title: Gold mine AMD Raw Water
design: Environmental DNA was extracted from three acid mine drainage (AMD) water samples using a Zymo Research DNA extraction kit according to the manufacturers instructions. DNA quantity and quality were assessed prior to library preparation. High-molecular-weight genomic DNA (1.5 g per sample) was fragmented using a g-TUBE device (Covaris Ltd.) to obtain the desired insert size distribution. SMRTbell libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences), following the manufacturers protocol, including DNA damage repair, end repair/A-tailing, adapter ligation, and bead-based purification. Libraries were quality-checked prior to sequencing. Whole-metagenome shotgun sequencing was performed at Inqaba Biotech (Pretoria, South Africa) using the PacBio Sequel II platform (Pacific Biosciences). Libraries were sequenced using Single-Molecule Real-Time (SMRT) sequencing chemistry in circular consensus sequencing (CCS) mode to generate high-fidelity (HiFi) long reads. CCS reads were generated using SMRT Link software with standard quality filtering parameters.