Date of Award


Document Type

Campus Access Thesis

Degree Name

Master of Science (MS)



First Advisor

Michael P. Shiaris

Second Advisor

Douglas C. Woodhams

Third Advisor

William E. Robinson


The Eastern Oyster, Crassostrea virginica, is a critical connection between pelagic and benthic environments for coastal microeukaryotic organisms. Through selective filter feeding on planktonic microeukaryotes, oysters contribute directly to the benthic food source for other organisms by depositing microeukaryotes in feces or pseudofeces to sediments. This role in nutrient cycling provides valuable ecosystem services in promoting biodiversity and clean water, and mitigating eutrophication in coastal waters. However, it is not known whether oysters have a eukaryotic microbiome, or “eukaryome.” The eukaryome may affect the important bivalve protozoan pathogens Perkinsus marinus and Haplosporidium nelsoni. This study is the first to use next generation sequencing to characterize the eukaryotic microbial communities associated with C. virginica. Gill and digestive tracts were dissected from a total of 25 oysters (13 juvenile and 12 adult) collected from two aquaculture sites in Duxbury Bay, Massachusetts. NGS was performed on the metagenomic samples, targeting the 18s rRNA gene. Taxonomic analyses, principal coordinate analyses (PCA) and network analysis revealed a distinct separation in the gill versus digestive tract eukaryomes. Both were very different from surrounding sediment and water eukaryomes. Digestive tract eukaryomes were composed mostly of diatoms and gill communities were dominated by ciliates. PCA showed no difference between rinsed gill samples and non-rinsed samples, suggesting that these microeukaryotes are closely associated with the gill tissue, perhaps as intracellular symbionts or components of a biofilm. One oyster showed systemic infection of H. nelsoni (97% of gill reads, 70% of digestive tract reads), the causative agent of MSX disease in the Eastern Oyster. A different oyster had 74% of its gill reads belonging to Alexandrium tamarense, a dinoflagellate species known to produce the saxitoxin responsible for Paralytic Shellfish Poisoning in humans.


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