The microbial community in a biological phosphorus removal process under different electron acceptor conditions was estimated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) assay and principal-component analysis (PCA). For this purpose, a lab-scale sequencing batch reactor (SBR) fed with municipal wastewater was operated under anaerobic–aerobic, anaerobic–anoxic–aerobic and anaerobic–anoxic conditions. The results of PCR-DGGE targeting the 16S rRNA gene indicated a significant shift in the microbial community with electron acceptor conditions. From the 16S rRNA-based PCA, the microbial shift implies that little oxygen supply caused the deterioration of aerobic bacteria, including aerobic polyphosphate-accumulating organisms (PAOs). Moreover, it also reflects the existence of nitrate-utilizing denitrifiers. On the other hand, although the band patterns of DGGE targeting a functional gene of denitrification (nirS) also showed the microbial shift, the result of PCA differed from that of 16S rRNA-based analysis. There is no conclusive proof that the bacteria represented as the dominant bands detected in the present study are denitrifying-PAOs so far, it should be worthwhile to identify the detected bacteria and to examine their traits as new denitrifying-PAO candidates.

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