Effect of intermittent aeration cycle (IAC = 15/45-60/60 min) on nutrient removal and microbial community structure was investigated using a novel fluidized bed reactor-membrane bioreactor (FBR-MBR) combo system. FBR alone was found more efficient for removing PO4-P (>85%) than NH4-N (<40%) and chemical oxygen demand (COD < 35%). However, in the combo system, COD and NH4-N removals were almost complete (>98%). Efficient nitrification, stable mixed liquor suspended solid and reduced transmembrane pressure was also achieved. Quantitative real-time polymerase chain reaction results of total bacteria 16S rRNA gene copies per mL of mixed-liquor varied from (2.48 +/- 0.42) x 10(9) initial to (2.74 +/- 0.10) x 10(8), (6.27 +/- 0.16) x 10(9) and (9.17 +/- 1.78) x 10(9) for 15/45, 45/15 and 60/60 min of IACs, respectively. The results of clone library analysis revealed that Proteobacteria (59%), Firmicutes (12%) and Bacteroidetes (11%) were the dominant bacterial group in all samples. Overall, the combo system performs optimum nutrient removal and host stable microbial communities at 45/15 min of IAC. (C) 2014 Elsevier Ltd. All rights reserved.