Bacterial and Archaeal Diversity in Nearshore Subtidal Sediments
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.