Dataset: Cell concentrations associated with genomics sampling to characterize bacterial responses to parasite-host metabolites from bottle incubation experiments in June of 2024

Location description:
Collected water and conducted bottle incubations off the UNH Coastal Marine Laboratory pier in June 2024.

Cultures and incubation set-up:

Amoebophrya sp. (RCC 4401) parasite spores were maintained by adding fresh host (Scrippsiella acuminata, strain RCC 1627)

every 2-3 d at a ratio of 1:1 spore to host by volume. Parasite and host cultures were kept at 18 °C on a 12:12 hour light: dark cycle at 80-100 µmol photon m^-2 s^-1. Prior to the incubation experiment, exudates from freshly lysed S. acuminata were collected by filtering parasite cultures through 0.2 µm filters (Long et al. 2021). As controls, exudates were also collected from healthy host cultures and f/2 media used for culturing. All exudates were stored at 4 °C for <1 h before being combined with natural seawater for incubation experiments.

Surface seawater (20 L) was collected at high tide from the UNH Coastal Marine Laboratory (CML) pier that is located at the mouth of Portsmouth Harbor in New Castle, NH. Seawater was immediately brought back to the lab and filtered through a 1.2-µm mesh filter to isolate natural bacterial communities. Filtered seawater (500 mL) was combined with 1.5 L of either filtrate from infected, healthy host, or the f/2 culture media in triplicate 2-L polycarbonate bottles (Maas et al. 2020) to explore the bacterial response to sources of dissolved organic carbon (DOC). These treatments are represented as "Infected", "Host", or "Media" within the data file in the Treatment column. The baseline community is represented by "Natural" and reflects the bacterial community at the initial time of sampling (Time zero = T0). A total of 9 bottles were allowed to incubate at ambient sweater conditions for a total of 48 h in a crab trap fixed to the dock. Bottles were sampled at 6, 24, and 48 h for DNA/RNA filtration (~500 ml per bottle) and flow cytometry. Triplicate flow cytometry samples were also taken from the natural bacterial community at T0.

Flow cytometry:

Samples (1.8 mL) from each bottle and time point were fixed with 1% glutaraldehyde, stored at 4 °C, and run on a Guava easyCyte HT (Millipore) flow cytometer within 4 months of collection to estimate bulk bacterial abundances. To prepare for the run, 198 µl per sample was loaded onto a 96-well plate, stained with 100x SYBR Green (Thermo Fisher), and set in the dark at room temperature for 30 min (Nunn et al. 2024). Samples were run on the flow cytometer at low flow rate (0.24 µl s^-1) for 3 min per well. Bulk heterotrophic bacteria populations were distinguished from pre-defined gates based on plots of forward scatter, which provides an indication of cell size, and green fluorescence (512 nm). In this case, green fluorescence at an emission wavelength of 512 nm reflects the binding of double-stranded DNA  to the SYBR Green dye that emits fluorescence upon excitation. 

Organism information:

TaxonomicName, Life Science Identifier (LSID), strain_identifier, organism_type
Scrippsiella acuminata, urn:lsid:marinespecies.org:taxname:1321853, RCC 1627, host
Amoebophrya sp., urn:lsid:marinespecies.org:taxname:109448, RCC 4401, parasite