Molar Ratios from an adult Eastern oyster ocean acidification exposure experiment at the Northeastern University Marine Science Center in 2017

Website: https://www.bco-dmo.org/dataset/888911
Data Type: Other Field Results
Version: 1
Version Date: 2023-02-02

Project
» Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters? (Epigenetics to Ocean)
ContributorsAffiliationRole
Lotterhos, KatieNortheastern UniversityPrincipal Investigator
Ries, Justin B.Northeastern UniversityCo-Principal Investigator, Contact
McNally, EliseNortheastern UniversityStudent
Heyl, TaylorWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager

Abstract
Trace, minor, and major element data from adult Eastern oyster ocean acidification exposure experiments were conducted at the Ries Lab at the Northeastern University Marine Science Center on samples from Plum Island Sound in 2017. This dataset represents molar ratio data that were processed using R, using the graphical interface RStudio and then converted to molar ratios to calcium.


Coverage

Spatial Extent: Lat:42.751636 Lon:-70.837023
Temporal Extent: 2017-04

Methods & Sampling

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.

 


Data Processing Description

Molar ratio data were processed using R (v. 4.0.3; R Core Team 2020) and the graphical interface RStudio (v. 1.0.1073).


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Data Files

File
traceelements_molarratios.csv
filename: traceelements_molarratios.csv
(Comma Separated Values (.csv), 99.63 KB)
MD5:58667fba22938afc2943e66f7f2f63f7
Primary data file for dataset 888911, version 1.

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Related Publications

Downey-Wall, A. M., Cameron, L. P., Ford, B. M., McNally, E. M., Venkataraman, Y. R., Roberts, S. B., Ries, J. B., & Lotterhos, K. E. (2020). Ocean Acidification Induces Subtle Shifts in Gene Expression and DNA Methylation in Mantle Tissue of the Eastern Oyster (Crassostrea virginica). Frontiers in Marine Science, 7. https://doi.org/10.3389/fmars.2020.566419
IsRelatedTo

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Related Datasets

References
Downey-Wall, A., Lotterhos, K., Ries, J. B., Cameron, L. (2023) Phenotypic responses of Eastern oyster in response to variable length OA exposure conducted in summer 2017 with oysters sampled in Plum Island. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-01-20 http://lod.bco-dmo.org/id/dataset/887553 [view at BCO-DMO]
IsRelatedTo
Lotterhos, K., Ries, J. B. (2023) Shell Concentrations from an adult Eastern oyster ocean acidification exposure experiment on adult Eastern oysters from Plum Island Sound in 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-02-02 doi:10.26008/1912/bco-dmo.888902.1 [view at BCO-DMO]
McNally, E., Lotterhos, K., Ries, J. B. (2023) Seawater concentration data from an ocean acidification exposure experiment on adult Eastern oysters from Plum Island Sound in 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-02-02 doi:10.26008/1912/bco-dmo.888887.1 [view at BCO-DMO]

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Parameters

ParameterDescriptionUnits
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


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Instruments

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.


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Project Information

Collaborative Research: Does ocean acidification induce a methylation response that affects the fitness of the next generation in oysters? (Epigenetics to Ocean)

Coverage: Coastal Massachusetts near Nahant: 42°25'06"N 70°54'14"W


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.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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