Marker gene sequencing of environmental sample
The v4-v5 hypervariable regions of the archaeal SSU rRNA gene were amplified using degenerate primers. The primers were 517F (GCCTAAAGCATCCGTAGC GCCTAAARCGTYCGTAGC GTCTAAAGGGTCYGTAGC GCTTAAAGNGTYCGTAGC GTCTAAARCGYYCGTAGC) and 958R (CCGGCGTTGANTCCAATT). Amplification was done with fusion primers containing the 16S-only sequences fused to Illumina adapters. The forward primers included a 5 nt multiplexing barcode and the reverse a 6 nt index. We generated PCR amplicons in triplicate 33 uL reaction volumes with an amplification cocktail containing 0.67 U SuperFi Taq Polymerase (Invitrogen, Carlsbad, CA), 1X enzyme buffer (includes MgCl2), 200 uM dNTP PurePeak DNA polymerase mix (ThermoFisher), and 0.3 uM of each primer. We added approximately 10-25 ng template DNA to each PCR and ran a no-template control for each primer pair. Amplification conditions were: initial 94C, 3 minute denaturation step; 30 cycles of 94C for 30s, 57C for 45s, and 72C for 60s; final 2 minute extension at 72C. The triplicate PCR reactions were pooled after amplification, visualized with the negative controls on a Caliper LabChipGX or Agilent TapeStation 4200, and purified using Ampure followed by PicoGreen quantitation and Ampure size selection.