DNA-Seq of river biofilm
DNA was extracted from a 0.2-g subsamples of biofilm using the PowerBiofilm DNA extraction kit (Qiagen, Germantown, MD, USA). Metagenomic sequencing was performed using the ZymoBIOMICS Shotgun Metagenomic Sequencing Service for Microbiome Analysis (Zymo Research, Irvine, CA, USA). Library preparation, where fragments were tagged with 8 bp internal dual-index barcode sequences with Nextera adapters (Illumina, San Diego, CA, USA), was completed by using Nextera DNA Flex Library Prep Kit (Illumina, San Diego, CA, USA) following manufacturer protocol. Library concentrations were quantified with TapeStation (Agilent Technologies, Santa Clara, CA, USA) to normalize abundances in the multiplexed pool for sequencing and quantified again using qPCR. The final library was sequenced using the NovaSeq (Illumina, San Diego, CA, USA) platform.