Dataset: Particle-associated microbial respiration from RESPIRE sediment trap deployments during R/V Atlantis cruise AT50-10 in the Eastern Tropical Pacific in May 2023 and R/V Sally Ride cruise SR1919 in the Santa Barbara Basin in Dec 2019

Sediment trap deployments and sample collection

REspiration on Sinking Particles In the subsuRface ocEan (RESPIRE) particle collection and incubation systems (Boyd et al., 2015; Bressac et al., 2024) were deployed on a drifting, surface-tethered trap (STT) array at each station for 2-3 days at depths between 80-225 m. RESPIRE traps were filled with 0.2 µm-filtered seawater collected from a CTD cast 2-3 hours prior to deployment. Upon recovery, overlying seawater in RESPIRE traps was siphoned off immediately after recovery, remaining RESPIRE water was collected for bacterial production, dissolved organic carbon (DOC), and cell count measurements, and remaining sample water was passed through a rotary wet splitter and divided into equal fractions. All trap samples were passed through screens to remove zooplankton “swimmers”. Split fractions of the sample water were then vacuum filtered onto pre-combusted 25mm GF/F (Whatman, Maidstone, Kent, United Kingdom) or quartz (Whatman) filters for CHN analyses. Samples collected for DNA were vacuum-filtered onto 25 mm or 47 mm 0.2 µm pore size polyethersulfone filters (Pall Supor, Port Washington, New York, USA), flash-frozen, then stored at -80°C until further processing in the lab. Filters for cell counts and CHN analyses were stored at -20°C and -80°C respectively until further processing in a shore-based lab.

Dissolved and total organic carbon measurements

Prior to each deployment, the 0.2 µm-filtered seawater used to fill RESPIRE traps prior to deployment was sampled for DOC and used as the DOC_initial timepoint. After recovery, particle-containing water was collected from RESPIRE traps for DOC or total organic carbon (TOC) determination (DOC_final or TOC_final). Combusted 40 mL glass vials with Teflon-lined caps were used for sample collection. For DOC samples, water was filtered into the vial using a 0.2 µm filter to a volume of ~30 mL and was acidified with 50 µL of DOC-free 4 N hydrochloric acid (Stephens et al., 2020). TOC samples were collected following the same protocol but without 0.2 µm filtration. All samples were stored at 4°C until measurements could be made in a shore-based lab. DOC and TOC concentrations were measured via the high temperature combustion method using modified Shimadzu TOC-V or TOC-L analyzers following Halewood et al. (2022).

DAPI staining and cell enumeration on particles

Particle-containing fluid (~15mL) from RESPIRE traps were collected and fixed with 0.405 mL of formalin for the purposes of DAPI staining and cell enumeration. Samples were vacuum filtered onto 25 mm, 0.2 µm poresize polycarbonate filters (Pall Supor). Five mL were pipetted into the filtration tower and filtered using vacuum filtration until ~0.5 mL remained above the filter. 0.5 mL DAPI solution (5 µg/mL) was added to the sample, and the filtration tower was covered with foil and left to stain for 3 min. After 3 min, the remaining sample was filtered. The filtered sample was removed from the filtration tower and mounted on a labeled glass microscope slide using a drop of immersion oil between the slide and filter and another drop between the filter and cover slip. Filters were stored at -20°C until imaging and counting on-shore. Epifluorescence microscopy (63X objective, Zeiss Axio Observer 7 Inverted microscope, Carl Zeiss Microscopy, LLC, White Plains, NY, USA) was used to take 12 digital images across different parts of each sample filter.