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Table S1. Characteristics of the environmental and operational parameters in Shatin WWTP from July 2007 to January 2011.

Table S2. Illumina sequencing metadata of the eight activated sludge samples in this study.

Table S3. The percentage abundances (%) of the major phyla (top 15 in each sample) in the eight AS samples.

Table S4. Abundances of the top 20 genera in each AS sample.

Table S5. Percentages of the shared genera and their corresponding sequences.

Table S6. The relative abundances of the 28 functional categories in four ecosystems based on SEED subsystems implemented in mg-rast.

Fig. S1. Reproducibility of Illumina high-throughput sequencing at different sequencing depths.

Fig. S2. Heat map of major genera (top 20 in each sample) of the eight AS samples.

Appendix S1. Variation of environmental and operational parameters.

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