Citation:

PANGAEA.990365

Name: Seawater carbonate chemistry and spine regeneration, coelomic fluid parameters and RNA/DNA ratio of sea‑urchin arbacia dufresnii
Published: 2026-02-05
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Acid-base regulation; Animalia; Arbacia dufresnii; Benthic animals; Benthos; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Echinodermata; Gene expression (incl. proteomics); Growth/Morphology; Laboratory experiment; Other studied parameter or process; Single species; South Atlantic; Temperate

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Published: 2026-02-05 • DOI registered: 2026-03-06

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Abstract:

The goal of this work was to assess the effects of Ocean Acidification (OA) on Arbacia dufresnii, a sub-Antarctic sea urchin species. Adult specimens were exposed to three pH treatments: 7.4, 7.7, and 8.0 (control), for 21 up to 23 days. We assessed spine regeneration, a proxy of calcification, by cutting spines at the base of the shaft and evaluating the magnesium content, height, and weight of the regenerated part. The coelomic fluid was sampled for pH assessment and magnesium and calcium content analysis. The RNA/DNA ratio, a proxy of metabolic activity, was assessed in the gonads and body walls.

This dataset is included in the OA-ICC data compilation maintained in the framework of the IAEA Ocean Acidification International Coordination Centre (see https://oa-icc.ipsl.fr). Original data were downloaded from Marine Data Archive, VLIZ, Belgium (see Source) by the OA-ICC data curator. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2024) 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 2026-01-30.

Keyword(s):

Acid-base regulation; Animalia; Arbacia dufresnii; Benthic animals; Benthos; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Echinodermata; Gene expression (incl. proteomics); Growth/Morphology; Laboratory experiment; Other studied parameter or process; Single species; South Atlantic; Temperate

Related to:

Grandjean, Juliette; González‑Aravena, Marcelo; Gallardo, Pablo; Dubois, Philippe; Catarino, Ana Isabel (2026): Short-term tolerance to ocean acidification of the sub-antarctic sea-urchin arbacia dufresnii. Polar Biology, 49(1), 3, https://doi.org/10.1007/s00300-025-03437-y

Source:

Grandjean, Juliette; González‑Aravena, Marcelo; Gallardo, Pablo; Dubois, Philippe; Catarino, Ana Isabel (2025): Experimental work for the assessment of ocean acidification effects on the sea-urchin Arbacia dufresnii [dataset]. Marine Data Archive (MDA), https://doi.org/10.14284/714

References:

Nisumaa, Anne-Marin; Pesant, Stephane; Bellerby, Richard G J; Delille, Bruno; Middelburg, Jack J; Orr, James C; Riebesell, Ulf; Tyrrell, Toby; Wolf-Gladrow, Dieter A; Gattuso, Jean-Pierre (2010): EPOCA/EUR-OCEANS data compilation on the biological and biogeochemical responses to ocean acidification. Earth System Science Data, 2(2), 167-175, https://doi.org/10.5194/essd-2-167-2010

Yang, Yan; Brockmann, Patrick; Galdino, Carolina; Schindler, Uwe; Gazeau, Frédéric (2024): An update of data compilation on the biological response to ocean acidification and overview of the OA-ICC data portal. Earth System Science Data, 16(8), 3771-3780, https://doi.org/10.5194/essd-16-3771-2024

Yang, Yan; Hansson, L; Gattuso, Jean-Pierre (2016): Data compilation on the biological response to ocean acidification: an update. Earth System Science Data, 8(1), 79-87, https://doi.org/10.5194/essd-8-79-2016

Related code / software:

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 (2024): seacarb: seawater carbonate chemistry with R. R package version 3.3.3. https://cran.r-project.org/web/packages/seacarb/index.html

Project(s):

Ocean Acidification International Coordination Centre (OA-ICC)

Coverage:

Latitude: -53.616600 * Longitude: -70.933300

Date/Time Start: 2008-11-03T00:00:00 * Date/Time End: 2009-09-09T00:00:00

Event(s):

Fuerte_Bulnes * Latitude: -53.616600 * Longitude: -70.933300 * Date/Time Start: 2008-11-03T00:00:00 * Date/Time End: 2009-09-09T00:00:00 * Method/Device: Experiment (EXP)

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type of study	Study type		Grandjean, Juliette
2	Species, unique identification	Species UID		Grandjean, Juliette
3	Species, unique identification (Semantic URI)	Species UID (Semantic URI)		Grandjean, Juliette
4	Species, unique identification (URI)	Species UID (URI)		Grandjean, Juliette
5	Identification	ID		Grandjean, Juliette		Aquarium
6	Code	Code		Grandjean, Juliette		Sea urchin codes according to the aquarium in which they are
7	Treatment: pH	T:pH		Grandjean, Juliette
8	pH, total scale	pHT		Grandjean, Juliette
9	Date/time analysis, experiment	Date/time analysis exp		Grandjean, Juliette
10	Carbonate ion	[CO3]2-	µmol/kg	Grandjean, Juliette
11	Calcite saturation state	Omega Cal		Grandjean, Juliette
12	Aragonite saturation state	Omega Arg		Grandjean, Juliette
13	Calcium	Ca	mg/kg	Grandjean, Juliette		seawater
14	Magnesium	Mg	mg/kg	Grandjean, Juliette		seawater
15	Calcium	Ca	mmol/g	Grandjean, Juliette
16	Magnesium	Mg	mmol/g	Grandjean, Juliette
17	Ion activity, calcium, seawater	a [Ca]2+ sw		Grandjean, Juliette
18	Ion activity, magnesium, seawater	a [Mg]2+ sw		Grandjean, Juliette
19	Ion activity, carbonate, seawater	a [CO3]2- sw		Grandjean, Juliette
20	Magnesium carbonate	MgCO3	%	Grandjean, Juliette		Mole percentage in the spinesof Arbacia dufresnii
21	Magnesium	Mg	%	Grandjean, Juliette		Mole percentage of Mg measured in the spines
22	Calcium	Ca	%	Grandjean, Juliette		Mole percentage of Ca measured in the spines
23	Logarithm	log		Grandjean, Juliette		Logarithmic transofrmation of the equilibrium constant Kx
24	Equilibrium constant, magnesium calcite dissolution	Kx		Grandjean, Juliette
25	Ion activity product	IAP		Grandjean, Juliette		at equilibrium
26	High magnesium calcite saturation state	Omega HMC		Grandjean, Juliette
27	pH, total scale	pHT		Grandjean, Juliette		adapted for marine water in the last 24 hours of the experiment
28	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Grandjean, Juliette		the last 24 hours of the experiment
29	Coelomic fluid, pH	pH (cf)		Grandjean, Juliette		total scale
30	Calcium ions, coelomic fluid	Ca2+ (cf)	mol	Grandjean, Juliette
31	Magnesium, coelomic fluid	Mg2+ (cf)	mol	Grandjean, Juliette
32	Coelomic fluid, magnesium/calcium ratio	Mg/Ca (cf)		Grandjean, Juliette
33	Gender	Gender		Grandjean, Juliette
34	RNA/DNA ratio	RNA/DNA		Grandjean, Juliette		gonads
35	Logarithm	log		Grandjean, Juliette		RNA/DNA (gonads)
36	RNA/DNA ratio	RNA/DNA		Grandjean, Juliette		bodywall
37	Logarithm	log		Grandjean, Juliette		RNA/DNA (bodywall)
38	Diameter	Ø	mm	Grandjean, Juliette		body
39	Mass	Mass	mg	Grandjean, Juliette		Average weight of three regenerated spine
40	Height	h	mm	Grandjean, Juliette		Mean regenerated spine height
41	Diameter	Ø	mm	Grandjean, Juliette		Mean regenerated spine base
42	Magnesium	Mg	mg/g	Grandjean, Juliette		in the regenerated spine
43	Logarithm	log		Grandjean, Juliette		Final concentration of magnesium in the regenerated spine
44	Magnesium	Mg	mmol/g	Grandjean, Juliette		Concentration of magnesium in the regenerated spine
45	Magnesium carbonate	MgCO3	g/g	Grandjean, Juliette		in the regenerated spine
46	Calcium carbonate, mass	CaCO3	g	Grandjean, Juliette		in the regenerated spine
47	Number	n	#	Grandjean, Juliette		CaCO3 moles in the regenerated spine
48	Magnesium carbonate	MgCO3	%	Grandjean, Juliette		mol percentage in the regenerated spine
49	Logarithm	log		Grandjean, Juliette		Mole percentage of concentration MgCO3 in the regenerated spine
50	Salinity	Sal		Grandjean, Juliette
51	Temperature, water	Temp	°C	Grandjean, Juliette
52	Alkalinity, total	AT	µmol/kg	Grandjean, Juliette
53	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
54	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
55	Fugacity of carbon dioxide (water) at sea surface temperature (wet air)	fCO2water_SST_wet	µatm	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
56	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
57	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
58	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
59	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
60	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
61	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)

License:

Creative Commons Attribution 4.0 International (CC-BY-4.0)

Status:

Curation Level: Enhanced curation (CurationLevelC)

Size:

10649 data points

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