Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Project Information
• Funding

This dataset represents Crassostrea virginica shell samples analyzed for trace and minor elements in adult Eastern oyster ocean acidification exposure experiments at the Ries Lab at the Northeastern University Marine Science Center on samples from Plum Island Sound in 2017.

The collection and culturing of C. virginica specimens are detailed in Downey-Wall, A.M., L.P. Cameron, B.M. Ford, E.M. McNally, Y.R. Venkataraman, S.B. Roberts, J.B. Ries, and K.E. Lotterhos. 2020. Ocean acidification induces subtle shifts in gene expression and DNA methylation in the mantle tissue of the Eastern oyster (Crassostrea virginica). Frontiers in Marine Science doi: 10.3389/fmars.2020.566419.

Shells were cleaned thoroughly in 90 percent ethanol (Fisher Reagent Alcohol CAS: 64-17-5). Cleaned shells were dried at room temperature for 48 hours and stored in sealed plastic bags. The inner (lamellar) layer of oyster shells was sampled for elemental analysis. Shells were sampled by gently moving a Shiyang-III dental drill outfitted with a round bit across the low-Mg calcite surfaces of the interior shell. The powdered shell was placed in 15-milliliter (mL) polypropylene centrifuge tubes leached in 5 percent ultra-pure nitric acid solution (Fisher TraceMetal Grade Nitric Acid UN2031).

Elemental analysis
Shell samples were analyzed for trace and minor elements by inductively coupled plasma mass spectrometry (ICPMS). Shell samples were also acidified with ultra-pure nitric acid for analysis. Shell samples were analyzed for a suite of 57 elements (including Ca) by ActLabs, Ontario, Canada using the ActLabs ICPMS Ultratrace 4 method. 

Concentration data were received from ActLabs:
https://actlabs.com/geochemistry/exploration-geochemistry/4-acid-near-total-digestion/

Concentration data were negative-corrected (i.e., for intercept correction of the calibration) by adding the lowest negative value along with a de minimis constant (0.000001) to each sample for each element that exhibited negative concentration values.

NSF Award Abstract:
Marine ecosystems worldwide are threatened by ocean acidification, a process caused by the unprecedented rate at which carbon dioxide is increasing in the atmosphere. Since ocean change is predicted to be rapid, extreme, and widespread, marine species may face an "adapt-or-die" scenario. However, modifications to the DNA sequence may be induced in response to a stress like ocean acidification and then inherited. Such "epigenetic" modifications may hold the key to population viability under global climate change, but they have been understudied. The aim of this research is to characterize the role of DNA methylation, a heritable epigenetic system, in the response of Eastern oysters (Crassostrea virginica) to ocean acidification. The intellectual merit lies in the integrative approach, which will characterize the role of DNA methylation in the intergenerational response of oysters to ocean acidification. These interdisciplinary data, spanning from molecular to organismal levels, will provide insight into mechanisms that underlie the capacity of marine invertebrates to respond to ocean acidification and lay the foundation for future transgenerational studies. Ocean acidification currently threatens marine species worldwide and has already caused significant losses in aquaculture, especially in Crassostrea species. This research has broader impacts for breeding, aquaculture, and the economy. Under the investigators' "Epigenetics to Ocean" (E2O) training program, the investigators will build STEM talent in bioinformatics and biogeochemistry, expose girls in low-income school districts to careers in genomics, and advance the field through open science and reproducibility.

This research will specifically test if intermittent exposure to low pH induces a methylation response with downstream beneficial effects for biomineralization. These methylation states could be inherited and confer a fitness advantage to larvae that possess them. Phase 1 of the project will use an exposure experiment to determine the degree to which DNA methylation is altered and regulates the response to OA. Data from this experiment will be used to test the hypotheses that (i) DNA methylation, induced in the tissue of shell formation (i.e., mantle tissue), is correlated with changes in transcription and regulation of pallial fluid pH (calcifying fluid pH, measured by microelectrode), and (ii) that methylation changes induced in the mantle tissue are also induced in the germline --indicating that such changes are potentially heritable. Phase 2 of the project will use a pair-mated cross experiment to test the hypothesis that parental exposure to OA alters larval traits (calcification rate, shell structure, and polymorph mineralogy). Larvae will be generated from parents exposed to OA or control seawater, and then raised under control or OA conditions. Results will be used to (i) characterize inheritance of induced methylation states, (ii) estimate the variance in larval traits explained by genotype, non-genetic maternal/paternal effects, adult OA exposure, larval OA exposure, and parental methylome, and (iii) test the hypothesis that adult exposure alters the heritability (a quantity that predicts evolutionary response) of larval traits. Since the effects of epigenetic phenomena on estimates of heritability are highly debated, the results would advance understanding of this important issue. Because the investigators could discover that DNA methylation is a mechanism for heritable plastic responses to OA, knowledge of this mechanism would significantly improve and potentially transform predictive models for how organisms respond to global change.