Groundwater 16S rRNA (PMA-treated), XB E00806, 5.5 m bgs, 2019-3-19
For selected samples, propidium monoazide (PMA) treatment was applied prior to DNA extraction to target DNA from viable cells. 16S rRNA gene amplicon libraries were prepared from groundwater DNA samples by Welgene Biotech Co., Ltd. (Taipei, Taiwan). The V3V4 hypervariable regions were amplified using primers Pro341F (5-CCTACGGGNBGCASCAG-3) and Pro805R (5-GACTACNVGGGTATCTAATCC-3). Libraries were generated using a two-step PCR protocol with dual-index barcoding and sequenced on the Illumina MiSeq platform. Raw reads were demultiplexed, PhiX reads were removed, and primer sequences were trimmed using the cutadapt plugin before QIIME 2 analysis.