Prokaryotic and eukaryotic microbiomes associated with Cochlodinium polykrikoides

High-throughput amplicon sequencing was used to assess bacterial (16S) and phytoplankton assemblages (18S) associated with blooms of the ichthyotoxic dinoflagellate, C. polykrikoides, during recurrent blooms on eastern Long Island, NY, USA. Over a three-year period, samples were collected inside (‘patch’) and outside (‘non-patch’) dense accumulations of C. polykrikoides to determine the core bacterial and eukaryotic microbiomes associated with these blooms.