Award: OCE-1634167

The objective of this project was to determine how ocean acidification influences DNA methylation in oysters and to what degree parental exposure to ocean acidification influences offspring. The rationale for this objective was to better understand how environmental conditions impact coastal ecosystems. Epigenetic processes such as DNA methylation are critical mechanisms linking environment to organismal physiology, and could drive effects on subsequent generations. In terms of characterizing the impact of ocean acidification on oyster DNA methylation, a series of experimental trials were performed. We were also able to provide an improved characterization of DNA methylation in this taxa as well as establish linkages with transcriptional activity. With respect to the influence of ocean acidification on adult oyster DNA methylation we examined mantle, gill, and gonad tissue. Mantle tissue demonstrated a global molecular response (both in the transcriptome and methylome) to acidification that shifted through time. A small number of ocean acidfication-induced differentially methylated loci were discovered, which corresponded with a weak association between ocean acidification induced changes in genome-wide gene body DNA methylation and gene expression. In a separate study, the response of the DNA methylome to ocean acidification was examined in gill tissue. In contrast to mantle tissue, there was a greater impact on the methylome with over 150 differentially methylated loci identified, many of which associated with genes involved in apoptosis, protein ubiquitination, zinc ion binding, and cytoskeletal processes commonly observed in oyster responses to ocean acidification. We were particularly interested in the influence of ocean acidification on DNA methylation in gonad tissue as any transgenerational effects facilitated by DNA methylation should be represented in this tissue. For this work, separate studies were carried out on both Crassostrea gigas and Crassostrea virginica. Interestingly there was a significantly greater impact on the gonad methylome in oysters exposed to low pH conditions compared to other tissues examined. As expected, a majority of differentially methylated loci were in gene bodies. This included genes involved in protein ubiquitination, biomineralization, and gonad development, indicating DNA methylation may be important for transcriptional control in response to ocean acidification. As part of our effort in examining DNA methylation in two oyster species we were able to perform comparative analysis that revealed that the general methylation landscape is similar. As a continuation of the Crassostrea gigas gonad DNA methylation analysis, we evaluated offspring performance. For this work, following ocean acidification exposure, oysters were held in ambient conditions, and subsequently reproductively conditioned under ambient pH. A sex-specific brood stock response was observed, where female exposure to low pH conditions resulted in fewer larvae. This study demonstrated that the effects of ocean acidification can last beyond the time from when the environmental perturbation is experienced. In summary, the combined effort demonstrates a strong tissue specific effect of ocean acidification on DNA methylation in oysters and alteration in DNA methylation pattens plays a role in responding to changing conditions. When characterizing DNA methylation in relation to gene expression we found limited evidence of direct regulation at the gene level, though did find consistency in changes at the physiological pathway level, suggesting interplay with other epigenetic mechanisms. Last Modified: 10/29/2021 Submitted by: Steven Roberts