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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
1 Type of studyStudy typeZhong, Kevin Xu
2 TreatmentTreatZhong, Kevin Xu
3 Temperature, waterTemp°CZhong, Kevin Xu
4 Temperature, water, standard deviationTemp std dev±Zhong, Kevin Xu
5 SalinitySalZhong, Kevin Xu
6 Salinity, standard deviationSal std dev±Zhong, Kevin Xu
7 Carbon, inorganic, dissolvedDICµmol/kgZhong, Kevin Xu
8 Carbon, inorganic, dissolved, standard deviationDIC std dev±Zhong, Kevin Xu
9 Alkalinity, totalATµmol/kgZhong, Kevin Xu
10 Alkalinity, total, standard deviationAT std dev±Zhong, Kevin Xu
11 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmZhong, Kevin Xu
12 Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Zhong, Kevin Xu
13 pHpHZhong, Kevin Xutotal scale
14 pH, standard deviationpH std dev±Zhong, Kevin Xutotal scale
15 Aragonite saturation stateOmega ArgZhong, Kevin Xu
16 Aragonite saturation state, standard deviationOmega Arg std dev±Zhong, Kevin Xu
17 Calcite saturation stateOmega CalZhong, Kevin Xu
18 Calcite saturation state, standard deviationOmega Cal std dev±Zhong, Kevin Xu
19 Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
20 Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
21 Carbon dioxide, standard deviationCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
22 Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
23 Fugacity of carbon dioxide in seawater, standard deviationfCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
24 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
25 Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
26 Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
27 Bicarbonate ion, standard deviation[HCO3]- std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
28 Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
29 Carbonate ion, standard deviation[CO3]2- std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
30 Alkalinity, totalATµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
31 Alkalinity, total, standard deviationAT std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
32 Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
33 Aragonite saturation state, standard deviationOmega Arg std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
34 Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
35 Calcite 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

Data

Download dataset as tab-delimited text — use the following character encoding:

1 
Study type		2 
Treat		3 
Temp [°C]		4 
Temp std dev [±]		5 
Sal		6 
Sal std dev [±]		7 
DIC [µmol/kg]		8 
DIC std dev [±]		9 
AT [µmol/kg]		10 
AT std dev [±]		11 
pCO2water_SST_wet [µatm]		12 
pCO2 std dev [±]		13 
pH
(total scale)		14 
pH std dev [±]
(total scale)		15 
Omega Arg		16 
Omega Arg std dev [±]		17 
Omega Cal		18 
Omega Cal std dev [±]		19 
CSC flag
(Calculated using seacarb afte...)		20 
CO2 [µmol/kg]
(Calculated using seacarb afte...)		21 
CO2 std dev [±]
(Calculated using seacarb afte...)		22 
fCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)		23 
fCO2 std dev [±]
(Calculated using seacarb afte...)		24 
pCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)		25 
pCO2 std dev [±]
(Calculated using seacarb afte...)		26 
[HCO3]- [µmol/kg]
(Calculated using seacarb afte...)		27 
[HCO3]- std dev [±]
(Calculated using seacarb afte...)		28 
[CO3]2- [µmol/kg]
(Calculated using seacarb afte...)		29 
[CO3]2- std dev [±]
(Calculated using seacarb afte...)		30 
AT [µmol/kg]
(Calculated using seacarb afte...)		31 
AT std dev [±]
(Calculated using seacarb afte...)		32 
Omega Arg
(Calculated using seacarb afte...)		33 
Omega Arg std dev [±]
(Calculated using seacarb afte...)		34 
Omega Cal
(Calculated using seacarb afte...)		35 
Omega Cal std dev [±]
(Calculated using seacarb afte...)
laboratory800 µatm+18 °C18.030.3128.950.212024.4578.372121.0180.89780.67192.807.790.091.360.242.130.38926.735.81754.79164.09757.42164.661912.8974.9884.8317.642120.7386.061.340.292.110.45
laboratory1600 µatm+18 °C18.140.2428.990.132110.4473.092122.0975.721564.73150.337.500.040.730.081.140.13954.605.441547.14154.101552.54154.642009.8969.6345.954.822122.4573.660.730.081.140.13
laboratory2800 µatm+18 °C18.170.2129.060.132222.4688.092156.8290.092954.77268.087.240.040.420.050.660.089103.3110.212930.86289.732941.09290.742092.7883.2426.372.882157.1686.020.420.050.660.08
laboratory800 µatm+24 °C24.040.4929.100.161941.6265.852056.8976.13814.33158.927.760.081.570.272.420.42924.024.68800.58155.90803.18156.411822.8063.1194.8017.492055.0574.061.540.292.390.45
laboratory1600 µatm+24 °C24.110.1929.180.142040.3193.402068.3898.751641.78175.297.480.050.870.111.340.17948.586.091622.32203.391627.57204.051938.5888.7753.166.822068.5994.720.870.121.340.18
laboratory2800 µatm+24 °C23.940.3129.230.142125.8158.662095.0355.022690.24247.107.280.040.560.050.870.07980.097.682663.79255.332672.45256.162011.1055.6634.623.622095.5558.650.560.060.870.10