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The inhibition of free ammonia (FA) to the granule-based enhanced biological phosphorus removal (EBPR) system and the recoverability from macro- to micro-scale were investigated in this study.FAwas found to seriously deteriorate the EBPR performance and sludge characteristic (settleability and morphology).The FA inhibitory threshold of 17.76 mg N L 1 was established.Acclimation phenomenon took place when poly-phosphate accumulating organisms (PAOs) were exposed for long time to constant FAconcentration (8.88 mg N L 1).The repressed polysaccharides excretion could lead to breaking the stability and integrity of the granules.Therefore,the reduced particle size and granule disintegration were observed.The molecular analysis revealed that FA had a significant influence on the microbial communities and FA inhibition may provide a competitive advantage to glycogen accumulating organisms(GAOs) over PAOs.Interestingly,the community composition was found irreversible by recovery (Dice coefficients,36.3%),although good EBPR performance was re-achieved.