Population genetic studies provide insights into intraspecific diversity and dispersal patterns of microorganisms such as protists, which help understanding invasions, harmful algal bloom development and occurrence of seafood poisoning. Spatial genetic differentiation has been reported in many microbial species indicating significant dispersal barriers among different habitats. Temporal differentiation has been less studied and its frequency, drivers, and magnitude are thus relatively poorly understood. The toxic dinoflagellate species Gambierdiscus caribaeus was sampled during 2 years in the Florida Keys, and repeatedly from 2006 to 2016 at St. Thomas, US Virgin Islands (USVI), including a 3-year period with monthly sampling, enabling a comparison of spatial and temporal genetic differentiation. Samples from the USVI site showed high temporal variability in local population structure, which correlated with changes in salinity and benthic habitat cover. In some cases, temporal variability exceeded spatial differentiation, despite apparent lack of connectivity and dispersal across the Greater Caribbean Region based on the spatial genetic data. Thus, local processes such as selection might have a stronger influence on population structure in microorganisms than geographic distance. The observed high temporal genetic diversity challenges the prediction of harmful algal blooms and toxin concentrations, but illustrates also the evolutionary potential of microalgae to respond to environmental change.

The genus Gambierdiscus is a recognized group of marine epiphytic-benthic dinoflagellates that produce the toxins that cause ciguatera fish poisoning (CFP). To date, thirteen species and six ribotypes of Gambierdiscus have been identified, and multiple species commonly co-occur within a single site or epiphyte community. Toxicity can vary by species, thus it is important to be able to differentiate among species for research and monitoring purposes. Gambierdiscus species have very similar morphological characteristics and are difficult or impossible to distinguish using light microscopy. DNA sequencing has been an important tool in the definition of Gambierdiscus species, but it can be time-consuming and relatively expensive. To provide an alternative approach, a PCR-RFLP protocol was developed for efficient, rapid, and cost-effective identification of Gambierdiscus strains isolated from the Gulf of Mexico and Caribbean Sea, where CFP cases and Gambierdiscus spp. have been reported. The assay targets the D1-D2 hypervariable regions of the large subunit ribosomal RNA gene and uses a single restriction enzyme, BsrI. This method produces distinct RFLP banding patterns for the six species of Gambierdiscus reported from the Gulf of Mexico and Caribbean Sea, and also distinguishes them from four Pacific endemic species. This method was successfully used to type 465 clonal isolates of Gambierdiscus from the U.S. Virgin Islands and Akumal Beach - Mexico This BsrI PCR-RFLP method expands the tools available to researchers and managers engaged in monitoring activities and ecological studies.