water sample of Citarum River downstream
Total genomic DNA from samples was extracted using the Cetyl trimethylammonium bromide/Sodium Dodecyl Sulfate (CTAB/SDS) method with the ZymoBIOMICS DNA Miniprep Kit (D4300) for water samples and PrestoTM Soil DNA Extraction (SLD100) for sediment samples. The concentration and purity of DNA were observed on 1% agarose gel. Based on the concentration, DNA was diluted to 1ng/L using sterile distilled water. The diversity and abundance of bacterial communities in water and sediment samples were analyzed by NGS using an Illumina HiSeq paired-end platform. Briefly, the hypervariable region (V4) of the bacterial 16S rRNA gene in the samples was amplified by PCR using the universal primer set 515F-806R and the Phusion High-Fidelity PCR Master Mix (New England Biolabs). The PCR reaction was carried out on each sample mixed with the same volume of loading buffer (containing SYB Green), then electrophoresed on 2% agarose gel, extracted, and purified using the Qiagen Gel Extraction Kit (Qiagen, Germany). Libraries were generated with the NEBNext UltraTM DNA Library Prep Kit for Illumina and measured via Qubit and Q-PCR, then analyzed by the Illumina platform.