Comparison of Quantitative Detection Methods for Enumeration of HAB Species: Applications for Resource Management

James Farm
             There has been a shift from microscopy to molecular methods for identifying and quantifying harmful algal bloom (HAB) species in environmental water samples. Molecular methods greatly increase the number of samples that can be processed each day while also increasing sensitivity and accuracy. While several molecular methods have been validated for HAB species quantification, they have not been rigorously compared, representing a key gap in our ability to provide recommendations to managers for a specific regulatory requirement. Our research provides a thorough assessment of two molecular methods currently used for HAB monitoring and research: quantitative real-time PCR (QPCR) and sandwich hybridization assay (SHA).QPCR and SHA are applicable to several HAB species, but the proposed study will focus on the globally-distributed harmful raphidophyte, Heterosigma akashiwo as a model species. Our objectives are to (1) Directly compare QPCR and SHA for quantification of H. akashiwo isolates spanning a range of cell abundances, growth phases, and nutrient conditions; (2) Determine the extent to which quantification of H. akashiwo is comparable using QPCR and SHA for natural phytoplankton communities (3) Synthesize comparisons according to a suite of criteria to enhance HAB monitoring and research activities.

            In this targeted study, QPCR and SHA will be critically compared, and recommendations will be made to managers for HAB monitoring strategies based upon specific criteria such as the range and limit of detection required, cost per sample, and sample throughput. Our results will provide management with the ability to make informed decisions when incorporating molecular methods into HAB monitoring programs.

        Investigators: Dianne Greenfield (, University of South Carolina, Belle Baruch Institute for Marine & Coastal Sciences and Kathryn J. Coyne ( Funded by a grant from the National Oceanic and Atmospheric Administration (NOAA).

Return to Research

  • Microbial Ecology Research Lab  •   700 Pilottown Road  •   Lewes, DE 19958  •   USA
    Phone: 302-645-4288  •   E-mail: