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.</p><p>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).