Universal Amplicon Sequences (mixed 16S/18S) from SCOPE Gradients 4 Cruise
The sequences are from a sampling campaign on the SCOPE Gradients 4 cruise (R/V Thompson; TN397) in November 2021. The sample sites are spaced approximately every 46 kilometers over a 3,000-kilometer northwestward transect from San Diego, California, through the California Current System, and across the North Pacific Subtropical Gyre. Three liters of surface seawater collected from the shipboard Underway system were aliquoted into three 1L bottles and each filtered through a 0.22 um Sterivex-GV filter (EMD Millipore; SVGVL10RC) with a peristaltic pump. Filters were sealed with Luer lock plug caps (MRO Supplies; 51525K333, 51525K334) and stored at -80 C.Before DNA extraction, the lysis buffer for each sample was spiked with 20 uL of three genomic standards of non-marine organisms to use as internal standards for analysis (Gifford et al., 2020, doi:10.3389/fmicb.2020.575194; Harrison et al., 2020, doi:10.1111/1755-0998.13247). The protocols followed for cell lysis and DNA recovery were adapted from Bostrom et al., 2004, doi:10.4319/lom.2004.2.365 (Manganelli et al., 2009, doi:10.1371/journal.pone.0006941; Signori et al., 2014, doi:10.3389/fmicb.2014.00647). The wet lab procedures followed for PCR are available at doi.org/10.17504/protocols.io.vb7e2rn. Here the GoTaq master mix (Promega, M5132/5133; Lot #0000520348) was used for DNA amplification with the 515Y (59-GTGYCAGCMGCCGCGGTAA) and 926R (59-CCGYCAATTYMTTTRAGTTT) primers (Parada et al., 2016, doi:10.1111/1462-2920.13023). Sequencing was done at Tufts University Medical School using HiSeq RapidRun technology (2x250 bp).