Comprehensive Microbial Community Analysis

One sludge sample was collected on November 15, 2018, from a well-operated one-stage PNA reactor under the same operating parameters as in our previous study [15 (link)]. Genomic DNA was extracted using the DNeasy PowerSoil Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. DNA concentration and purity were determined using a Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and NanoDrop 1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA) as previously described [25 (link)]. The total DNA was divided into two equal parts, with one part sequenced by Novogene Company Limited (Beijing, China) using shotgun sequencing on an Illumina HiSeq 4000 PE150 sequencer (Illumina, CA, USA) to generate 150 bp paired-end reads with a 350-bp insert size, and the other sequenced by the Chinese University of Hong Kong (Hong Kong, China) using a Nanopore PromethION sequencer (Oxford Nanopore Technology, UK).