Dataset: OC1703A Sediment 16S rRNA and 16S rRNA gene amplicon sequences
Deployment: OC1703A

Sediment was collected with an MC-800 multicorer aboard the R/V Oceanus (expedition 1703A) approximately 0-300 km off the coast of San Francisco, CA, USA. Cores were stored at 4C until extrusion and sectioning within 24h of collection. Cores were sectioned into 2.5-5cm vertical horizons, and approximately 2g of sediment were sampled from each horizon with a cut-off syringe, flash frozen in liquid nitrogen, and stored at -80C until extraction of nucleic acids. DNA was extracted with an RNeasy PowerSoil DNA elution kit (Qiagen, cat. no 12867-25) in combination with an RNeasy PowerSoil Total RNA kit (Qiagen, cat. no 12866-25). The manufacturer's protocol was modified to include a bead-beating step of 5.5 m/s for 2x45s with a FastPrep-24 instrument. DNA and RNA was eluted in 100 microliters of DNAse and RNAse-free water or 1xTE and stored at -80C. Total RNA was treated with DNAse (Thermo Fisher Scientific,cat. no AM1907). RNA was then reverse transcribed to cDNA using the SuperScript III First Strand RT PCR kit according to the manufacturer’s instructions (Thermo Fisher Scientific, cat. no 18080-400). DNA and cDNA were amplified wtih universal V4/V5 primers, 515F/926R (Parada et al., 2016). The loci-specific cycling conditions included an initial heating step at 95 C for 180 s, followed by 25 cycles of 95 C for 45 s, 50 C for 45 s, 68 C for 90 s, and a final extension of 68 C for 5 min. Barcodes were added to individual samples by a second PCR step consisting of an initial denaturation step at 95 C for 180 s, followed by 8 cycles of 95 C for 30 s, 55 C for 30 s, 72 C for 30 s and a final extension step at 72 C for 300 s. Sequencing was performed at the UC Davis Genome Center using Illumina MiSeq 2 x 250 bp paired-end technology.