Column-type combined reactors were designed to cultivate micro-aerobic pentachlorophenol (PCP) degrading granular sludge under oxygen-limited conditions (0.1-0.2 mg L-1) over 39-day experimental period. Micro-aerobic granular had both anaerobic activity (SMA: 2.34 mMCH(4)/h g VSS) and aerobic activity (SOUR: 2.21 mMO(2)/h g VSS). Metabolite analysis results revealed that PCP was sequentially dechlorinated to TCP, DCP, and eventually to MCP. Methanogens were not directly involved in the dechlorination of PCP, but might played a vital role in stabilizing the overall structure of the granule sludge. For Eubacteria, the Shannon Index (2.09 in inoculated granular sludge) increased both in micro-aerobic granular sludge (2.61) and PCP-degradation granular sludge (2.55). However, for Archaea, it decreased from 2.53 to 1.85 and 1.84, respectively. Although the Shannon Index demonstrated slight difference between micro-aerobic granular sludge and PCP-degradation granular sludge, the Principal Component Analysis (PCA) indicated obvious variance of the microbial composition, revealing significant effect of micro-aerobic condition and PCP on microbial community. Furthermore, nucleotide sequencing indicated that the main microorganisms for PCP degradation might be related to Actinobacterium and Sphingomonas. These results provided insights into situ bioremediation of environments contaminated by PCP and had practical implications for the strategies of PCP degradation. (C) 2014 Elsevier B.V. All rights reserved.