Date of Completion


Embargo Period


Major Advisor

J. Evan Ward

Associate Advisor

Marta Gomez-Chiarri

Associate Advisor

Spencer Nyholm

Associate Advisor

Senjie Lin

Associate Advisor

Milton Levin

Field of Study



Doctor of Philosophy

Open Access

Open Access


Prokaryotic communities are ubiquitous in every environment on earth. In the oceans they are integral to a number of biogeochemical processes and form the base of marine food webs. Microbes have also coevolved with eukaryotes, aiding in a variety of host functions including digestion and nutrient absorption, development of the immune system, and protection against pathogens. The disruption of these microbial communities, especially in the gut, has been linked to altered health statuses and physiological functions in a range of hosts. The eastern oyster, Crassostrea virginica (Gmelin, 1791), is a valuable economic and ecological resource in near-shore environments. As a result of their suspension-feeding activities, oyster tissues are in constant contact with bacteria in the water column. Considering such interactions, and the value of oysters to ecosystem functioning, the relationships of oysters and their associated microbial communities are surprisingly poorly understood. As such, the temporal and spatial distribution of the oyster microbiome within Long Island Sound was evaluated, as well as the role of environmental reservoirs of bacterial communities, both free-living and particle-associated. The oyster-associated gut microbiome was also compared to that of the blue mussel, Mytilus edulis Linnaeus, 1758. Finally, the role of these bacterial communities in oyster digestive activity and pathogen accumulation was assessed.

Major results indicate that oysters maintain similar microbial communities over time and space which are largely influenced by seawater temperature. Both genetic and functional diversity of the oyster-associated microbial communities decreased in the winter, as did environmental microbial communities. The stability of these communities across spatial scales may be due to oyster genetic factors, and the high gene flow in Long Island Sound. Oysters maintained a common community of microbes, or “core,” in their gut throughout the summer and fall. This core gut microbiome was also shared with mussels. In contrast to oysters, however, mussels maintained gut microbiomes which did not experience a decrease in functional diversity in winter months. This functional stability is likely due to the higher feeding activity of mussels in the winter compared to oysters. In individual microcosm experiments, a disturbance of the gut microbiota by antibiotics resulted in variable impacts on oyster physiological enantiostasis. Digestive enzyme activity and absorption efficiency showed few significant differences between antibiotic treated and control groups. When challenged with the pathogen Vibrio coralliilyticus, however, an advantage was seen in depuration of pathogens for those oysters which did not have a microbiome disturbed by antibiotics. Stability of digestive activity may be due to functional redundancy in the gut microbial community, the continued contribution of enzymes from lysed cells, and horizontal transfer of metabolic genes. Extended experiments with more time points, as well as repeated challenges, would help to further elucidate the role of oyster-associated microbial communities to the overall physiological functioning of the host. This research provides a vital baseline for future research aimed at understanding the role gut microbes have in oyster physiology.