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Zhong, Kevin Xu; Chan, Amy M; Collicutt, Brenna; Daspe, Maxim; Finke, Jan F; Foss, Megan; Green, Timothy J; Harley, Christopher D G; Hesketh, Amelia V; Miller, Kristina M; Otto, Sarah P; Rolheiser, Kate; Saunders, Rob; Sutherland, Ben J G; Suttle, C A (2024): Seawater carbonate chemistry and prokaryotic and eukaryotic microbiome of Pacific oyster spat [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.967412

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Abstract:
Pacific oysters (Magallana gigas, a.k.a. Crassostrea gigas), the most widely farmed oysters, are under threat from climate change and emerging pathogens. In part, their resilience may be affected by their microbiome, which, in turn, may be influencedinfluencedinfluencedby ocean warming and acidification. To understand these impacts, we exposed early-development Pacific oyster spat to different temperatures (18°C and 24°C) and pCO2 levels (800, 1,600, and 2,800 μatm) in a fully crossed design for 3 weeks.
Keyword(s):
Animalia; Benthic animals; Benthos; Community composition and diversity; Containers and aquaria (20-1000 L or < 1 m**2); Crassostrea gigas; Entire community; Laboratory experiment; Laboratory strains; Mollusca; Not applicable; Other studied parameter or process; Pelagos; Single species; Temperature
Related to:
Zhong, Kevin Xu; Chan, Amy M; Collicutt, Brenna; Daspe, Maxim; Finke, Jan F; Foss, Megan; Green, Timothy J; Harley, Christopher D G; Hesketh, Amelia V; Miller, Kristina M; Otto, Sarah P; Rolheiser, Kate; Saunders, Rob; Sutherland, Ben J G; Suttle, C A; Biddle, Jennifer F (2024): The prokaryotic and eukaryotic microbiome of Pacific oyster spat is shaped by ocean warming but not acidification. Applied and Environmental Microbiology, 90(4), e00052-24, https://doi.org/10.1128/aem.00052-24
Source:
Zhong, Kevin Xu (2024): ASV tables, metadata and codes for the article titled "The Prokaryotic and Eukaryotic Microbiome of Pacific Oyster Spat is Shaped by Ocean Warming but not Acidification". figshare, https://doi.org/10.6084/M9.FIGSHARE.25180460
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)
Comment:
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 2024-04-23.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Type of studyStudy typeZhong, Kevin Xu
2TreatmentTreatZhong, Kevin Xu
3Temperature, waterTemp°CZhong, Kevin Xu
4Temperature, water, standard deviationTemp std dev±Zhong, Kevin Xu
5SalinitySalZhong, Kevin Xu
6Salinity, standard deviationSal std dev±Zhong, Kevin Xu
7Carbon, inorganic, dissolvedDICµmol/kgZhong, Kevin Xu
8Carbon, inorganic, dissolved, standard deviationDIC std dev±Zhong, Kevin Xu
9Alkalinity, totalATµmol/kgZhong, Kevin Xu
10Alkalinity, total, standard deviationAT std dev±Zhong, Kevin Xu
11Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmZhong, Kevin Xu
12Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Zhong, Kevin Xu
13pHpHZhong, Kevin Xutotal scale
14pH, standard deviationpH std dev±Zhong, Kevin Xutotal scale
15Aragonite saturation stateOmega ArgZhong, Kevin Xu
16Aragonite saturation state, standard deviationOmega Arg std dev±Zhong, Kevin Xu
17Calcite saturation stateOmega CalZhong, Kevin Xu
18Calcite saturation state, standard deviationOmega Cal std dev±Zhong, Kevin Xu
19Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
20Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
21Carbon dioxide, standard deviationCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
22Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
23Fugacity of carbon dioxide in seawater, standard deviationfCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
24Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
25Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
26Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
27Bicarbonate ion, standard deviation[HCO3]- std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
28Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
29Carbonate ion, standard deviation[CO3]2- std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
30Alkalinity, totalATµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
31Alkalinity, total, standard deviationAT std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
32Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
33Aragonite saturation state, standard deviationOmega Arg std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
34Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
35Calcite 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:
210 data points

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