Data Description

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Citation:
Stumpp, M et al. (2011): Seawater carbonate chemistry and Strongylocentrotus purpuratus body length and gene expression pattern changes during experiments, 2011. doi:10.1594/PANGAEA.774447,
Supplement to: Stumpp, Meike; Dupont, Sam; Thorndyke, Mike; Melzner, Frank (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, doi:10.1016/j.cbpa.2011.06.023
Abstract:
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.
Project(s):
Comment:
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).
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethodComment
1Experimental treatment *Exp trtmStumpp, Meike *
2Experiment day *Exp daydayStumpp, Meike *
3Salinity *SalStumpp, Meike *
4Salinity, standard deviation *Sal std dev±Stumpp, Meike *
5Temperature, water *Temp°CStumpp, Meike *
6Temperature, standard deviation *T std dev±Stumpp, Meike *
7Alkalinity, total *ATµmol/kgStumpp, Meike *Measured *
8Alkalinity, total, standard deviation *AT std dev±Stumpp, Meike *
9pH *pHStumpp, Meike *Measured *NBS scale
10pH, standard deviation *pH std dev±Stumpp, Meike *
11Relative density per sample per individual *Density/ind#/#Stumpp, Meike *
12Relative density per sample, standard deviation *Density std dev±Stumpp, Meike *
13Strongylocentrotus purpuratus, body length *S. purpuratus B lµmStumpp, Meike *
14Strongylocentrotus purpuratus, body length, standard deviation *S. purpuratus B l std dev±Stumpp, Meike *
15Change in anion exchanger 3-like protein, SLC4A3 expression *AE3a%Stumpp, Meike *see reference(s) *
16Change in anion exchanger 3-like protein SLC4A3 expression, standard deviation *AE3a std dev±Stumpp, Meike *see reference(s) *
17Change in carbonic anhydrase 15-subfamily expression *CA15%Stumpp, Meike *see reference(s) *
18Change in carbonic anhydrase 15-subfamily expression, standard deviation *CA15 std dev±Stumpp, Meike *see reference(s) *
19Change in carbonic anhydrase related protein expression *CA10%Stumpp, Meike *see reference(s) *
20Change in carbonic anhydrase related protein expression, standard deviation *CA10 std dev±Stumpp, Meike *see reference(s) *
21Change in Echinonectin expression *EN%Stumpp, Meike *see reference(s) *
22Change in Echinonectin expression, standard deviation *EN std dev±Stumpp, Meike *see reference(s) *
23Change in Lysosomal H+ ATPase expression *lys H-ATPase%Stumpp, Meike *see reference(s) *
24Change in Lysosomal H+ ATPase expression, standard deviation *lys H-ATPase std dev±Stumpp, Meike *see reference(s) *
25Change in Matrix-metalloproteinase 14 expression *MMP%Stumpp, Meike *see reference(s) *
26Change in Matrix-metalloproteinase 14 expression, standard deviation *MMP std dev±Stumpp, Meike *see reference(s) *
27Change in Mesenchyme-msp 130 expression *msp 130%Stumpp, Meike *see reference(s) *
28Change in Mesenchyme-msp 130 expression, standard deviation *msp 130 std dev±Stumpp, Meike *see reference(s) *
29Change in Sodium/potassium ATPase alpha subunit expression *NaK-ATPase%Stumpp, Meike *see reference(s) *
30Change in Sodium/potassium ATPase alpha subunit expression, standard deviation *NaK-ATPase std dev±Stumpp, Meike *see reference(s) *
31Change in Anion exchanger 3, SLC4A3 expression *AE3b%Stumpp, Meike *see reference(s) *
32Change in Anion exchanger 3, SLC4A3 expression, standard deviation *AE3b std dev±Stumpp, Meike *see reference(s) *
33Change in Sodium/hydrogen exchanger 3, SLC9A3 expression *NHE3%Stumpp, Meike *see reference(s) *
34Change in Sodium/hydrogen exchanger 3, SLC9A3 expression, standard deviation *NHE3 std dev±Stumpp, Meike *see reference(s) *
35Change in Sarco/endoplasmic reticulum Ca transporting ATPase expression *SERCA%Stumpp, Meike *see reference(s) *
36Change in Sarco/endoplasmic reticulum Ca transporting ATPase expression, std dev *SERCA std dev±Stumpp, Meike *see reference(s) *
37Change in Spicule matrix protein 30 B expression *SM30B%Stumpp, Meike *see reference(s) *
38Change in Spicule matrix protein 30 B expression, standard deviation *SM30B std dev±Stumpp, Meike *see reference(s) *
39Change in Spicule matrix protein 30 E expression *SM30E%Stumpp, Meike *see reference(s) *
40Change in Spicule matrix protein 30 E expression, standard deviation *SM30E std dev±Stumpp, Meike *see reference(s) *
41Change in Spicule matrix protein 50 expression *SM50%Stumpp, Meike *see reference(s) *
42Change in Spicule matrix protein 50 expression, standard deviation *SM50 std dev±Stumpp, Meike *see reference(s) *
43Change in Voltage gated proton channel expression *VSOP%Stumpp, Meike *see reference(s) *
44Change in Voltage gated proton channel expression, standard deviation *VSOP std dev±Stumpp, Meike *see reference(s) *
45Change in Vacuolar H+ ATPase B subunit expression *V-H-ATPase%Stumpp, Meike *see reference(s) *
46Change in Vacuolar H+ ATPase B subunit expression, standard deviation *V-H-ATPase std dev±Stumpp, Meike *see reference(s) *
47Change in FACT complex subunit SPT16 expression *FACT%Stumpp, Meike *see reference(s) *
48Change in FACT complex subunit SPT16 expression, standard deviation *FACT std dev±Stumpp, Meike *see reference(s) *
49Change in ß-Actin expression *beta Actin%Stumpp, Meike *see reference(s) *
50Change in ß-Actin expression, standard deviation *beta Actin std dev±Stumpp, Meike *see reference(s) *
51Change in TATA-box binding protein expression *TBP%Stumpp, Meike *see reference(s) *
52Change in TATA-box binding protein expression, standard deviation *TBP std dev±Stumpp, Meike *see reference(s) *
53Change in Heat shock protein gp96 expression *gp96%Stumpp, Meike *see reference(s) *
54Change in Heat shock protein gp96 expression, standard deviation *gp96 std dev±Stumpp, Meike *see reference(s) *
55Change in Heat shock protein 70 kDa expression *HSP70%Stumpp, Meike *see reference(s) *
56Change in Heat shock protein 70 kDa expression, standard deviation *HSP70 std dev±Stumpp, Meike *see reference(s) *
57Change in ATP-synthase beta-subunit expression *ATP-S%Stumpp, Meike *see reference(s) *
58Change in ATP-synthase beta-subunit expression, standard deviation *ATP-S std dev±Stumpp, Meike *see reference(s) *
59Change in Citrate synthase expression *CS%Stumpp, Meike *see reference(s) *
60Change in Citrate synthase expression, standard deviation *CS std dev±Stumpp, Meike *see reference(s) *
61Change in Mannose-6-phosphate growth factor expression *IR%Stumpp, Meike *see reference(s) *
62Change in Mannose-6-phosphate growth factor expression, standard deviation *IR std dev±Stumpp, Meike *see reference(s) *
63Change in Pyruvat kinase expression *PK%Stumpp, Meike *see reference(s) *
64Change in Pyruvat kinase expression, standard deviation *PK std dev±Stumpp, Meike *see reference(s) *
65Change in Thiolase expression *Thiolase%Stumpp, Meike *see reference(s) *
66Change in Thiolase expression, standard deviation *Thiolase std dev±Stumpp, Meike *see reference(s) *
67Carbonate system computation flag *CSC flagNisumaa, Anne-Marin *Calculated using seacarb after Nisumaa et al. (2010) *
68pH *pHNisumaa, Anne-Marin *Calculated using seacarb after Nisumaa et al. (2010) *Total scale
69Carbon dioxide *CO2µmol/kgNisumaa, Anne-Marin *Calculated using seacarb after Nisumaa et al. (2010) *
70Partial pressure of carbon dioxide (water) at sea surface temperature (wet air) *pCO2water_SST_wetµatmNisumaa, Anne-Marin *Calculated using seacarb after Nisumaa et al. (2010) *
71Fugacity of carbon dioxide (water) at sea surface temperature (wet air) *fCO2water_SST_wetµatmNisumaa, Anne-Marin *Calculated using seacarb after Nisumaa et al. (2010) *
72Bicarbonate ion *[HCO3]-µmol/kgNisumaa, Anne-Marin *Calculated using seacarb after Nisumaa et al. (2010) *
73Carbonate ion *[CO3]2-µmol/kgNisumaa, Anne-Marin *Calculated using seacarb after Nisumaa et al. (2010) *
74Carbon, inorganic, dissolved *DICµmol/kgNisumaa, Anne-Marin *Calculated using seacarb after Nisumaa et al. (2010) *
75Aragonite saturation state *Omega ArgNisumaa, Anne-Marin *Calculated using seacarb after Nisumaa et al. (2010) *
76Calcite saturation state *Omega CalNisumaa, Anne-Marin *Calculated using seacarb after Nisumaa et al. (2010) *
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632 data points

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