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Stumpp, Meike; Dupont, Sam; Thorndyke, Mike; Melzner, Frank (2011): Seawater carbonate chemistry and Strongylocentrotus purpuratus body length and gene expression pattern changes during experiments, 2011. PANGAEA,, Supplement to: Stumpp, M et al. (2011): CO2 induced seawater acidification impacts sea urchin larval development II: Gene expression patterns in pluteus larvae. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 160(3), 320-330,

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Extensive use of fossil fuels is leading to increasing CO2 concentrations in the atmosphere and causes changes in the carbonate chemistry of the oceans which represents a major sink for anthropogenic CO2. As a result, the oceans' surface pH is expected to decrease by ca. 0.4 units by the year 2100, a major change with potentially negative consequences for some marine species. Because of their carbonate skeleton, sea urchins and their larval stages are regarded as likely to be one of the more sensitive taxa. In order to investigate sensitivity of pre-feeding (2 days post-fertilization) and feeding (4 and 7 days post-fertilization) pluteus larvae, we raised Strongylocentrotus purpuratus embryos in control (pH 8.1 and pCO2 41 Pa e.g. 399 µatm) and CO2 acidified seawater with pH of 7.7 (pCO2 134 Pa e.g. 1318 µatm) and investigated growth, calcification and survival. At three time points (day 2, day 4 and day 7 post-fertilization), we measured the expression of 26 representative genes important for metabolism, calcification and ion regulation using RT-qPCR.
After one week of development, we observed a significant difference in growth. Maximum differences in size were detected at day 4 (ca. 10 % reduction in body length). A comparison of gene expression patterns using PCA and ANOSIM clearly distinguished between the different age groups (Two way ANOSIM: Global R = 1) while acidification effects were less pronounced (Global R = 0.518). Significant differences in gene expression patterns (ANOSIM R = 0.938, SIMPER: 4.3% difference) were also detected at day 4 leading to the hypothesis that differences between CO2 treatments could reflect patterns of expression seen in control experiments of a younger larva and thus a developmental artifact rather than a direct CO2 effect. We found an up regulation of metabolic genes (between 10 to 20% in ATP-synthase, citrate synthase, pyruvate kinase and thiolase at day 4) and down regulation of calcification related genes (between 23 and 36% in msp130, SM30B, SM50 at day 4). Ion regulation was mainly impacted by up regulation of Na+/K+-ATPase at day 4 (15%) and down regulation of NHE3 at day 4 (45%). We conclude that in studies in which a stressor induces an alteration in the speed of development, it is crucial to employ experimental designs with a high time resolution in order to correct for developmental artifacts. This helps prevent misinterpretation of stressor effects on organism physiology.
Animalia; Bottles or small containers/Aquaria (<20 L); Coast and continental shelf; Echinodermata; Gene expression (incl. proteomics); Growth/Morphology; Laboratory experiment; Mortality/Survival; North Pacific; Pelagos; Single species; Strongylocentrotus purpuratus; Temperate; Zooplankton
Seventh Framework Programme (FP7), grant/award no. 211384: European Project on Ocean Acidification
Sixth Framework Programme (FP6), grant/award no. 511106: European network of excellence for Ocean Ecosystems Analysis
In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Lavigne and Gattuso, 2011) 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).
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Experimental treatmentExp treatStumpp, Meike
2Experiment dayExp daydayStumpp, Meike
3SalinitySalStumpp, Meike
4Salinity, standard deviationSal std dev±Stumpp, Meike
5Temperature, waterTemp°CStumpp, Meike
6Temperature, standard deviationT std dev±Stumpp, Meike
7Alkalinity, totalATµmol/kgStumpp, MeikeMeasured
8Alkalinity, total, standard deviationAT std dev±Stumpp, Meike
9pHpHStumpp, MeikeMeasuredNBS scale
10pH, standard deviationpH std dev±Stumpp, Meike
11Relative density per sample per individualDensity/ind#/#Stumpp, Meike
12Relative density per sample, standard deviationDensity std dev±Stumpp, Meike
13Strongylocentrotus purpuratus, body lengthS. purpuratus B lµmStumpp, Meike
14Strongylocentrotus purpuratus, body length, standard deviationS. purpuratus B l std dev±Stumpp, Meike
15Change in anion exchanger 3-like protein, SLC4A3 expressionAE3a%Stumpp, Meikesee reference(s)
16Change in anion exchanger 3-like protein SLC4A3 expression, standard deviationAE3a std dev±Stumpp, Meikesee reference(s)
17Change in carbonic anhydrase 15-subfamily expressionCA15%Stumpp, Meikesee reference(s)
18Change in carbonic anhydrase 15-subfamily expression, standard deviationCA15 std dev±Stumpp, Meikesee reference(s)
19Change in carbonic anhydrase related protein expressionCA10%Stumpp, Meikesee reference(s)
20Change in carbonic anhydrase related protein expression, standard deviationCA10 std dev±Stumpp, Meikesee reference(s)
21Change in Echinonectin expressionEN%Stumpp, Meikesee reference(s)
22Change in Echinonectin expression, standard deviationEN std dev±Stumpp, Meikesee reference(s)
23Change in Lysosomal H+ ATPase expressionlys H-ATPase%Stumpp, Meikesee reference(s)
24Change in Lysosomal H+ ATPase expression, standard deviationlys H-ATPase std dev±Stumpp, Meikesee reference(s)
25Change in Matrix-metalloproteinase 14 expressionMMP%Stumpp, Meikesee reference(s)
26Change in Matrix-metalloproteinase 14 expression, standard deviationMMP std dev±Stumpp, Meikesee reference(s)
27Change in Mesenchyme-msp 130 expressionmsp 130%Stumpp, Meikesee reference(s)
28Change in Mesenchyme-msp 130 expression, standard deviationmsp 130 std dev±Stumpp, Meikesee reference(s)
29Change in Sodium/potassium ATPase alpha subunit expressionNaK-ATPase%Stumpp, Meikesee reference(s)
30Change in Sodium/potassium ATPase alpha subunit expression, standard deviationNaK-ATPase std dev±Stumpp, Meikesee reference(s)
31Change in Anion exchanger 3, SLC4A3 expressionAE3b%Stumpp, Meikesee reference(s)
32Change in Anion exchanger 3, SLC4A3 expression, standard deviationAE3b std dev±Stumpp, Meikesee reference(s)
33Change in Sodium/hydrogen exchanger 3, SLC9A3 expressionNHE3%Stumpp, Meikesee reference(s)
34Change in Sodium/hydrogen exchanger 3, SLC9A3 expression, standard deviationNHE3 std dev±Stumpp, Meikesee reference(s)
35Change in Sarco/endoplasmic reticulum Ca transporting ATPase expressionSERCA%Stumpp, Meikesee reference(s)
36Change in Sarco/endoplasmic reticulum Ca transporting ATPase expression, std devSERCA std dev±Stumpp, Meikesee reference(s)
37Change in Spicule matrix protein 30 B expressionSM30B%Stumpp, Meikesee reference(s)
38Change in Spicule matrix protein 30 B expression, standard deviationSM30B std dev±Stumpp, Meikesee reference(s)
39Change in Spicule matrix protein 30 E expressionSM30E%Stumpp, Meikesee reference(s)
40Change in Spicule matrix protein 30 E expression, standard deviationSM30E std dev±Stumpp, Meikesee reference(s)
41Change in Spicule matrix protein 50 expressionSM50%Stumpp, Meikesee reference(s)
42Change in Spicule matrix protein 50 expression, standard deviationSM50 std dev±Stumpp, Meikesee reference(s)
43Change in Voltage gated proton channel expressionVSOP%Stumpp, Meikesee reference(s)
44Change in Voltage gated proton channel expression, standard deviationVSOP std dev±Stumpp, Meikesee reference(s)
45Change in Vacuolar H+ ATPase B subunit expressionV-H-ATPase%Stumpp, Meikesee reference(s)
46Change in Vacuolar H+ ATPase B subunit expression, standard deviationV-H-ATPase std dev±Stumpp, Meikesee reference(s)
47Change in FACT complex subunit SPT16 expressionFACT%Stumpp, Meikesee reference(s)
48Change in FACT complex subunit SPT16 expression, standard deviationFACT std dev±Stumpp, Meikesee reference(s)
49Change in ß-Actin expressionbeta Actin%Stumpp, Meikesee reference(s)
50Change in ß-Actin expression, standard deviationbeta Actin std dev±Stumpp, Meikesee reference(s)
51Change in TATA-box binding protein expressionTBP%Stumpp, Meikesee reference(s)
52Change in TATA-box binding protein expression, standard deviationTBP std dev±Stumpp, Meikesee reference(s)
53Change in Heat shock protein gp96 expressiongp96%Stumpp, Meikesee reference(s)
54Change in Heat shock protein gp96 expression, standard deviationgp96 std dev±Stumpp, Meikesee reference(s)
55Change in Heat shock protein 70 kDa expressionHSP70%Stumpp, Meikesee reference(s)
56Change in Heat shock protein 70 kDa expression, standard deviationHSP70 std dev±Stumpp, Meikesee reference(s)
57Change in ATP-synthase beta-subunit expressionATP-S%Stumpp, Meikesee reference(s)
58Change in ATP-synthase beta-subunit expression, standard deviationATP-S std dev±Stumpp, Meikesee reference(s)
59Change in Citrate synthase expressionCS%Stumpp, Meikesee reference(s)
60Change in Citrate synthase expression, standard deviationCS std dev±Stumpp, Meikesee reference(s)
61Change in Mannose-6-phosphate growth factor expressionIR%Stumpp, Meikesee reference(s)
62Change in Mannose-6-phosphate growth factor expression, standard deviationIR std dev±Stumpp, Meikesee reference(s)
63Change in Pyruvat kinase expressionPK%Stumpp, Meikesee reference(s)
64Change in Pyruvat kinase expression, standard deviationPK std dev±Stumpp, Meikesee reference(s)
65Change in Thiolase expressionThiolase%Stumpp, Meikesee reference(s)
66Change in Thiolase expression, standard deviationThiolase std dev±Stumpp, Meikesee reference(s)
67Carbonate system computation flagCSC flagNisumaa, Anne-MarinCalculated using seacarb after Nisumaa et al. (2010)
68pHpHNisumaa, Anne-MarinCalculated using seacarb after Nisumaa et al. (2010)Total scale
69Carbon dioxideCO2µmol/kgNisumaa, Anne-MarinCalculated using seacarb after Nisumaa et al. (2010)
70Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmNisumaa, Anne-MarinCalculated using seacarb after Nisumaa et al. (2010)
71Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmNisumaa, Anne-MarinCalculated using seacarb after Nisumaa et al. (2010)
72Bicarbonate ion[HCO3]-µmol/kgNisumaa, Anne-MarinCalculated using seacarb after Nisumaa et al. (2010)
73Carbonate ion[CO3]2-µmol/kgNisumaa, Anne-MarinCalculated using seacarb after Nisumaa et al. (2010)
74Carbon, inorganic, dissolvedDICµmol/kgNisumaa, Anne-MarinCalculated using seacarb after Nisumaa et al. (2010)
75Aragonite saturation stateOmega ArgNisumaa, Anne-MarinCalculated using seacarb after Nisumaa et al. (2010)
76Calcite saturation stateOmega CalNisumaa, Anne-MarinCalculated using seacarb after Nisumaa et al. (2010)
632 data points

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