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Li, Yixin; Zhao, Hongwei; Zhao, Yunpeng; Liao, Xin; Chen, J Y; Qin, Yanping; Lu, Zuhong; Zhang, Yuehuan; He, Chunpeng (2025): Seawater carbonate chemistry and skeleton-forming responses of reef-building corals under ocean acidification [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.984672

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Published: 2025-09-01 • DOI registered: 2025-09-30

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Abstract:
Here, we studied the skeleton-forming strategies of 4 widely distributed coral species in a simulated acidified habitat with a pH of 7.6 to 7.8. We reconstructed and visualized the skeleton-forming process, quantified elemental calcium loss, and determined gene expression changes.
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 extracted from tables in the related paper (see Related to) 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 2025-09-01.
Keyword(s):
Acropora muricata; Animalia; Benthic animals; Benthos; Biomass/Abundance/Elemental composition; Cnidaria; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Gene expression (incl. proteomics); Growth/Morphology; Laboratory experiment; Montipora capricornis; Montipora foliosa; North Pacific; Pocillopora damicornis; Single species; Tropical
Related to:
Li, Yixin; Zhao, Hongwei; Zhao, Yunpeng; Liao, Xin; Chen, J Y; Qin, Yanping; Lu, Zuhong; Zhang, Yuehuan; He, Chunpeng (2025): Skeleton-Forming Responses of Reef-Building Corals under Ocean Acidification. Research, 8, 0736, https://doi.org/10.34133/research.0736
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:
Median Latitude: 16.416600 * Median Longitude: 112.000000 * South-bound Latitude: 15.666600 * West-bound Longitude: 111.000000 * North-bound Latitude: 17.166600 * East-bound Longitude: 113.000000
Event(s):
Xisha_Island_OA * Latitude Start: 15.666600 * Longitude Start: 111.000000 * Latitude End: 17.166600 * Longitude End: 113.000000 * Method/Device: Experiment (EXP)
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Type of studyStudy typeLi, Yixin
2Species, unique identificationSpecies UIDLi, Yixin
3Species, unique identification (URI)Species UID (URI)Li, Yixin
4Species, unique identification (Semantic URI)Species UID (Semantic URI)Li, Yixin
5GroupGroupLi, Yixin
6Experiment dayExp daydayLi, Yixin
7RatioRatioLi, Yixinskeleton to void
8ElementsElementsLi, Yixin
9ElementsElements%Li, Yixin
10ErrorErrorLi, YixinAbs
11TypeTypeLi, YixinGene
12Protein nameProteinLi, Yixin
13Gene expressionGene expressionLi, YixinChange
14Temperature, waterTemp°CLi, Yixin
15SalinitySalLi, Yixin
16pH, NBS scalepH NBSLi, Yixin
17Alkalinity, totalATµmol/kgLi, Yixin
18Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
19pH, total scalepHTYang, YanCalculated using seacarb after Nisumaa et al. (2010)
20Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
21Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
22Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
23Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
24Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
25Carbon, inorganic, dissolvedDICµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
26Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
27Calcite saturation stateOmega CalYang, YanCalculated 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:
27456 data points

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