Defense Date


Document Type


Degree Name

M.S. Coastal Zone Management

First Advisor

Donald McCorquodale

Second Advisor

George Duncan


When analyzing the water quality of the coastal zone, culture-based techniques have been utilized most often to identify Fecal Indicator Bacteria in samples. Since the advent of the Sanger Method for DNA sequencing, other techniques have arisen that provide significantly more information on the microorganisms in sample, but they are still not the mainstream for water quality analysis. This capstone reviews and compares culture-based techniques, DNA sequencing, RNA sequencing, qPCR for biomarker, and 16S rDNA sequencing to highlight their merits and shortcomings for analyzing environmental water samples. The technique presented that provides the broadest range of information (including the identification of bacteria, viruses, fungi, pathogens, virulence factors, and antibiotic resistance genes) is whole genome shotgun sequencing paired with k-mer based microbial identification. This technique allows researchers and managers not only to identify all microorganisms present in a given sample, but to identify sources of these microorganisms and infection potential to humans as well. This has huge implications for the future of water quality management and provides invaluable information that recreational water managers can use to determine risk to human health. As modern methods drop in price, they are becoming more accessible to user groups. This capstone is designed to help users determine the best method for their individual needs.