studied in controlled laboratory-scale systems with defined influent at a constant temperature. 16S rRNA- and ammonia oxidising amoA-gene-defined bacterial community structure was investigated in industrial and laboratory-scale moving bed biofilm bioreactors (MBBRs) treating municipal wastewater (WIN) or synthetic ammonium solution (AS). Nitrification activity, 16S rRNA and amoA gene T-RFLP profiles were comparable between industrial and laboratory scale WW bioreactors. AS bioreactors exhibited higher nitrification and higher relative abundances of Nitrosomonadaceae and Nitrospiraceae families but only small changes in the general bacterial community structure was detected compared to WW MBBRs. Nitrosomonas europaea lineage dominated WW, while uncultivated Nitrosomonas-like sequences prevailed in AS bioreactors. These results suggest that influent type has a stronger influence on community structure than operational conditions, such as temperature or bioreactor size. (C) 2012 Elsevier Ltd. All rights reserved.