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To characterize the effects of pentachlorophenol (PCP) on the performance and microbial community of aerobic granular sludge insequencing batch reactor (SBR), the web-based terminal restriction fragment length polymorphism (T-RFLP) and real-time PCR (RT-PCR) techniques were used to explore the bacterial community structure. When PCP increased from 0 to 50 mg/L, the COD removalrate changed little, while the ammonia removal rate dropped from 100% to 64.9%. The results of molecular characterization showedthat the quantity of ammonia oxidizing bacteria (AOB) kept constantly, although the number of bacteria species decreased with theincrease of PCP concentation. Significant shift in bacterial community structure at different PCP stresses was observed within aerobicgranular sludge. When the PCP was absent, there are 69 strains in aerobic granular sludge detected by T-RFLP method. With theincrease of PCP, most of bacteria disappeared and only 19 bacteria existed at all five PCP concentrations. These results contributed tocomprehensive understanding of the microbial community structure under the PCP stress and its relationship with the performance forwastewater treatment by aerobic granular sludge.