Dataset: Eukaryotic and prokaryotic microbial taxa retained by wild-caught doliolids collected during bloom events at three different shelf locations in the northern California Current system in June 2019.

Samples were collected during daylight from the R/V Atlantis (AGOR-25) along the Newport Hydrographic (NH) Line at station “NH5” (N 44° 39.084’, W 125° 7.151’) on July 22nd as well as along the Trinidad Head (TR) Line at stations “TR1” (N 41° 3.467, W 124° 16.016) and “TR3” (N 41° 3.448, W 124° 26.7) on July 17th and 19th, respectively.

Doliolids were sampled using a modified coupled Multiple Opening and Closing Net and Environmental Sensing System (MOCNESS). Doliolids were rinsed three times with 0.2 µm filtered seawater to remove unattached microbes, collected in a 1-mL sterile bead-beater tube containing 0.55- and 0.25-mm beads, and then frozen at -80 °C.