Dataset: Salp and pteropod associated microorganisms from the Western Edge of the Gulf Stream sampled in September 2019.

Collected from the western edge of the Gulf Stream (26°43′93″ N, 79° 59′15″ W) in September 2019, 5–8 km east of West Palm Beach, Florida. All samples were collected during daylight in the upper 15 m. Sampling was done by hand.

Jars with animals and jars with seawater were brought on the deck of a 10 m dive vessel for processing. Within 30 min of divers surfacing, samples were archived or processed as follows. Salps and pteropods were gently poured onto a metal sieve then rinsed with 0.2 μm filtered seawater. Each gut was then removed with dissecting scissors, avoiding as much of the gelatinous tissue as possible. Guts were placed into sterile bead-beating tubes with 0.55 and 0.25 mm sterile glass beads and stored on dry ice until archiving at −80°C in a shore-based laboratory. Salp faecal pellets were sampled from different salp specimens incubated in jars for approximately 1-h after collection. Faecal pellets were collected on a mesh sieve (500 μm), rinsed with 0.2 μm filtered seawater, then stored as above. Jars containing seawater collected near sampled animals were transported on blue ice to the shore-based laboratory. For flow cytometry samples, 2 ml of seawater was fixed at a final concentration of 0.125% TEM grade glutaraldehyde (Tousimis), incubated at room temperature for 10 min, then flash frozen in ethanol cooled with dry ice. Seawater DNA samples were taken by peristaltic pumping onto 0.2 μm membrane filters and were stored on dry ice until archiving at −80°C.