DNA extraction, 16S rRNA gene amplicon library preparation, sequencing, and bioinformatic analysis of sediment microbial fuel cell samples v1

This protocol describes DNA extraction, 16S rRNA gene amplicon library preparation, sequencing, and bioinformatic processing procedures used for the analysis of microbial communities associated with sediment microbial fuel cell (SMFC) systems. DNA was extracted from freeze-dried sediment and soil samples using mechanical disruption, Lysis Solution F treatment, and subsequent purification with the LabAid824s DNA Extraction Kit. Libraries targeting the V4 region of the prokaryotic 16S rRNA gene were prepared using a two-step tailed PCR strategy and sequenced on an Illumina NextSeq 1000 platform. Sequence processing was performed using FASTX-Toolkit, sickle, FLASH, QIIME 2, DADA2, and the SILVA database. This protocol provides detailed methodological information supporting the associated sequencing dataset and manuscript.