Genomic DNA Extraction and Sequencing Protocol

Using the method described by Marmur [32 (link)], the genomic DNA from strain F20-122^T was extracted and purified for 16S rRNA and rpoB´ gene analysis and for genome sequencing. The quality of the DNA was checked by (1%) agarose gel electrophoresis. DNA quantification was determined by spectrophotometry (DeNovix DS-11 FX, DeNovix Technologies, Wilmington, Delaware, USA) and fluorometry (Qubit 3.0 Fluorometer, Thermofisher Scientific, USA). The 16S rRNA and rpoB´ genes were amplified by PCR [33 ] with the universal primers ArchF and ArchR [34 (link),35 (link)] and the primers designed by Fullmer et al. [36 (link)], respectively. The PCR products were sequenced by StabVida (Oeiras, Portugal) using the Sanger method and the same primers. For the 16S rRNA gene sequencing, primers 16RB36 (GGA CTA CCA GGG TAT CTA) and 16RD34 (GGT CTC GCT CGT TGC CTG) were also used. Sequencing reactions were carried out using a BigDye terminator kit version 3.1 from Applied Biosystems. A draft genome sequence of strain F20-122^T was also determined in this study using a whole-genome shotgun strategy. After the DNA quality control, a library was constructed using the Kappa HyperPrep library preparation kit. The generated DNA libraries were sequenced in the lllumina Hiseq 4000 platform, using 150 bp paired-end sequencing reads (StabVida, Oeiras, Portugal).