Disruption and stability in the oyster microbiome
Creators: name: Yeh, Heidi
Publisher: name: No Publisher Supplied
Year: 2023

description: This dissertation profiled the microbiome of the Eastern oyster Crassostrea virginica to explore its dynamics in the Delaware Bay and beyond. This body of work features the first application of the relatively new ONT MinION sequencing platform to study the oyster microbiome using the whole rRNA operon to generate strain-level taxonomic identifications of bacteria. The experiments described herein employed increasing levels of manipulation, starting from simple field collections in chapter 2, progressing to manipulations on oyster farms in chapters 3-4, and culminated in a highly-controlled laboratory experiment in chapter 5. To develop a baseline understanding of the oyster microbiome in the Delaware Bay, oysters were collected from a variety of locations along a salinity gradient, multiple timepoints, and subtidal/intertidal contexts. The extent to which each of these factors influenced the microbiome was characterized, as well as the relationship of oysters to the surrounding water. Oyster and water samples collected from the New York City harbor collected under similar circumstances were then used as a point of comparison to the Delaware Bay oysters. In both harbors, water and oyster microbiota were significantly different. Seasonal changes in the environment drove significant microbiome changes in both estuaries, but geographic variation within the estuary was only significant in the NYC Harbor. There was more similarity between oysters of the two estuaries than there was to their respective water samples, or between the water samples themselves. A core microbiome was identified for oysters from both bays, which shared 41% of their strains in common. The core microbiome identified for the Delaware Bay was used in subsequent chapters to quantify disturbance to the core microbiome of oysters originating from this estuary. The oyster microbiome response to disturbance was studied in the aquaculture context through a series of overwintering and heat shock experiments. In both cases, oysters were sampled at multiple timepoints to describe the progression of seasonal changes, changes that resulted from the various treatments, and the persistence of microbiome changes in the weeks or months after a disturbance event. When comparing oysters subjected to different overwintering treatments, the relative abundance of core Delaware Bay oyster microbiota provided clearer evidence of disturbance than typical measures of alpha- and beta-diversity provided. In both experiments, regardless of the level of disturbance that was caused by experimental manipulations, any evidence of this change was absent from the microbiome by the time that one or two weeks had elapsed. These experiments provided evidence that aquaculture disruption to the oyster microbiome does not have consequences for its overall composition in the long-term (on the scale of months), and that core microbiome analysis has utility for quantifying disturbance. To further investigate the topic of microbiome disruption, a series of highly-controlled experiments were performed in a laboratory setting. Oysters were subjected to treatment with antibiotics and/or challenged with Perkinsus marinus in a 2-way factorial design. Although antibiotics did not induce a difference in susceptibility to dermo disease as a result of the challenge, significant changes were observed in the microbiome as a result of a primary disturbance (antibiotic exposure) followed by a secondary disturbance (P. marinus challenge or oyster death). Throughout this dissertation, no evidence was found for a pathobiome of dermo disease that would manifest as significant whole-microbiome changes, but specific taxa like the Mycoplasma genus appeared to be correlated with oyster health. Given the enormous amount of sequencing data that was generated for this dissertation (with millions of sequence reads, identified as 11,000+ strains), seemingly limitless opportunities remain to continue to further refine the taxonomic identities of the oyster microbiota, as well as their significance to the oyster host and its ecosystem function.