Dataset: Bacterial transcriptional response to picoeukaryote Micromonas commoda

Axenic cultures of Micromonas commoda RCC299 (National Center for Marine Algae, NMCA) were grown in 1 L of organic-carbon free defined medium L1-Si [31] as modified by NCMA (https://ncma.bigelow.org/) at a salinity of 35 in 1900 mL vented polystyrene tissue culture flasks. Flasks were maintained at 18 oC under 16 h light at 160 μmol photons m−2s−1 and 8 h dark. Pre-cultures of Micromonas were sequentially upscaled (50 ml, 200 ml, 1 L) with transfers occurring during the exponential growth phase. After growing for 7 d (early stationary growth phase; ~2.7 × 106 cells ml−1), three marine bacteria pre-grown in YTSS medium (Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, and Polaribacter dokdonensis MED152 were washed 5 times in sterile L1 medium at 6000 RCF and inoculated into the axenic cultures at ~106 cells ml−1. Three or four replicate co-cultures were established for each bacterial strain and also for an axenic phytoplankton control. Three additional treatments were established with bacterial strains introduced individually into L1 medium with 400 μM C glucose as the sole carbon source (which supports all 3) at the same initial cell concentration as the co-cultures. As this treatment contained a single, known metabolite, it served as a control for co-culture transcriptome analysis. Bacterial contamination of the axenic phytoplankton cultures was ruled out based on lack of colony formation from culture aliquots spread onto YTSS plates and absence of bacterial-size particles in flow cytometry scattergrams.