PCR Negative Control
All samples were amplified and sequenced with the Archaea-Specific primers; For the PCR control, in light of DNA elutions, nuclease free water was amplified using GoTaq Green Mastermix (Promega, Madison, WI, USA) and primers with index sequences for 2-step Illumina library preparation (Illumina, San Diego, CA, USA). Primer sequences are as follows with the index in italics and the target sequence in bold: Indexed516F (ACACTCTTTCCCTACACGACGCTCTTCCGATCTTGYCAGCCGCCGCGGTAAHACCVGC); Indexed915R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGTGCTCCCCCGCCAATTCCT). The PCR reaction included an initial incubation at 95C for 2 minutes, then 30 cycles of 95C for 60 seconds, 64C for 60 seconds, and 72C for 60 seconds and a final extension at 72C for 5 minutes. Amplification was confirmed using gel electrophoresis. Samples were sequenced on the Illumina MiSeq (Illumina, San Diego, CA, USA) platform at the University of Connecticut MARS core lab following library preparation.