Dynamics of finely resolved, abundant symbiotic marine plankton and other interacting microbes via automated high-frequency sampling

Short time-scale observations are valuable for understanding microbial ecological processes. We assessed dynamics in relative abundance and potential activities by sequencing the small sub-unit ribosomal RNA gene (rDNA) and rRNA molecules (rRNA), of Bacteria, Archaea and Eukaryotes once to twice-daily between March and May in the surface ocean off Catalina Island, California. Typically Ostreococcus, Braarudosphaera, Teleaulax, and Synechococcus dominated phytoplankton sequences while SAR11, Sulfitobacter and Fluvicola dominated non-phytoplankton prokaryotes. We observed short-lived increases of diatoms, mostly Pseudo-nitzschia and Chaetoceros, with quickly-responding prokaryotes including Flavobacteria (Polaribacter, Formosa), Roseovarius, and Euryarchaea (MGII), which were the exact sequence variants we also observed as temporally most-abundant in another diatom bloom at a nearby location, 3 years prior. We observed positive correlations representing known interactions among abundant taxa in chloroplastic rRNA sequences, demonstrating the ecological relevance of such interactions and their influence on the environment: 1) The kleptochlorplastidic ciliate Myrionecta 18S and Teleaulax chloroplasts (16S) were correlated (Spearman r =0.83) yet uncorrelated to Teleaulax nuclear 18S, nor any other taxon and 2) the photosynthetic prymnesiophyte Braarudosphaera bigelowii and 2 strains of diazotrophic cyanobacterium UCYN-A were correlated and each was correlated to multiple other taxa, including Braarudosphaera to a Verrucomicrobium and a Dictyophyte phytoplankter (all r > 0.8). We also report strong correlations (r > 0.7) between ciliates and bacteria and phytoplankton, possibly representing mutually beneficial interactions. These data reiterate the utility of high-frequency time-series to show rapid microbial reactions to stimuli, and provide new information about in-situ dynamics of previously recognized and hypothesized interactions.