CDPM_S3
The genomic DNA extraction was performed using NucleoSpin Soil kit (Macherey-Nagel, Germany). By calculating the A260/280 ratio, a spectrophotometer (NanoDrop One, made by Thermo Fisher Scientific, U.S.A.) quantified the isolated genomic DNA concentration. The quality of the isolated DNA was confirmed using agarose gel electrophoresis. Then, the quality control passed genomic DNA samples were processed for amplicon generation via polymerase chain reaction (PCR). Specific primers such as 16S rRNA F (GCCTACGGGNGGCWGCAG) and 16S rRNA R (ACTACHVGGGTATCTAATCC) were used for amplification of bacterial hypervariable regions (V3-V4). The ITS 1F (GCATCGATGAAGAACGCAGC) and ITS 2R (TCCTCCGCTTATTGATATGC) primers were used for the amplification of the fungal ITS region. For making copies of the 16S rRNA gene of archaea, the 16S rRNA Arch-F (GYGCASCAGKCGMGAAW) and 16S rRNA Arch-R (GGACTACVSGGGTATCTAAT) primers were used. Samples that passed the quality control test were used to prepare an NGS library using an index kit (Nextera XT Illumina Inc.) and the library preparation protocol for 16S metagenomic sequencing (part # 15044223 Rev.B) (Illumina, 2013). The libraries were sequenced on the Illumina MiSeq platform using 2x300 bp chemistry (Illumina, San Diego, USA). The amplicon libraries were cleaned with AMPureXP beads, measured with a Qubit Fluorometer, and checked for size distribution on an Agilent Technologies 4200 Tape Station system with a D1000 ScreenTape, following the manufacturer's instructions.