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Decisions to close shellfisheries and beaches due to microbial contamination are often based on water quality assays of microbial contaminants that are slow, labor-intensive and do not differentiate between human and animal sources of waste.

This DNA hybridization assay was adapted by researchers at NOAA’s National Atlantic Oceanic and Meteorological Laboratories and the University of Miami to detect a variety of microbial contaminants important to coastal water quality.The development and transfer of the assay was funded by CICEET, the Cooperative Institute for Coastal and Estuarine Environmental Technology. It can provide sensitive and specific molecular analysis in a convenient, adaptable, and relatively inexpensive format. Water quality managers can adapt this technique to the molecular probes of their choice, or it can be used as an introduction to molecular methods for educational purposes.

This assay is in a microtiter plate format that can be used to provide quick, colorimetric detection of a variety of organisms. Molecular probes for the species of interest are bound to the surface of microtiter plates. DNA is amplified and labeled with biotin during thermal cycling, hybridized to the probe bound on the plates, and detected by a HRP chemistry-based colorimetric reaction.

The assay provides immediate visual results, is more specific and convenient than a series of species-specific PCR reactions, and is faster, easier and less expensive than cloning. It is simple to add and adapt probes to the assay. The technique conserves the amount of genomic DNA utilized, which can be critical to certain applications. It also allow screening of samples without the microscopic or culturing expertise normally required.

These web pages offer step-by-step written instructions and a video tutorial on this assay. Questions about the approach should be directed to Dr. Kelly Goodwin at NOAA's National Atlantic Oceanic and Meteorologic Laboratories: