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Daviray, Maxime; Lesut, Milla; Geslin, Emmanuelle; Metzger, Edouard; van Dijk, Inge; Courtial, Julia (2025): Seawater carbonate chemistry and shell dissolution of benthic foraminifera [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.984757

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Published: 2025-09-05 • DOI registered: 2025-10-07

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Abstract:
Ammonia confertitesta and Haynesina germanica are two common estuarine benthic foraminifera subject to sediment acidification. Nevertheless, mechanisms involved in their response to acidification are still poorly understood. Since H. germanica is kleptoplastic and photosynthetically active, unlike A. confertitesta, these species were cultured in controlled experiments to determine whether these mechanisms could mitigate acidification-induced shell dissolution. Both living and dead specimens were incubated at two pH (8.0 and 6.8) and two light conditions (0 and 24 μmol photon m-2.s-1) for 18 days. For each species, respiration and photosynthesis rates were calculated based on oxygen measurements. At the end of incubation, foraminiferal viability was assessed with CellTracker Green™ biomarker, and each test was categorised according to a dissolution scale (DS) using SEM.
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 2025-09-05.
Keyword(s):
Ammonia confertitesta; Benthos; Bottles or small containers/Aquaria (<20 L); Calcification/Dissolution; Chromista; Coast and continental shelf; Foraminifera; Haynesina germanica; Laboratory experiment; Light; Mortality/Survival; North Atlantic; Primary production/Photosynthesis; Respiration; Single species; Temperate; Zooplankton
Related to:
Daviray, Maxime; Lesut, Milla; Geslin, Emmanuelle; Metzger, Edouard; van Dijk, Inge; Courtial, Julia (2025): Species-specific mechanisms of benthic foraminifera in response to shell dissolution. Marine Micropaleontology, 200, 102490, https://doi.org/10.1016/j.marmicro.2025.102490
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: 47.013000 * Longitude: -2.019000
Date/Time Start: 2024-03-06T00:00:00 * Date/Time End: 2024-03-06T00:00:00
Event(s):
Bourgneuf_Bay_mudflat * Latitude: 47.013000 * Longitude: -2.019000 * Date/Time: 2024-03-06T00:00:00 * Method/Device: Experiment (EXP)
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Type of studyStudy typeDaviray, Maxime
2Species, unique identificationSpecies UIDDaviray, Maxime
3Species, unique identification (Semantic URI)Species UID (Semantic URI)Daviray, Maxime
4Species, unique identification (URI)Species UID (URI)Daviray, Maxime
5Time in daysTime ddaysDaviray, Maxime
6Light modeL modeDaviray, Maxime
7Treatment: pHT:pHDaviray, Maxime
8Cell biovolumeCell biovolµm3Daviray, Maxime
9Cell biovolume, standard deviationCell biovol std dev±Daviray, Maxime
10Oxygen consumptionO2 conpmol/s/mm3Daviray, Maximelight off
11Oxygen consumption, standard deviationO2 con std dev±Daviray, Maximelight off
12Oxygen consumptionO2 conpmol/s/mm3Daviray, Maximelight on
13Oxygen consumption, standard deviationO2 con std dev±Daviray, Maximelight on
14Net photosynthesis rate, oxygenPN O2pmol/s/mm3Daviray, Maxime
15Net photosynthesis rate, standard deviationPN std dev±Daviray, Maxime
16GroupGroupDaviray, MaximeViability
17Dissolution stageDS%Daviray, MaximeDS-0
18Dissolution stageDS%Daviray, MaximeDS-1
19Dissolution stageDS%Daviray, MaximeDS-2
20Dissolution stageDS%Daviray, MaximeDS-3
21Dissolution stageDS%Daviray, MaximeDS-4
22Dissolution stageDS%Daviray, MaximeDS-5
23Dissolution stageDS%Daviray, Maximelost
24ReplicatesRepl#Daviray, Maxime
25Temperature, waterTemp°CDaviray, Maxime
26Temperature, water, standard deviationTemp std dev±Daviray, Maxime
27SalinitySalDaviray, Maxime
28Salinity, standard deviationSal std dev±Daviray, Maxime
29pH, NBS scalepH NBSDaviray, MaximePotentiometric
30pH, standard deviationpH std dev±Daviray, MaximePotentiometric
31Alkalinity, totalATµmol/lDaviray, MaximePotentiometric titration
32Alkalinity, total, standard deviationAT std dev±Daviray, MaximePotentiometric titration
33Carbon, inorganic, dissolvedDICmmol/lDaviray, MaximeCalculated using CO2SYS
34Carbon, inorganic, dissolved, standard deviationDIC std dev±Daviray, MaximeCalculated using CO2SYS
35Calcite saturation stateOmega CalDaviray, MaximeCalculated using CO2SYS
36Calcite saturation state, standard deviationOmega Cal std dev±Daviray, MaximeCalculated using CO2SYS
37Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
38pH, total scalepHTYang, YanCalculated using seacarb after Nisumaa et al. (2010)
39Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
40Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
41Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
42Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
43Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
44Carbon, inorganic, dissolvedDICµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
45Alkalinity, totalATµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
46Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
47Calcite 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:
1438 data points

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