An advanced side-stream reactor process with alkaline treatment (SIPER) has been demonstrated excellent sludge reduction potential and nutrient removal in the previous pilot-scale studies. The microbial community characteristic of the process was investigated in this study. The results indicated that the return of alkaline-treated sludge did not influence microbial activity of the activated sludge containing a higher diversity of bacteria in the SIPER process. Sludge in the biological nutrient removal (BNR) system and in the side-stream reactor (SSR) showed significantly different microbial composition, although two systems were connected via sludge recycle. The unique bacterial community was attributed to high pH environment in the SSR. Sequences represented by predominant DGGE bands were affiliated with Proteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, and Chlamydiae. The predominant bacteria in the system were nitrifying, denitrifying, and hydrolytic acid producing bacteria. The hydrolytic acid producing bacteria played an important role in achieving lysis-cryptic growth of cells while nitrifying and denitrifying bacteria laid the foundation for effective nitrogen removal. Plenty of nitrifying and denitrifying bacteria existed in the SSR, which improved the utility of the supernatant of alkaline-treated sludge as an additional carbon source and enhanced nitrogen removal of the system. (C) 2015 Elsevier Ltd. All rights reserved.