The top 3cm of sediment was collected and mixed from each core. Sediment was stored a -80C before being processed. DNA was extracted using 10.5 g of sediment and the PowerMax soil DNA Isolation Kit (MoBio Labs). Bacteria 16S rRNA gene fragments were amplified using a mixture of 5 forward and 4 reverse primers targeting the V6 hypervariable region. The same region was targeted for the archaeal 16S rRNA gene using a mixture of 1 forward and 2 reverse primers. Primers were modified to include a 5-bp barcode (forward primers) and adapter sequences for the Ion Torrent PGM sequencer (Life Technologies). Triplicate reactions were combined and cleaned up with the Qiagen MinElute PCR Clean-up kit. Barcoded samples were pooled to achieve equalmolar concentrations and sequenced using the 100 bp V2.0 kit from Life Technologies using 316 chips.
The top 3cm of sediment was collected and mixed from each core. Sediment was stored a -80C before being processed. DNA was extracted using 10.5 g of sediment and the PowerMax soil DNA Isolation Kit (MoBio Labs). Bacteria 16S rRNA gene fragments were amplified using a mixture of 5 forward and 4 reverse primers targeting the V6 hypervariable region. The same region was targeted for the archaeal 16S rRNA gene using a mixture of 1 forward and 2 reverse primers. Primers were modified to include a 5-bp barcode (forward primers) and adapter sequences for the Ion Torrent PGM sequencer (Life Technologies). Triplicate reactions were combined and cleaned up with the Qiagen MinElute PCR Clean-up kit. Barcoded samples were pooled to achieve equalmolar concentrations and sequenced using the 100 bp V2.0 kit from Life Technologies using 316 chips.