Contributors | Affiliation | Role |
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Lotterhos, Katie | Northeastern University | Principal Investigator |
Ries, Justin B. | Northeastern University | Co-Principal Investigator, Contact |
McNally, Elise | Northeastern University | Student |
Heyl, Taylor | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
In this study, we examined the phenotypic and molecular responses in the extrapallial fluid in the adult eastern oyster (Crassostrea virginica) exposed to experimental ocean acidification (OA) over 80 days. 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.
Elemental analysis
Extrapallial fluid, seawater, and shell samples were analyzed for trace and minor elements by inductively coupled plasma mass spectrometry (ICPMS). Liquid samples (i.e., EPF, seawater) were diluted to less than 0.05 percent total dissolved solid content with ultra-pure deionized water in 15 mL polypropylene centrifuge tubes leached in the same manner as those for shell samples. The samples were acidified with ultra-pure nitric acid (Fisher TraceMetal Grade Nitric Acid UN2031). Shell samples were also acidified with ultra-pure nitric acid for analysis.
Extrapallial fluid, seawater, and shell samples were analyzed for a suite of 57 elements (including Ca) by ActLabs, Ontario, Canada. In addition to the common suite of elements, liquid samples were analyzed for Si and shell samples were analyzed for S, P, Au, B, and Re. Liquid samples were analyzed using the ActLabs ICPMS method. Shell samples were analyzed using the ActLabs ICPMS Ultratrace 4 method:
https://actlabs.com/geochemistry/exploration-geochemistry/4-acid-near-total-digestion/
This dataset represents molar ratio data that were processed using R (v. 4.0.3; R Core Team 2020) using the graphical interface RStudio (v. 1.0.1073) and then converted to molar ratios to calcium. For each sample type (EPF, seawater, shell), values were identified as outliers if the E/Ca ratio deviated by more than 103 from the mean E/Ca ratio for that element. This approach to identifying outliers removes those caused by sampling or equipment error but is more conservative than Tukey's method to identify and remove outliers.
Molar ratio data were processed using R (v. 4.0.3; R Core Team 2020) and the graphical interface RStudio (v. 1.0.1073).
File |
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traceelements_molarratios.csv filename: traceelements_molarratios.csv (Comma Separated Values (.csv), 99.63 KB) MD5:58667fba22938afc2943e66f7f2f63f7 Primary data file for dataset 888911, version 1. |
Parameter | Description | Units |
SampleType | type of sample EPF= extrapallial fluid, seawater, or shell | unitless |
Species | Species that the sample was taken from. C_virginica is Crassostrea virginica | unitless |
SampleID | Unique identifier for the sample | unitless |
TankID | Unique identifier for the tank | unitless |
ShellType | sample shell type; M = mantle R = repair AM = above mud UM = under mud | unitless |
Ag_Ca | molar ratio of silver to calcium | unitless |
Al_Ca | molar ratio of aluminum to calcium | unitless |
As_Ca | molar ratio of arsenic to calcium | unitless |
Au_Ca | molar ratio of gold to calcium | unitless |
B_Ca | molar ratio of boron to calcium | unitless |
Ba_Ca | molar ratio of barium to calcium | unitless |
Be_Ca | molar ratio of beryllium to calcium | unitless |
Bi_Ca | molar ratio of bismuth to calcium | unitless |
Ca_Ca | molar ratio of calcium to calcium | unitless |
Cd_Ca | molar ratio of cadmium to calcium | unitless |
Ce_Ca | molar ratio of cerium to calcium | unitless |
Co_Ca | molar ratio of cobalt to calcium | unitless |
Cr_Ca | molar ratio of chromium to calcium | unitless |
Cs_Ca | molar ratio of cesium to calcium | unitless |
Cu_Ca | molar ratio of copper to calcium | unitless |
Dy_Ca | molar ratio of dysrosium to calcium | unitless |
Er_Ca | molar ratio of erbium to calcium | unitless |
Eu_Ca | molar ratio of europium to calcium | unitless |
Fe_Ca | molar ratio of iron to calcium | unitless |
Ga_Ca | molar ratio of gallium to calcium | unitless |
Gd_Ca | molar ration of gadolinium to calcium | unitless |
Ge_Ca | molar ratio of germanium to calcium | unitless |
Hf_Ca | molar ratio of hafnium to calcium | unitless |
Hg_Ca | molar ratio of mercury to calcium | unitless |
Ho_Ca | molar ratio of holmium to calcium | unitless |
In_Ca | molar ratio of indium to calcium | unitless |
K_Ca | molar ratio of potassium to calcium | unitless |
La_Ca | molar ratio of lanthanum to calcium | unitless |
Li_Ca | molar ratio of lithium to calcium | unitless |
Lu_Ca | molar ratio of lutetium to calcium | unitless |
Mg_Ca | molar ratio of magnesium to calcium | unitless |
Mn_Ca | molar ratio of manganese to calcium | unitless |
Mo_Ca | molar ratio of molybdenum to calcium | unitless |
Na_Ca | molar ratio of sodium to calcium | unitless |
Nb_Ca | molar ratio of niobium to calcium | unitless |
Nd_Ca | molar ratio of neodymium to calcium | unitless |
Ni_Ca | molar ratio of nickel to calcium | unitless |
P_Ca | molar ratio of phosphorous to calcium | unitless |
Pb_Ca | molar ratio of lead to calcium | unitless |
Pr_Ca | molar ratio of praseodymium to calcium | unitless |
Rb_Ca | molar ratio of rubidium to calcium | unitless |
Re_Ca | molar ratio of rhenium to calcium | unitless |
S_Ca | molar ratio of sulfur to calcium | unitless |
Sb_Ca | molar ratio of antimony to calcium | unitless |
Sc_Ca | molar ratio of scandium to calcium | unitless |
Se_Ca | molar ratio of selenium to calcium | unitless |
Si_Ca | molar ratio of silicon to calcium | unitless |
Sm_Ca | molar ratio of samarium to calcium | unitless |
Sn_Ca | molar ratio of tin to calcium | unitless |
Sr_Ca | molar ratio of strontium to calcium | unitless |
Ta_Ca | molar ratio of tantalum to calcium | unitless |
Tb_Ca | molar ratio of terbium to calcium | unitless |
Te_Ca | molar ratio of thorium to calcium | unitless |
Th_Ca | molar ratio of titanium to calcium | unitless |
Ti_Ca | molar ratio of thulium to calcium | unitless |
Tl_Ca | molar ratio of vanadium to calcium | unitless |
Tm_Ca | molar ratio of tungsten to calcium | unitless |
U_Ca | molar ratio of uranium to calcium | unitless |
V_Ca | molar ratio of tellerium to calcium | unitless |
W_Ca | molar ratio of thallium to calcium | unitless |
Y_Ca | molar ratio of yttrium to calcium | unitless |
Yb_Ca | molar ratio of ytterbium to calcium | unitless |
Zn_Ca | molar ratio of zinc to calcium | unitless |
Zr_Ca | molar ratio of zirconium to calcium | unitless |
Dataset-specific Instrument Name | Shiyang-III dental drill |
Generic Instrument Name | Drill |
Generic Instrument Description | A drill is a tool used for making round holes or driving fasteners. There are many types of drills: some are powered manually, and others use electricity (electric drill) or compressed air as the motive power. Drills with a percussive action (hammer drills) are mostly used in hard materials such as masonry (brick, concrete, and stone) or rock. Some types of hand-held drills are also used to drive screws and other fasteners. |
Dataset-specific Instrument Name | |
Generic Instrument Name | Inductively Coupled Plasma Mass Spectrometer |
Generic Instrument Description | An ICP Mass Spec is an instrument that passes nebulized samples into an inductively-coupled gas plasma (8-10000 K) where they are atomized and ionized. Ions of specific mass-to-charge ratios are quantified in a quadrupole mass spectrometer. |
Dataset-specific Instrument Name | Mettler Toledo scale |
Generic Instrument Name | scale |
Dataset-specific Description | Mettler Toledo scale (precision = 0.001g) |
Generic Instrument Description | An instrument used to measure weight or mass. |
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.
Funding Source | Award |
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NSF Division of Ocean Sciences (NSF OCE) |