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Schwaner, Caroline; Espinosa, Emmanuelle Pales; Allam, Bassem (2023): Seawater carbonate chemistry and larval viability, size, development, and shell mineralization of the eastern oyster (Crassostrea virginica) [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.957629

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Abstract:
Calcifying marine organisms, including the eastern oyster (Crassostrea virginica), are vulnerable to ocean acidification (OA) because it is more difficult to precipitate calcium carbonate (CaCO3). Previous investigations of the molecular mechanisms associated with resilience to OA in C. virginica demonstrated significant differences in single nucleotide polymorphism and gene expression profiles among oysters reared under ambient and OA conditions. Converged evidence generated by both of these approaches highlighted the role of genes related to biomineralization, including perlucins. Here, gene silencing via RNA interference (RNAi) was used to evaluate the protective role of a perlucin gene under OA stress. Larvae were exposed to short dicer-substrate small interfering RNA (DsiRNA-perlucin) to silence the target gene or to one of two control treatments (control DsiRNA or seawater) before cultivation under OA (pH ~7.3) or ambient (pH ~8.2) conditions. Two transfection experiments were performed in parallel, one during fertilization and one during early larval development (6 h post-fertilization), before larval viability, size, development, and shell mineralization were monitored. Silenced oysters under acidification stress were the smallest, had shell abnormalities, and had significantly reduced shell mineralization, thereby suggesting that perlucin significantly helps larvae mitigate the effects of OA.
Keyword(s):
Animalia; Bottles or small containers/Aquaria (<20 L); Crassostrea virginica; Development; Gene expression (incl. proteomics); Growth/Morphology; Laboratory experiment; Laboratory strains; Mollusca; Mortality/Survival; Not applicable; Other studied parameter or process; Pelagos; Single species; Zooplankton
Supplement to:
Schwaner, Caroline; Espinosa, Emmanuelle Pales; Allam, Bassem (2023): RNAi Silencing of the Biomineralization Gene Perlucin Impairs Oyster Ability to Cope with Ocean Acidification. International Journal of Molecular Sciences, 24(4), 3661, https://doi.org/10.3390/ijms24043661
Documentation:
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 (2022): seacarb: seawater carbonate chemistry with R. R package version 3.3.1. https://cran.r-project.org/web/packages/seacarb/index.html
Comment:
In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2022) 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 2023-04-18.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
Type of studyStudy typeSchwaner, Caroline
Species, unique identificationSpecies UIDSchwaner, Caroline
Species, unique identification (URI)Species UID (URI)Schwaner, Caroline
Species, unique identification (Semantic URI)Species UID (Semantic URI)Schwaner, Caroline
ExperimentExpSchwaner, Caroline
TreatmentTreatSchwaner, Caroline
Treatment: pHT:pHSchwaner, Caroline
Gene expression, fold change, relativeGene expressionSchwaner, Carolineperlucin
Gene expression, fold change, relative, standard deviationGene expression std dev±Schwaner, Carolineperlucin
10 ViabilityViab%Schwaner, Caroline
11 Viability, standard deviationViab std dev±Schwaner, Caroline
12 Larval deformity rateLarval def rate%Schwaner, Caroline
13 Larval deformity rate, standard deviationLarval def rate std dev±Schwaner, Caroline
14 LengthlµmSchwaner, Caroline
15 Length, standard deviationl std dev±Schwaner, Caroline
16 Day of experimentDOEdaySchwaner, Caroline
17 Birefringence intensityBirefringence IpixelSchwaner, Caroline
18 Birefringence intensity, standard deviationBirefringence I std dev±Schwaner, Caroline
19 pHpHSchwaner, CarolineTotal scale
20 pH, standard deviationpH std dev±Schwaner, Caroline
21 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmSchwaner, Caroline
22 Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Schwaner, Caroline
23 Calcite saturation stateOmega CalSchwaner, Caroline
24 Calcite saturation state, standard deviationOmega Cal std dev±Schwaner, Caroline
25 Aragonite saturation stateOmega ArgSchwaner, Caroline
26 Aragonite saturation state, standard deviationOmega Arg std dev±Schwaner, Caroline
27 Carbon, inorganic, dissolvedDICµmol/kgSchwaner, Caroline
28 Carbon, inorganic, dissolved, standard deviationDIC std dev±Schwaner, Caroline
29 Carbonate ion[CO3]2-µmol/kgSchwaner, Caroline
30 Carbonate ion, standard deviation[CO3]2- std dev±Schwaner, Caroline
31 Alkalinity, totalATµmol/kgSchwaner, Caroline
32 Alkalinity, total, standard deviationAT std dev±Schwaner, Caroline
33 Temperature, waterTemp°CSchwaner, Caroline
34 SalinitySalSchwaner, Caroline
35 Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
36 pHpHYang, YanCalculated using seacarb after Nisumaa et al. (2010)Total scale
37 Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
38 Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
39 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
40 Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
41 Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
42 Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
43 Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
1410 data points

Data

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


Study type

Species UID

Species UID (URI)

Species UID (Semantic URI)

Exp

Treat

T:pH

Gene expression
(perlucin)

Gene expression std dev [±]
(perlucin)
10 
Viab [%]
11 
Viab std dev [±]
12 
Larval def rate [%]
13 
Larval def rate std dev [±]
14 
l [µm]
15 
l std dev [±]
16 
DOE [day]
17 
Birefringence I [pixel]
18 
Birefringence I std dev [±]
19 
pH
(Total scale)
20 
pH std dev [±]
21 
pCO2water_SST_wet [µatm]
22 
pCO2 std dev [±]
23 
Omega Cal
24 
Omega Cal std dev [±]
25 
Omega Arg
26 
Omega Arg std dev [±]
27 
DIC [µmol/kg]
28 
DIC std dev [±]
29 
[CO3]2- [µmol/kg]
30 
[CO3]2- std dev [±]
31 
AT [µmol/kg]
32 
AT std dev [±]
33 
Temp [°C]
34 
Sal
35 
CSC flag
36 
pH
(Total scale)
37 
CO2 [µmol/kg]
38 
fCO2water_SST_wet [µatm]
39 
pCO2water_SST_wet [µatm]
40 
[HCO3]- [µmol/kg]
41 
[CO3]2- [µmol/kg]
42 
Omega Arg
43 
Omega Cal
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Seawater8.20.02-0.458.20.014020.054.20.102.70.101909381613.021263925.2025158.0511.98402.69403.981732.19164.822.744.29
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Negative Control8.20.370.418.20.004074.004.20.032.70.021914191601.021311924.6025158.0611.93394.80396.071737.27164.802.734.28
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Gene Silencing8.2-1.05-1.248.20.0141112.004.10.102.60.101927351585.021414024.6725158.0512.27406.71408.021751.62163.122.704.24
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Seawater7.30.750.947.30.033508151.000.60.100.40.04206282222.019878724.5025157.15107.073534.043545.471932.2622.680.380.59
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Negative Control7.30.540.527.30.023335229.000.60.010.40.01208180240.420137224.3325157.18102.173357.643368.511954.5824.240.400.63
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Gene Silencing7.3-0.77-1.257.30.04341338.000.61.000.40.04208864242.020186524.7625157.17103.963454.783465.911959.9024.130.400.63
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Seawater8.20.200.058.20.0238011.004.40.202.80.101936481709.021675824.6725158.0811.38377.39378.601749.29175.322.914.56
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Negative Control8.20.13-0.288.20.013683.004.30.202.80.101891321601.021311924.6025158.1110.45345.73346.851700.29180.262.994.68
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Gene Silencing8.2-0.51-0.348.20.003862.004.10.022.60.01186791591.020841025.0025158.0611.49384.09385.321692.04163.482.714.25
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Seawater7.30.560.497.30.103861436.000.60.100.40.03214933222.020622324.4325157.13118.053889.603902.182008.7522.200.370.58
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Negative Control7.30.300.447.30.023571120.000.60.040.40.02216415241.0208812124.4025157.17109.933618.983630.692029.7424.330.400.63
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Gene Silencing7.3-1.55-1.837.30.013708239.000.50.020.30.01201797201.019349024.8325157.12112.413742.093754.141883.9420.650.340.54
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Gene Silencing8.27511.070.7009.10054.0992.2518.20.0141112.004.10.102.60.101927351585.021414024.6725158.0512.27406.71408.021751.62163.122.704.24
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Gene Silencing7.37010.092.3005.50044.3683.3107.30.04341338.000.61.000.40.04208864242.020186524.7625157.17103.963454.783465.911959.9024.130.400.63
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Negative Control8.2523.017.0008.00062.6231.9608.20.004074.004.20.032.70.021914191601.021311924.6025158.0611.93394.80396.071737.27164.802.734.28
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Negative Control7.37221.058.7004.90079.9801.9607.30.023335229.000.60.010.40.01208180240.420137224.3325157.18102.173357.643368.511954.5824.240.400.63
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Seawater8.26319.00.0000.00093.8293.8008.20.014020.054.20.102.70.101909381613.021263925.2025158.0511.98402.69403.981732.19164.822.744.29
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Seawater7.37315.054.70010.20071.0952.1707.30.033508151.000.60.100.40.04206282222.019878724.5025157.15107.073534.043545.471932.2622.680.380.59
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Gene Silencing8.2852.019.6678.50590.2912.7548.20.003862.004.10.022.60.01186791591.020841025.0025158.0611.49384.09385.321692.04163.482.714.25
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Gene Silencing7.3852.028.00010.14985.8444.5837.30.013708239.000.50.020.30.01201797201.019349024.8325157.12112.413742.093754.141883.9420.650.340.54
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Negative Control7.3854.07.00012.12490.5871.4227.30.023571120.000.60.040.40.02216415241.0208812124.4025157.17109.933618.983630.692029.7424.330.400.63
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Negative Control8.2890.817.33310.40896.5654.5508.20.013683.004.30.202.80.101891321601.021311924.6025158.1110.45345.73346.851700.29180.262.994.68
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Seawater8.2731.30.0000.00097.3703.8448.20.0238011.004.40.202.80.101936481709.021675824.6725158.0811.38377.39378.601749.29175.322.914.56
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Seawater7.3756.00.0000.00089.8450.4987.30.103861436.000.60.100.40.03214933222.020622324.4325157.13118.053889.603902.182008.7522.200.370.58
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Gene Silencing8.2361.5004.6008.20.003862.004.10.022.60.01186791591.020841025.0025158.0611.49384.09385.321692.04163.482.714.25
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Gene Silencing7.3343.70012.4007.30.013708239.000.50.020.30.01201797201.019349024.8325157.12112.413742.093754.141883.9420.650.340.54
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Negative Control7.3362.5000.6307.30.023571120.000.60.040.40.02216415241.0208812124.4025157.17109.933618.983630.692029.7424.330.400.63
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Negative Control8.2375.0005.0008.20.013683.004.30.202.80.101891321601.021311924.6025158.1110.45345.73346.851700.29180.262.994.68
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Seawater8.2379.8008.5008.20.0238011.004.40.202.80.101936481709.021675824.6725158.0811.38377.39378.601749.29175.322.914.56
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Seawater7.3361.7003.5007.30.103861436.000.60.100.40.03214933222.020622324.4325157.13118.053889.603902.182008.7522.200.370.58
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Gene Silencing8.2557.4551.1508.20.003862.004.10.022.60.01186791591.020841025.0025158.0611.49384.09385.321692.04163.482.714.25
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Gene Silencing7.3551.4891.7607.30.013708239.000.50.020.30.01201797201.019349024.8325157.12112.413742.093754.141883.9420.650.340.54
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Negative Control7.3563.4150.8977.30.023571120.000.60.040.40.02216415241.0208812124.4025157.17109.933618.983630.692029.7424.330.400.63
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Negative Control8.2561.4422.4008.20.013683.004.30.202.80.101891321601.021311924.6025158.1110.45345.73346.851700.29180.262.994.68
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Seawater8.2570.4562.1908.20.0238011.004.40.202.80.101936481709.021675824.6725158.0811.38377.39378.601749.29175.322.914.56
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406572Seawater7.3561.5071.6007.30.103861436.000.60.100.40.03214933222.020622324.4325157.13118.053889.603902.182008.7522.200.370.58
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Gene Silencing8.2358.88522.3218.20.0141112.004.10.102.60.101927351585.021414024.6725158.0512.27406.71408.021751.62163.122.704.24
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Gene Silencing7.3328.60915.4037.30.04341338.000.61.000.40.04208864242.020186524.7625157.17103.963454.783465.911959.9024.130.400.63
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Negative Control7.3322.1816.7547.30.023335229.000.60.010.40.01208180240.420137224.3325157.18102.173357.643368.511954.5824.240.400.63
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Negative Control8.2350.79110.4298.20.004074.004.20.032.70.021914191601.021311924.6025158.0611.93394.80396.071737.27164.802.734.28
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Seawater8.2363.28912.7898.20.014020.054.20.102.70.101909381613.021263925.2025158.0511.98402.69403.981732.19164.822.744.29
laboratoryCrassostrea virginicamarinespecies.orgurn:lsid:marinespecies.org:taxname:1406571Seawater7.3337.42921.0677.30.033508151.000.60.100.40.04206282222.019878724.5025157.15107.073534.043545.471932.2622.680.380.59