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Timmins-Schiffman, Emma; Coffey, William D; Hua, Wilber; Nunn, Brook L; Dickinson, Gary H; Roberts, Steven B (2014): Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.837671

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Abstract:
Background. Ocean acidification as a result of increased anthropogenic CO2 emissions is occurring in marine and estuarine environments worldwide. The coastal ocean experiences additional daily and seasonal fluctuations in pH that can be lower than projected end of century open ocean pH reductions. Projected and current ocean acidification have wide-ranging effects on many aquatic organisms, however the exact mechanisms of the impacts of ocean acidification on many of these animals remains to be characterized.
Methods. In order to assess the impact of ocean acidification on marine invertebrates, Pacific oysters (Crassostrea gigas) were exposed to one of four different pCO2 levels for four weeks: 400 µatm (pH 8.0), 800 µatm (pH 7.7), 1000 µatm (pH 7.6), or 2800 µatm (pH 7.3). At the end of 4 weeks a variety of physiological parameters were measured to assess the impacts of ocean acidification: tissue glycogen content and fatty acid profile, shell micromechanical properties, and response to acute heat shock. To determine the effects of ocean acidification on the underlying molecular physiology of oysters and their stress response, some of the oysters from 400 µatm and 2800 µatm were exposed to an additional mechanical stress and shotgun proteomics were done on oysters from high and low pCO2 and from with and without mechanical stress.
Results. At the end of the four week exposure period, oysters in all four pCO2 environments deposited new shell, but growth rate was not different among the treatments. However, micromechanical properties of the new shell were compromised by elevated pCO2. Elevated pCO2 affected neither whole body fatty acid composition, nor glycogen content, nor mortality rate associated with acute heat shock. Shotgun proteomics revealed that several physiological pathways were significantly affected by ocean acidification, including antioxidant response, carbohydrate metabolism, and transcription and translation. Additionally, the proteomic response to a second stress differed with pCO2, with numerous processes significantly affected by mechanical stimulation at high versus low pCO2 (all proteomics data are available in the ProteomeXchange under the identifier PXD000835).
Discussion. Oyster physiology is significantly altered by exposure to elevated pCO2, indicating changes in energy resource use. This is especially apparent in the assessment of the effects of pCO2 on the proteomic response to a second stress. The altered stress response illustrates that ocean acidification may impact how oysters respond to other changes in their environment. These data contribute to an integrative view of the effects of ocean acidification on oysters as well as physiological trade-offs during environmental stress.
Keyword(s):
Animalia; Benthic animals; Benthos; Biomass/Abundance/Elemental composition; Bottles or small containers/Aquaria (<20 L); Coast and continental shelf; Crassostrea gigas; Gene expression (incl. proteomics); Laboratory experiment; Mollusca; Mortality/Survival; North Pacific; Other studied parameter or process; Single species; Temperate
Related to:
Timmins-Schiffman, Emma; Coffey, William D; Hua, Wilber; Nunn, Brook L; Dickinson, Gary H; Roberts, Steven B (2014): Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas. PeerJ PrePrints, https://doi.org/10.7287/PEERJ.PREPRINTS.388V1
Timmins-Schiffman, Emma; Coffey, William D; Hua, Wilber; Nunn, Brook L; Dickinson, Gary H; Roberts, Steven B (2014): Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas. BMC Genomics, 15(1), 951, https://doi.org/10.1186/1471-2164-15-951
Original version:
Roberts, Steven B; Timmins-Schiffman, Emma (2014): Data accompanying "Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas". Figshare, https://doi.org/10.6084/M9.FIGSHARE.1192933
Further details:
Lavigne, Héloïse; Epitalon, Jean-Marie; Gattuso, Jean-Pierre (2014): seacarb: seawater carbonate chemistry with R. R package version 3.0. https://cran.r-project.org/package=seacarb
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 (Lavigne et al, 2014) 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 is 2014-10-30.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1SpeciesSpeciesRoberts, Steven B
2TableTabRoberts, Steven B
3FigureFigRoberts, Steven B
4Sample IDSample IDRoberts, Steven B
5Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmRoberts, Steven Btreatment
6ReplicateReplRoberts, Steven B
7Vickers hardness numberVH nrRoberts, Steven B
8Fracture toughnessK_IckPa m**(1/2)Roberts, Steven B
9Duration, number of daysDurationdaysRoberts, Steven B
10Temperature, waterTemp°CRoberts, Steven Btreatment
11MortalityMortalityRoberts, Steven B
12GlycogenGLYµg/mgRoberts, Steven B
13MassMassmgRoberts, Steven Btissue
14MassMassmgRoberts, Steven Bbuoyant, at start
15Confidence intervalCIRoberts, Steven B95%
16MassMassmgRoberts, Steven Bbuoyant, at 29 Days
17Confidence intervalCIRoberts, Steven B95%
18Protein spots, totalProtein spots#Roberts, Steven Btotal
19Protein spots, totalProtein spots#Roberts, Steven Btechnical replicate #1
20Protein spots, totalProtein spots#Roberts, Steven Btechnical replicate #2
21Protein spots, totalProtein spots#Roberts, Steven Btechnical replicate #3
22Protein spots, totalProtein spots#Roberts, Steven Bacross all 3 replicates
23ProteinsProtein%Roberts, Steven B
24GroupGroupRoberts, Steven Bfatty acid
25Peak areaPeak areaRoberts, Steven Bfatty acid
26ProportionPropRoberts, Steven Bfatty acid, normalized
27pHpHRoberts, Steven BSpectrophotometrictotal scale
28pH, standard deviationpH std dev±Roberts, Steven BSpectrophotometrictotal scale
29Temperature, waterTemp°CRoberts, Steven B
30Temperature, water, standard deviationTemp std dev±Roberts, Steven B
31SalinitySalRoberts, Steven B
32Salinity, standard deviationSal std dev±Roberts, Steven B
33Alkalinity, totalATµmol/kgRoberts, Steven BPotentiometric titration
34Alkalinity, total, standard deviationAT std dev±Roberts, Steven BPotentiometric titration
35Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmRoberts, Steven BCalculated using CO2calc
36Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Roberts, Steven BCalculated using CO2calc
37Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmRoberts, Steven BCalculated using CO2calc
38Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Roberts, Steven BCalculated using CO2calc
39Calcite saturation stateOmega CalRoberts, Steven BCalculated using CO2calc
40Calcite saturation state, standard deviationOmega Cal std dev±Roberts, Steven BCalculated using CO2calc
41Aragonite saturation stateOmega ArgRoberts, Steven BCalculated using CO2calc
42Aragonite saturation state, standard deviationOmega Arg std dev±Roberts, Steven BCalculated using CO2calc
43Carbonate ion[CO3]2-µmol/kgRoberts, Steven BCalculated using CO2calc
44Carbonate ion, standard deviation[CO3]2- std dev±Roberts, Steven BCalculated using CO2calc
45Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
46Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
47Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
48Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
49Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
50Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
51Carbon, inorganic, dissolvedDICµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
52Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
53Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
License:
Creative Commons Attribution 3.0 Unported (CC-BY-3.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
23319 data points

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