Single-cell PCR of the luciferase conserved catalytic domain reveals a unique cluster in the toxic bioluminescent dinoflagellate Pyrodinium bahamense

Pyrodinium bahamense is a toxic, bioluminescent dinoflagellate with a record of intense bloom formation in both the Atlantic-Caribbean and Indo-Pacific regions. To date, limited genetic information exists for P. bahamense in comparison to other closely related harmful algal bloom taxa such as Alexandrium, or other bioluminescent taxa such as Pyrocystis. This study utilized single-cell PCR to explore the molecular diversity of P. bahamense within the Indian River Lagoon (IRL), Florida, USA, and a bioluminescent bay in Puerto Rico. Pyrodinium-specific primers targeting a ca.1.2-kb region of the 18S rRNA gene and degenerate primers targeting the conserved catalytic domain of the luciferase gene (lcf) were applied to single cells isolated from both geographic regions as well as single cells of clonal isolates from the IRL. Phylogenetic analysis revealed that while P. bahamense is more closely related to Alexandrium spp. at the 18S rRNA gene level, its lcf sequences are more closely related to Pyrocystis spp. than Alexandrium spp. Pyrodinium bahamense lcf sequences from the Western Atlantic formed 2 distinct clusters. These clusters were defined by a set of core amino acid substitutions, and the extent of variation was greater than that recorded between the established variants of Pyrocystis lcf. lcf sequences from an Indo-Pacific strain formed a third distinct cluster. Based on these results, the potential of lcf for use in tracking sub-populations of P. bahamense is discussed