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Lopez, Mark Louie D; Rolheiser, Kate C; Etzkorn, Jacob; Imbery, Jacob J; Lemay, Matthew A; Gimenez, Iria; Helbing, Caren C (2025): Seawater carbonate chemistry and environmental DNA and RNA Shedding and Persistence [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.986892

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Published: 2025-10-23 • DOI registered: 2025-11-21

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Abstract:
In the present study, we conducted mesocosm experiments to determine the shedding and decay rate constants of eDNA and eRNA in M. gigas (Magallana [Crassostrea] gigas) using mitochondrially encoded tRNA leucine 1 (mt-tl1) marker at various partial pressures of CO2 in seawater. To our knowledge, this is the first study manipulating seawater pH using CO2. We developed a sensitive and specific quantitative PCR-based assay to detect M. gigas eDNA and eRNA.
This dataset is included in the OA-ICC data compilation maintained in the framework of the IAEA Ocean Acidification International Coordination Centre (see https://oa-icc.ipsl.fr). Original data were provided by the author of the related paper (see Related to) to the OA-ICC data curator. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2024) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2025-10-23.
Keyword(s):
Animalia; Benthic animals; Benthos; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Gene expression (incl. proteomics); Laboratory experiment; Magallana gigas; Mollusca; North Pacific; Single species; Temperate
Related to:
Lopez, Mark Louie D; Rolheiser, Kate C; Etzkorn, Jacob; Imbery, Jacob J; Lemay, Matthew A; Gimenez, Iria; Helbing, Caren C (2025): Impact of CO 2 -Induced Aquatic Acidification on Environmental DNA and RNA Shedding and Persistence. Environmental DNA, 7(4), e70158, https://doi.org/10.1002/edn3.70158
References:
Nisumaa, Anne-Marin; Pesant, Stephane; Bellerby, Richard G J; Delille, Bruno; Middelburg, Jack J; Orr, James C; Riebesell, Ulf; Tyrrell, Toby; Wolf-Gladrow, Dieter A; Gattuso, Jean-Pierre (2010): EPOCA/EUR-OCEANS data compilation on the biological and biogeochemical responses to ocean acidification. Earth System Science Data, 2(2), 167-175, https://doi.org/10.5194/essd-2-167-2010
Yang, Yan; Brockmann, Patrick; Galdino, Carolina; Schindler, Uwe; Gazeau, Frédéric (2024): An update of data compilation on the biological response to ocean acidification and overview of the OA-ICC data portal. Earth System Science Data, 16(8), 3771-3780, https://doi.org/10.5194/essd-16-3771-2024
Yang, Yan; Hansson, L; Gattuso, Jean-Pierre (2016): Data compilation on the biological response to ocean acidification: an update. Earth System Science Data, 8(1), 79-87, https://doi.org/10.5194/essd-8-79-2016
Related code / software:
Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James; Gentili, Bernard; Hagens, Mathilde; Hofmann, Andreas; Mueller, Jens-Daniel; Proye, Aurélien; Rae, James; Soetaert, Karline (2024): seacarb: seawater carbonate chemistry with R. R package version 3.3.3. https://cran.r-project.org/web/packages/seacarb/index.html
Project(s):
Ocean Acidification International Coordination Centre (OA-ICC)
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Type of studyStudy typeLopez, Mark Louie D
2Species, unique identificationSpecies UIDLopez, Mark Louie D
3Species, unique identification (URI)Species UID (URI)Lopez, Mark Louie D
4Species, unique identification (Semantic URI)Species UID (Semantic URI)Lopez, Mark Louie D
5DateDateLopez, Mark Louie D
6IdentificationIDLopez, Mark Louie D
7TreatmentTreatLopez, Mark Louie D
8TypeTypeLopez, Mark Louie DNucleic acid
9Time in hoursTime hhLopez, Mark Louie D
10PhasePhaseLopez, Mark Louie D
11TreatmentTreatLopez, Mark Louie DWith control treatment
12Replicate, biologicalRepl bioLopez, Mark Louie D
13Gene copiesGCN#Lopez, Mark Louie D
14Temperature, waterTemp°CLopez, Mark Louie D
15Temperature, water, standard deviationTemp std dev±Lopez, Mark Louie D
16SalinitySalLopez, Mark Louie D
17Salinity, standard deviationSal std dev±Lopez, Mark Louie D
18Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmLopez, Mark Louie D
19Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Lopez, Mark Louie D
20pH, total scalepHTLopez, Mark Louie DCalculated with seacarb package in R
21pH, standard deviationpH std dev±Lopez, Mark Louie DCalculated with seacarb package in Rtotal scale
22Carbon, inorganic, dissolvedDICµmol/kgLopez, Mark Louie D
23Carbon, inorganic, dissolved, standard deviationDIC std dev±Lopez, Mark Louie D
24Alkalinity, totalATµmol/kgLopez, Mark Louie DCalculated with seacarb package in R
25Alkalinity, total, standard deviationAT std dev±Lopez, Mark Louie DCalculated with seacarb package in R
26Aragonite saturation stateOmega ArgLopez, Mark Louie DCalculated with seacarb package in R
27Aragonite saturation state, standard deviationOmega Arg std dev±Lopez, Mark Louie DCalculated with seacarb package in R
28Calcite saturation stateOmega CalLopez, Mark Louie DCalculated with seacarb package in R
29Calcite saturation state, standard deviationOmega Cal std dev±Lopez, Mark Louie DCalculated with seacarb package in R
30IndividualsInd#Lopez, Mark Louie D
31Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
32pH, total scalepHTYang, YanCalculated using seacarb after Nisumaa et al. (2010)
33pH, standard deviationpH std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)total scale
34Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
35Carbon dioxide, standard deviationCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
36Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
37Fugacity of carbon dioxide in seawater, standard deviationfCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
38Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
39Bicarbonate ion, standard deviation[HCO3]- std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
40Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
41Carbonate ion, standard deviation[CO3]2- std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
42Alkalinity, totalATµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
43Alkalinity, total, standard deviationAT std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
44Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
45Aragonite saturation state, standard deviationOmega Arg std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
46Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
47Calcite saturation state, standard deviationOmega Cal std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
10800 data points

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