Citation:

j.cbpa.2011.06.023

Name: Seawater carbonate chemistry and Strongylocentrotus purpuratus body length and gene expression pattern changes during experiments, 2011
Published: 2011
License: https://creativecommons.org/licenses/by/3.0/
Keywords: 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

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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.

Keyword(s):

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

Project(s):

Biological Impacts of Ocean Acidification (BIOACID)

European network of excellence for Ocean Ecosystems Analysis (EUR-OCEANS)

European Project on Ocean Acidification (EPOCA)

Ocean Acidification International Coordination Centre (OA-ICC)

Funding:

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

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):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Experimental treatment	Exp treat		Stumpp, Meike
2	Experiment day	Exp day	day	Stumpp, Meike
3	Salinity	Sal		Stumpp, Meike
4	Salinity, standard deviation	Sal std dev	±	Stumpp, Meike
5	Temperature, water	Temp	°C	Stumpp, Meike
6	Temperature, standard deviation	T std dev	±	Stumpp, Meike
7	Alkalinity, total	AT	µmol/kg	Stumpp, Meike	Measured
8	Alkalinity, total, standard deviation	AT std dev	±	Stumpp, Meike
9	pH	pH		Stumpp, Meike	Measured	NBS scale
10	pH, standard deviation	pH std dev	±	Stumpp, Meike
11	Relative density per sample per individual	Density/ind	#/#	Stumpp, Meike
12	Relative density per sample, standard deviation	Density std dev	±	Stumpp, Meike
13	Strongylocentrotus purpuratus, body length	S. purpuratus B l	µm	Stumpp, Meike
14	Strongylocentrotus purpuratus, body length, standard deviation	S. purpuratus B l std dev	±	Stumpp, Meike
15	Change in anion exchanger 3-like protein, SLC4A3 expression	AE3a	%	Stumpp, Meike	see reference(s)
16	Change in anion exchanger 3-like protein SLC4A3 expression, standard deviation	AE3a std dev	±	Stumpp, Meike	see reference(s)
17	Change in carbonic anhydrase 15-subfamily expression	CA15	%	Stumpp, Meike	see reference(s)
18	Change in carbonic anhydrase 15-subfamily expression, standard deviation	CA15 std dev	±	Stumpp, Meike	see reference(s)
19	Change in carbonic anhydrase related protein expression	CA10	%	Stumpp, Meike	see reference(s)
20	Change in carbonic anhydrase related protein expression, standard deviation	CA10 std dev	±	Stumpp, Meike	see reference(s)
21	Change in Echinonectin expression	EN	%	Stumpp, Meike	see reference(s)
22	Change in Echinonectin expression, standard deviation	EN std dev	±	Stumpp, Meike	see reference(s)
23	Change in Lysosomal H+ ATPase expression	lys H-ATPase	%	Stumpp, Meike	see reference(s)
24	Change in Lysosomal H+ ATPase expression, standard deviation	lys H-ATPase std dev	±	Stumpp, Meike	see reference(s)
25	Change in Matrix-metalloproteinase 14 expression	MMP	%	Stumpp, Meike	see reference(s)
26	Change in Matrix-metalloproteinase 14 expression, standard deviation	MMP std dev	±	Stumpp, Meike	see reference(s)
27	Change in Mesenchyme-msp 130 expression	msp 130	%	Stumpp, Meike	see reference(s)
28	Change in Mesenchyme-msp 130 expression, standard deviation	msp 130 std dev	±	Stumpp, Meike	see reference(s)
29	Change in Sodium/potassium ATPase alpha subunit expression	NaK-ATPase	%	Stumpp, Meike	see reference(s)
30	Change in Sodium/potassium ATPase alpha subunit expression, standard deviation	NaK-ATPase std dev	±	Stumpp, Meike	see reference(s)
31	Change in Anion exchanger 3, SLC4A3 expression	AE3b	%	Stumpp, Meike	see reference(s)
32	Change in Anion exchanger 3, SLC4A3 expression, standard deviation	AE3b std dev	±	Stumpp, Meike	see reference(s)
33	Change in Sodium/hydrogen exchanger 3, SLC9A3 expression	NHE3	%	Stumpp, Meike	see reference(s)
34	Change in Sodium/hydrogen exchanger 3, SLC9A3 expression, standard deviation	NHE3 std dev	±	Stumpp, Meike	see reference(s)
35	Change in Sarco/endoplasmic reticulum Ca transporting ATPase expression	SERCA	%	Stumpp, Meike	see reference(s)
36	Change in Sarco/endoplasmic reticulum Ca transporting ATPase expression, std dev	SERCA std dev	±	Stumpp, Meike	see reference(s)
37	Change in Spicule matrix protein 30 B expression	SM30B	%	Stumpp, Meike	see reference(s)
38	Change in Spicule matrix protein 30 B expression, standard deviation	SM30B std dev	±	Stumpp, Meike	see reference(s)
39	Change in Spicule matrix protein 30 E expression	SM30E	%	Stumpp, Meike	see reference(s)
40	Change in Spicule matrix protein 30 E expression, standard deviation	SM30E std dev	±	Stumpp, Meike	see reference(s)
41	Change in Spicule matrix protein 50 expression	SM50	%	Stumpp, Meike	see reference(s)
42	Change in Spicule matrix protein 50 expression, standard deviation	SM50 std dev	±	Stumpp, Meike	see reference(s)
43	Change in Voltage gated proton channel expression	VSOP	%	Stumpp, Meike	see reference(s)
44	Change in Voltage gated proton channel expression, standard deviation	VSOP std dev	±	Stumpp, Meike	see reference(s)
45	Change in Vacuolar H+ ATPase B subunit expression	V-H-ATPase	%	Stumpp, Meike	see reference(s)
46	Change in Vacuolar H+ ATPase B subunit expression, standard deviation	V-H-ATPase std dev	±	Stumpp, Meike	see reference(s)
47	Change in FACT complex subunit SPT16 expression	FACT	%	Stumpp, Meike	see reference(s)
48	Change in FACT complex subunit SPT16 expression, standard deviation	FACT std dev	±	Stumpp, Meike	see reference(s)
49	Change in beta-Actin expression	b Actin	%	Stumpp, Meike	see reference(s)
50	Change in beta-Actin expression, standard deviation	b Actin std dev	±	Stumpp, Meike	see reference(s)
51	Change in TATA-box binding protein expression	TBP	%	Stumpp, Meike	see reference(s)
52	Change in TATA-box binding protein expression, standard deviation	TBP std dev	±	Stumpp, Meike	see reference(s)
53	Change in Heat shock protein gp96 expression	gp96	%	Stumpp, Meike	see reference(s)
54	Change in Heat shock protein gp96 expression, standard deviation	gp96 std dev	±	Stumpp, Meike	see reference(s)
55	Change in Heat shock protein 70 kDa expression	HSP70	%	Stumpp, Meike	see reference(s)
56	Change in Heat shock protein 70 kDa expression, standard deviation	HSP70 std dev	±	Stumpp, Meike	see reference(s)
57	Change in ATP-synthase beta-subunit expression	ATP-S	%	Stumpp, Meike	see reference(s)
58	Change in ATP-synthase beta-subunit expression, standard deviation	ATP-S std dev	±	Stumpp, Meike	see reference(s)
59	Change in Citrate synthase expression	CS	%	Stumpp, Meike	see reference(s)
60	Change in Citrate synthase expression, standard deviation	CS std dev	±	Stumpp, Meike	see reference(s)
61	Change in Mannose-6-phosphate growth factor expression	IR	%	Stumpp, Meike	see reference(s)
62	Change in Mannose-6-phosphate growth factor expression, standard deviation	IR std dev	±	Stumpp, Meike	see reference(s)
63	Change in Pyruvat kinase expression	PK	%	Stumpp, Meike	see reference(s)
64	Change in Pyruvat kinase expression, standard deviation	PK std dev	±	Stumpp, Meike	see reference(s)
65	Change in Thiolase expression	Thiolase	%	Stumpp, Meike	see reference(s)
66	Change in Thiolase expression, standard deviation	Thiolase std dev	±	Stumpp, Meike	see reference(s)
67	Carbonate system computation flag	CSC flag		Nisumaa, Anne-Marin	Calculated using seacarb after Nisumaa et al. (2010)
68	pH	pH		Nisumaa, Anne-Marin	Calculated using seacarb after Nisumaa et al. (2010)	Total scale
69	Carbon dioxide	CO2	µmol/kg	Nisumaa, Anne-Marin	Calculated using seacarb after Nisumaa et al. (2010)
70	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Nisumaa, Anne-Marin	Calculated using seacarb after Nisumaa et al. (2010)
71	Fugacity of carbon dioxide (water) at sea surface temperature (wet air)	fCO2water_SST_wet	µatm	Nisumaa, Anne-Marin	Calculated using seacarb after Nisumaa et al. (2010)
72	Bicarbonate ion	[HCO3]-	µmol/kg	Nisumaa, Anne-Marin	Calculated using seacarb after Nisumaa et al. (2010)
73	Carbonate ion	[CO3]2-	µmol/kg	Nisumaa, Anne-Marin	Calculated using seacarb after Nisumaa et al. (2010)
74	Carbon, inorganic, dissolved	DIC	µmol/kg	Nisumaa, Anne-Marin	Calculated using seacarb after Nisumaa et al. (2010)
75	Aragonite saturation state	Omega Arg		Nisumaa, Anne-Marin	Calculated using seacarb after Nisumaa et al. (2010)
76	Calcite saturation state	Omega Cal		Nisumaa, Anne-Marin	Calculated 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:

632 data points

Data

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

1 Exp treat	2 Exp day [day]	3 Sal	4 Sal std dev [±]	5 Temp [°C]	6 T std dev [±]	7 AT [µmol/kg] (Measured)	8 AT std dev [±]	9 pH (NBS scale, Measured)	10 pH std dev [±]	11 Density/ind [#/#]	12 Density std dev [±]	13 S. purpuratus B l [µm]	14 S. purpuratus B l std dev [±]	15 AE3a [%] (see reference(s))	16 AE3a std dev [±] (see reference(s))	17 CA15 [%] (see reference(s))	18 CA15 std dev [±] (see reference(s))	19 CA10 [%] (see reference(s))	20 CA10 std dev [±] (see reference(s))	21 EN [%] (see reference(s))	22 EN std dev [±] (see reference(s))	23 lys H-ATPase [%] (see reference(s))	24 lys H-ATPase std dev [±] (see reference(s))	25 MMP [%] (see reference(s))	26 MMP std dev [±] (see reference(s))	27 msp 130 [%] (see reference(s))	28 msp 130 std dev [±] (see reference(s))	29 NaK-ATPase [%] (see reference(s))	30 NaK-ATPase std dev [±] (see reference(s))	31 AE3b [%] (see reference(s))	32 AE3b std dev [±] (see reference(s))	33 NHE3 [%] (see reference(s))	34 NHE3 std dev [±] (see reference(s))	35 SERCA [%] (see reference(s))	36 SERCA std dev [±] (see reference(s))	37 SM30B [%] (see reference(s))	38 SM30B std dev [±] (see reference(s))	39 SM30E [%] (see reference(s))	40 SM30E std dev [±] (see reference(s))	41 SM50 [%] (see reference(s))	42 SM50 std dev [±] (see reference(s))	43 VSOP [%] (see reference(s))	44 VSOP std dev [±] (see reference(s))	45 V-H-ATPase [%] (see reference(s))	46 V-H-ATPase std dev [±] (see reference(s))	47 FACT [%] (see reference(s))	48 FACT std dev [±] (see reference(s))	49 b Actin [%] (see reference(s))	50 b Actin std dev [±] (see reference(s))	51 TBP [%] (see reference(s))	52 TBP std dev [±] (see reference(s))	53 gp96 [%] (see reference(s))	54 gp96 std dev [±] (see reference(s))	55 HSP70 [%] (see reference(s))	56 HSP70 std dev [±] (see reference(s))	57 ATP-S [%] (see reference(s))	58 ATP-S std dev [±] (see reference(s))	59 CS [%] (see reference(s))	60 CS std dev [±] (see reference(s))	61 IR [%] (see reference(s))	62 IR std dev [±] (see reference(s))	63 PK [%] (see reference(s))	64 PK std dev [±] (see reference(s))	65 Thiolase [%] (see reference(s))	66 Thiolase std dev [±] (see reference(s))	67 CSC flag (Calculated using seacarb afte...)	68 pH (Total scale, Calculated using...)	69 CO2 [µmol/kg] (Calculated using seacarb afte...)	70 pCO2water_SST_wet [µatm] (Calculated using seacarb afte...)	71 fCO2water_SST_wet [µatm] (Calculated using seacarb afte...)	72 [HCO3]- [µmol/kg] (Calculated using seacarb afte...)	73 [CO3]2- [µmol/kg] (Calculated using seacarb afte...)	74 DIC [µmol/kg] (Calculated using seacarb afte...)	75 Omega Arg (Calculated using seacarb afte...)	76 Omega Cal (Calculated using seacarb afte...)
pH=8.1	1	32	0.7	16	0.8	2243	40	8.17	0.04	1.0000	0.0000																																																							26	8.05	14.58	395.75	394.35	1871.46	150.96	2037.00	2.35	3.67
pH=8.1	2	32	0.7	16	0.8	2243	40	8.17	0.04	1.0000	0.0000	148.34	7.40	0.828	0.086	1.396	0.124	0.237	0.016	0.320	0.037	1.286	0.128	0.707	0.062	6.398	0.311	14.831	0.983	0.114	0.012	0.344	0.023	4.194	0.292	15.607	2.081	0.101	0.010	5.101	0.359	0.370	0.038	2.529	0.278	0.527	0.024	1.588	0.144	0.149	0.010	6.164	0.788	3.540	0.287	11.707	0.907	2.745	0.242	0.464	0.058	0.545	0.034	2.325	0.162	26	8.05	14.58	395.75	394.35	1871.46	150.96	2037.00	2.35	3.67
pH=8.1	3	32	0.7	16	0.8	2243	40	8.17	0.04	0.9750	0.0250																																																							26	8.05	14.58	395.75	394.35	1871.46	150.96	2037.00	2.35	3.67
pH=8.1	4	32	0.7	16	0.8	2243	40	8.17	0.04	0.9393	0.0139	240.68	12.50	0.374	0.024	0.729	0.082	0.462	0.035	0.573	0.046	1.278	0.142	0.224	0.019	2.014	0.111	17.075	0.914	0.071	0.003	0.316	0.018	5.095	0.277	9.528	0.627	0.116	0.011	2.549	0.124	0.134	0.007	2.646	0.227	0.652	0.047	1.074	0.127	0.234	0.017	6.459	0.417	10.196	0.509	21.989	2.098	4.110	0.445	0.432	0.037	1.180	0.121	3.277	0.296	26	8.05	14.58	395.75	394.35	1871.46	150.96	2037.00	2.35	3.67
pH=8.1	5	32	0.7	16	0.8	2243	40	8.17	0.04	0.9427	0.0573																																																							26	8.05	14.58	395.75	394.35	1871.46	150.96	2037.00	2.35	3.67
pH=8.1	6	32	0.7	16	0.8	2243	40	8.17	0.04	0.9218	0.0018																																																							26	8.05	14.58	395.75	394.35	1871.46	150.96	2037.00	2.35	3.67
pH=8.1	7	32	0.7	16	0.8	2243	40	8.17	0.04	0.9418	0.0182	293.62	14.34	0.341	0.031	0.502	0.042	0.562	0.022	1.265	0.105	1.521	0.092	0.128	0.015	0.762	0.075	12.683	0.754	0.106	0.006	0.330	0.023	3.709	0.158	4.045	0.233	0.059	0.005	1.266	0.074	0.309	0.017	3.567	0.220	0.431	0.031	1.420	0.076	0.141	0.008	4.321	0.321	3.842	0.278	25.918	1.361	4.562	0.250	0.846	0.015	0.726	0.052	1.481	0.114	26	8.05	14.58	395.75	394.35	1871.46	150.96	2037.00	2.35	3.67
pH=7.7	1	32	0.7	16	0.8	2233	17	7.70	0.04	1.0000	0.0000																																																							26	7.58	48.14	1307.06	1302.46	2092.23	57.13	2197.50	0.89	1.39
pH=7.7	2	32	0.7	16	0.8	2233	17	7.70	0.04	0.9900	0.0100	137.18	9.75	0.854	0.071	1.233	0.081	0.192	0.017	0.283	0.022	1.272	0.083	0.668	0.051	6.160	0.447	14.785	0.856	0.110	0.009	0.376	0.032	4.308	0.141	13.745	1.456	0.118	0.016	4.924	0.455	0.368	0.035	2.416	0.201	0.513	0.031	1.446	0.113	0.141	0.014	5.611	0.444	3.461	0.277	11.251	0.957	2.609	0.302	0.410	0.025	0.530	0.048	2.162	0.193	26	7.58	48.14	1307.06	1302.46	2092.23	57.13	2197.50	0.89	1.39
pH=7.7	3	32	0.7	16	0.8	2233	17	7.70	0.04	0.9656	0.0344																																																							26	7.58	48.14	1307.06	1302.46	2092.23	57.13	2197.50	0.89	1.39
pH=7.7	4	32	0.7	16	0.8	2233	17	7.70	0.04	0.9603	0.0360	216.70	8.27	0.332	0.031	0.730	0.056	0.437	0.030	0.465	0.045	1.337	0.096	0.169	0.010	1.283	0.083	19.740	1.573	0.071	0.004	0.173	0.021	5.443	0.280	6.786	0.803	0.106	0.009	1.958	0.134	0.131	0.014	2.631	0.094	0.741	0.049	1.261	0.063	0.241	0.015	6.857	0.205	12.084	0.669	25.836	1.924	4.619	0.310	0.435	0.020	1.293	0.088	3.922	0.242	26	7.58	48.14	1307.06	1302.46	2092.23	57.13	2197.50	0.89	1.39
pH=7.7	5	32	0.7	16	0.8	2233	17	7.70	0.04	0.9618	0.0382																																																							26	7.58	48.14	1307.06	1302.46	2092.23	57.13	2197.50	0.89	1.39
pH=7.7	6	32	0.7	16	0.8	2233	17	7.70	0.04	0.8514	0.0686																																																							26	7.58	48.14	1307.06	1302.46	2092.23	57.13	2197.50	0.89	1.39
pH=7.7	7	32	0.7	16	0.8	2233	17	7.70	0.04	0.8640	0.1160	276.22	22.22	0.278	0.019	0.538	0.034	0.516	0.040	1.243	0.119	1.441	0.118	0.119	0.014	0.708	0.046	12.136	1.059	0.104	0.009	0.278	0.019	2.907	0.164	4.229	0.333	0.083	0.015	1.183	0.140	0.359	0.025	3.227	0.189	0.411	0.034	1.666	0.145	0.147	0.011	3.892	0.361	3.397	0.290	28.013	2.895	4.906	0.472	0.928	0.061	0.863	0.092	1.475	0.156	26	7.58	48.14	1307.06	1302.46	2092.23	57.13	2197.50	0.89	1.39