Citation:

PANGAEA.987275

Name: Seawater carbonate chemistry and protein oxidative damage and ubiquitination in Penaeus vannamei
Published: 2025-11-07
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Animalia; Arthropoda; Benthic animals; Benthos; Bottles or small containers/Aquaria (<20 L); Laboratory experiment; Laboratory strains; Not applicable; Ocean acidification; Other studied parameter or process; Penaeus vannamei; Respiration; Single species

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Published: 2025-11-07 • DOI registered: 2025-12-06

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Abstract:

In this study, we investigated the effects of increasing environmental PCO2 (ambient, 5000 and 10,000 µatm) on metabolism, oxidative stress and protein ubiquitination (an indicator of protein degradation) in whiteleg shrimp (Penaeus vannamei).

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 Figshare (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 2025-11-07.

Keyword(s):

Animalia; Arthropoda; Benthic animals; Benthos; Bottles or small containers/Aquaria (<20 L); Laboratory experiment; Laboratory strains; Not applicable; Ocean acidification; Other studied parameter or process; Penaeus vannamei; Respiration; Single species

Related to:

Sanders, Trystan; Derjean, Hélisoa Amadeus; Costello, Joseph L; Ellis, Robert P; Wilson, Rod W (2025): The effects of high seawater PCO2 on protein oxidative damage and ubiquitination in Penaeus vannamei. Journal of Experimental Biology, 228(16), jeb249906, https://doi.org/10.1242/jeb.249906

Source:

Sanders, Trystan (2025): Sanders_2025_JEB_data.xlsx [dataset]. figshare, https://doi.org/10.6084/M9.FIGSHARE.29927741.V1

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)

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type of study	Study type		Sanders, Trystan
2	Species, unique identification	Species UID		Sanders, Trystan
3	Species, unique identification (URI)	Species UID (URI)		Sanders, Trystan
4	Species, unique identification (Semantic URI)	Species UID (Semantic URI)		Sanders, Trystan
5	Treatment: partial pressure of carbon dioxide	T:pCO2	µatm	Sanders, Trystan
6	Metabolic rate of oxygen	MR O2	µmol/h/g	Sanders, Trystan		Standard
7	Specific dynamic action, oxygen, magnitude	SDA O2 mag	µmol/g	Sanders, Trystan
8	Protein carbonyl, per protein mass	Prot carbo/prot	nmol/mg	Sanders, Trystan
9	Intensity	Intensity		Sanders, Trystan		K48 Ubiquitin-conjugated protein 900 vs 10000
10	Intensity	Intensity		Sanders, Trystan		K48 Ubiquitin-conjugated protein 900 vs 5000
11	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Sanders, Trystan
12	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Sanders, Trystan
13	Temperature, water	Temp	°C	Sanders, Trystan
14	Temperature, water, standard deviation	Temp std dev	±	Sanders, Trystan
15	Salinity	Sal		Sanders, Trystan
16	Salinity, standard deviation	Sal std dev	±	Sanders, Trystan
17	pH, NBS scale	pH NBS		Sanders, Trystan
18	pH, standard deviation	pH std dev	±	Sanders, Trystan		NBS scale
19	Alkalinity, total	AT	µmol/l	Sanders, Trystan
20	Alkalinity, total, standard deviation	AT std dev	±	Sanders, Trystan
21	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
22	pH, total scale	pHT		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
23	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
24	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)
25	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)
26	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
27	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
28	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
29	Alkalinity, total	AT	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
30	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
31	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:

553 data points

Data

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

1 Study type	2 Species UID	3 Species UID (URI)	4 Species UID (Semantic URI)	5 T:pCO2 [µatm]	6 MR O2 [µmol/h/g] (Standard)	7 SDA O2 mag [µmol/g]	8 Prot carbo/prot [nmol/mg]	9 Intensity (K48 Ubiquitin-conjugated prot...)	10 Intensity (K48 Ubiquitin-conjugated prot...)	11 pCO2water_SST_wet [µatm]	12 pCO2 std dev [±]	13 Temp [°C]	14 Temp std dev [±]	15 Sal	16 Sal std dev [±]	17 pH NBS	18 pH std dev [±] (NBS scale)	19 AT [µmol/l]	20 AT std dev [±]	21 CSC flag	22 pHT	23 CO2 [µmol/kg]	24 fCO2water_SST_wet [µatm]	25 pCO2water_SST_wet [µatm]	26 [HCO3]- [µmol/kg]	27 [CO3]2- [µmol/kg]	28 DIC [µmol/kg]	29 AT [µmol/kg]	30 Omega Arg	31 Omega Cal
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	900	9.3	447.4	11.5	9.63	9.41	881	75	27.0	0.4	26.2	0.1	8.069	0.01	2912	136	26	7.92	21.71	768.32	770.72	2433.25	188.53	2643.50	2865.80	3.16	4.89
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	900	7.9	274.6	13.6	2.40	2.25	881	75	27.0	0.4	26.2	0.1	8.069	0.01	2912	136	26	7.92	21.71	768.32	770.72	2433.25	188.53	2643.50	2865.80	3.16	4.89
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	900	11.5	184.9	10.2	1.92	1.43	881	75	27.0	0.4	26.2	0.1	8.069	0.01	2912	136	26	7.92	21.71	768.32	770.72	2433.25	188.53	2643.50	2865.80	3.16	4.89
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	900	6.4	152.7	9.8	4.12	4.77	881	75	27.0	0.4	26.2	0.1	8.069	0.01	2912	136	26	7.92	21.71	768.32	770.72	2433.25	188.53	2643.50	2865.80	3.16	4.89
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	900	1.8	148.5	17.4			881	75	27.0	0.4	26.2	0.1	8.069	0.01	2912	136	26	7.92	21.71	768.32	770.72	2433.25	188.53	2643.50	2865.80	3.16	4.89
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	900	6.7	156.5				881	75	27.0	0.4	26.2	0.1	8.069	0.01	2912	136	26	7.92	21.71	768.32	770.72	2433.25	188.53	2643.50	2865.80	3.16	4.89
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	5000	32.4	367.5	10.2		1.49	4654	538	26.8	0.8	25.8	0.2	7.609	0.02	4919	82	26	7.46	118.88	4176.85	4189.99	4579.77	120.85	4819.50	4842.20	2.02	3.14
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	5000	21.2	368.8	10.0		1.31	4654	538	26.8	0.8	25.8	0.2	7.609	0.02	4919	82	26	7.46	118.88	4176.85	4189.99	4579.77	120.85	4819.50	4842.20	2.02	3.14
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	5000	24.4	94.7	11.7		6.80	4654	538	26.8	0.8	25.8	0.2	7.609	0.02	4919	82	26	7.46	118.88	4176.85	4189.99	4579.77	120.85	4819.50	4842.20	2.02	3.14
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	5000	12.4	389.4	17.5		11.24	4654	538	26.8	0.8	25.8	0.2	7.609	0.02	4919	82	26	7.46	118.88	4176.85	4189.99	4579.77	120.85	4819.50	4842.20	2.02	3.14
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	5000	16.1	192.8	11.5		1.29	4654	538	26.8	0.8	25.8	0.2	7.609	0.02	4919	82	26	7.46	118.88	4176.85	4189.99	4579.77	120.85	4819.50	4842.20	2.02	3.14
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	5000	21.3	121.5				4654	538	26.8	0.8	25.8	0.2	7.609	0.02	4919	82	26	7.46	118.88	4176.85	4189.99	4579.77	120.85	4819.50	4842.20	2.02	3.14
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	5000	5.6	292.0				4654	538	26.8	0.8	25.8	0.2	7.609	0.02	4919	82	26	7.46	118.88	4176.85	4189.99	4579.77	120.85	4819.50	4842.20	2.02	3.14
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	10000	27.2	143.7	13.8	1.23		10413	2104	27.2	0.0	26.3	0.1	7.573	0.05	10079	441	26	7.42	262.51	9339.11	9368.52	9428.55	235.33	9926.40	9919.10	3.95	6.11
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	10000	10.7	501.9	9.7	1.79		10413	2104	27.2	0.0	26.3	0.1	7.573	0.05	10079	441	26	7.42	262.51	9339.11	9368.52	9428.55	235.33	9926.40	9919.10	3.95	6.11
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	10000	13.8	217.5	12.1	0.54		10413	2104	27.2	0.0	26.3	0.1	7.573	0.05	10079	441	26	7.42	262.51	9339.11	9368.52	9428.55	235.33	9926.40	9919.10	3.95	6.11
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	10000	25.0	511.7	11.5	0.65		10413	2104	27.2	0.0	26.3	0.1	7.573	0.05	10079	441	26	7.42	262.51	9339.11	9368.52	9428.55	235.33	9926.40	9919.10	3.95	6.11
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	10000	10.5	506.2	7.7	0.66		10413	2104	27.2	0.0	26.3	0.1	7.573	0.05	10079	441	26	7.42	262.51	9339.11	9368.52	9428.55	235.33	9926.40	9919.10	3.95	6.11
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	10000	5.0	465.2				10413	2104	27.2	0.0	26.3	0.1	7.573	0.05	10079	441	26	7.42	262.51	9339.11	9368.52	9428.55	235.33	9926.40	9919.10	3.95	6.11
laboratory	Penaeus vannamei	marinespecies.org	urn:lsid:marinespecies.org:taxname:377748	10000	20.9	287.0				10413	2104	27.2	0.0	26.3	0.1	7.573	0.05	10079	441	26	7.42	262.51	9339.11	9368.52	9428.55	235.33	9926.40	9919.10	3.95	6.11