Not logged in
PANGAEA.
Data Publisher for Earth & Environmental Science

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

Always quote citation above when using data! You can download the citation in several formats below.

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

RIS CitationBibTeX Citation ShareShow MapGoogle Earth

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
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
Type of studyStudy typeDaviray, Maxime
Species, unique identificationSpecies UIDDaviray, Maxime
Species, unique identification (Semantic URI)Species UID (Semantic URI)Daviray, Maxime
Species, unique identification (URI)Species UID (URI)Daviray, Maxime
Time in daysTime ddaysDaviray, Maxime
Light modeL modeDaviray, Maxime
Treatment: pHT:pHDaviray, Maxime
Cell biovolumeCell biovolµm3Daviray, Maxime
Cell biovolume, standard deviationCell biovol std dev±Daviray, Maxime
10 Oxygen consumptionO2 conpmol/s/mm3Daviray, Maximelight off
11 Oxygen consumption, standard deviationO2 con std dev±Daviray, Maximelight off
12 Oxygen consumptionO2 conpmol/s/mm3Daviray, Maximelight on
13 Oxygen consumption, standard deviationO2 con std dev±Daviray, Maximelight on
14 Net photosynthesis rate, oxygenPN O2pmol/s/mm3Daviray, Maxime
15 Net photosynthesis rate, standard deviationPN std dev±Daviray, Maxime
16 GroupGroupDaviray, MaximeViability
17 Dissolution stageDS%Daviray, MaximeDS-0
18 Dissolution stageDS%Daviray, MaximeDS-1
19 Dissolution stageDS%Daviray, MaximeDS-2
20 Dissolution stageDS%Daviray, MaximeDS-3
21 Dissolution stageDS%Daviray, MaximeDS-4
22 Dissolution stageDS%Daviray, MaximeDS-5
23 Dissolution stageDS%Daviray, Maximelost
24 ReplicatesRepl#Daviray, Maxime
25 Temperature, waterTemp°CDaviray, Maxime
26 Temperature, water, standard deviationTemp std dev±Daviray, Maxime
27 SalinitySalDaviray, Maxime
28 Salinity, standard deviationSal std dev±Daviray, Maxime
29 pH, NBS scalepH NBSDaviray, MaximePotentiometric
30 pH, standard deviationpH std dev±Daviray, MaximePotentiometric
31 Alkalinity, totalATµmol/lDaviray, MaximePotentiometric titration
32 Alkalinity, total, standard deviationAT std dev±Daviray, MaximePotentiometric titration
33 Carbon, inorganic, dissolvedDICmmol/lDaviray, MaximeCalculated using CO2SYS
34 Carbon, inorganic, dissolved, standard deviationDIC std dev±Daviray, MaximeCalculated using CO2SYS
35 Calcite saturation stateOmega CalDaviray, MaximeCalculated using CO2SYS
36 Calcite saturation state, standard deviationOmega Cal std dev±Daviray, MaximeCalculated using CO2SYS
37 Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
38 pH, total scalepHTYang, YanCalculated using seacarb after Nisumaa et al. (2010)
39 Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
40 Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
41 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
42 Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
43 Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
44 Carbon, inorganic, dissolvedDICµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
45 Alkalinity, totalATµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
46 Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
47 Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
1438 data points

Data

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


Study type

Species UID

Species UID (Semantic URI)

Species UID (URI)

Time d [days]

L mode

T:pH

Cell biovol [µm3]

Cell biovol std dev [±]
10 
O2 con [pmol/s/mm3]
(light off)
11 
O2 con std dev [±]
(light off)
12 
O2 con [pmol/s/mm3]
(light on)
13 
O2 con std dev [±]
(light on)
14 
PN O2 [pmol/s/mm3]
15 
PN std dev [±]
16 
Group
(Viability)
17 
DS [%]
(DS-0)
18 
DS [%]
(DS-1)
19 
DS [%]
(DS-2)
20 
DS [%]
(DS-3)
21 
DS [%]
(DS-4)
22 
DS [%]
(DS-5)
23 
DS [%]
(lost)
24 
Repl [#]
25 
Temp [°C]
26 
Temp std dev [±]
27 
Sal
28 
Sal std dev [±]
29 
pH NBS
(Potentiometric)
30 
pH std dev [±]
(Potentiometric)
31 
AT [µmol/l]
(Potentiometric titration)
32 
AT std dev [±]
(Potentiometric titration)
33 
DIC [mmol/l]
(Calculated using CO2SYS)
34 
DIC std dev [±]
(Calculated using CO2SYS)
35 
Omega Cal
(Calculated using CO2SYS)
36 
Omega Cal std dev [±]
(Calculated using CO2SYS)
37 
CSC flag
(Calculated using seacarb afte...)
38 
pHT
(Calculated using seacarb afte...)
39 
CO2 [µmol/kg]
(Calculated using seacarb afte...)
40 
fCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)
41 
pCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)
42 
[HCO3]- [µmol/kg]
(Calculated using seacarb afte...)
43 
[CO3]2- [µmol/kg]
(Calculated using seacarb afte...)
44 
DIC [µmol/kg]
(Calculated using seacarb afte...)
45 
AT [µmol/kg]
(Calculated using seacarb afte...)
46 
Omega Arg
(Calculated using seacarb afte...)
47 
Omega Cal
(Calculated using seacarb afte...)
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.org2light/dark cycle8.0710000036000000.570.02-0.480.021.040.021017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.org2light/dark cycle8.0620000036000001.270.17-0.580.031.740.391017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.org2light/dark cycle8.051000009000000.890.06-0.910.081.800.031017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.org2light/dark cycle8.0510000014000001.460.052.000.151017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.org2light/dark cycle8.0470000024000002.430.012.300.231017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.org2light/dark cycle8.0410000012000002.970.032.620.261017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.org12light/dark cycle8.052000008000001.340.52-0.850.022.200.141017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.org12light/dark cycle8.018000005000003.800.27-1.420.045.230.271017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.org12light/dark cycle8.0710000028000000.910.041.120.011017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.org12dark8.020000006000004.880.032.020.252.860.231017.30.727.10.17.890.112310702.220.042.160.50267.7632.22881.67884.772074.6279.632186.462266.051.262.00
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.org12dark8.0600000017000001.260.121017.30.727.10.17.890.112310702.220.042.160.50267.7632.22881.67884.772074.6279.632186.462266.051.262.00
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.org12light/dark cycle6.8410000021000002.320.021.320.180.980.181017.11.127.10.16.810.052490902.950.130.200.02266.68455.1412381.0812425.382424.487.672887.292442.520.120.19
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.org12light/dark cycle6.8520000022000002.690.062.370.011017.11.127.10.16.810.052490902.950.130.200.02266.68455.1412381.0812425.382424.487.672887.292442.520.120.19
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.org12dark6.813000007000007.060.284.990.472.080.321017.20.727.10.16.800.0425101002.980.140.200.02266.67468.7112787.7512833.462444.397.592920.682462.190.120.19
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.org12dark6.8650000027000002.300.021017.20.727.10.16.800.0425101002.980.140.200.02266.67468.7112787.7512833.462444.397.592920.682462.190.120.19
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.org18light/dark cycle8.0490000015000002.370.061.840.110.530.121017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.org18light/dark cycle8.0490000015000001.410.060.480.040.930.091017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.org18light/dark cycle8.0680000016000000.580.010.510.031017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.org18dark8.0480000015000001.590.051.280.090.300.051017.30.727.10.17.890.112310702.220.042.160.50267.7632.22881.67884.772074.6279.632186.462266.051.262.00
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.org18dark8.0630000016000001.340.051.110.101017.30.727.10.17.890.112310702.220.042.160.50267.7632.22881.67884.772074.6279.632186.462266.051.262.00
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.org18light/dark cycle6.8260000015000001.690.091.350.070.340.161017.11.127.10.16.810.052490902.950.130.200.02266.68455.1412381.0812425.382424.487.672887.292442.520.120.19
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.org18light/dark cycle6.8480000022000001.660.021.450.041017.11.127.10.16.810.052490902.950.130.200.02266.68455.1412381.0812425.382424.487.672887.292442.520.120.19
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.org18dark6.8270000012000002.590.062.440.050.180.081017.20.727.10.16.800.0425101002.980.140.200.02266.67468.7112787.7512833.462444.397.592920.682462.190.120.19
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.org18dark6.840000005000002.010.061.670.101017.20.727.10.16.800.0425101002.980.140.200.02266.67468.7112787.7512833.462444.397.592920.682462.190.120.19
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.orglight/dark cycle8.0living foraminifera6622100001017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.orglight/dark cycle8.0living foraminifera5130200001017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.orgdark8.0living foraminifera5830000001017.30.727.10.17.890.112310702.220.042.160.50267.7632.22881.67884.772074.6279.632186.462266.051.262.00
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.orgdark8.0living foraminifera40301320001017.30.727.10.17.890.112310702.220.042.160.50267.7632.22881.67884.772074.6279.632186.462266.051.262.00
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.orglight/dark cycle6.8living foraminifera0235022201017.11.127.10.16.810.052490902.950.130.200.02266.68455.1412381.0812425.382424.487.672887.292442.520.120.19
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.orglight/dark cycle6.8living foraminifera07271219201017.11.127.10.16.810.052490902.950.130.200.02266.68455.1412381.0812425.382424.487.672887.292442.520.120.19
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.orgdark6.8living foraminifera01115211001017.20.727.10.16.800.0425101002.980.140.200.02266.67468.7112787.7512833.462444.397.592920.682462.190.120.19
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.orgdark6.8living foraminifera41817126401017.20.727.10.16.800.0425101002.980.140.200.02266.67468.7112787.7512833.462444.397.592920.682462.190.120.19
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.orglight/dark cycle8.0dead foraminifera5330400001017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.orglight/dark cycle8.0dead foraminifera7422100001017.40.527.10.17.970.132330302.210.062.590.62267.8426.52727.85730.412057.1195.262178.892285.721.512.40
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.orgdark8.0dead foraminifera7314100001017.30.727.10.17.890.112310702.220.042.160.50267.7632.22881.67884.772074.6279.632186.462266.051.262.00
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.orgdark8.0dead foraminifera21402010001017.30.727.10.17.890.112310702.220.042.160.50267.7632.22881.67884.772074.6279.632186.462266.051.262.00
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.orglight/dark cycle6.8dead foraminifera0000022531017.11.127.10.16.810.052490902.950.130.200.02266.68455.1412381.0812425.382424.487.672887.292442.520.120.19
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.orglight/dark cycle6.8dead foraminifera0000041341017.11.127.10.16.810.052490902.950.130.200.02266.68455.1412381.0812425.382424.487.672887.292442.520.120.19
laboratoryHaynesina germanicaurn:lsid:marinespecies.org:taxname:113294marinespecies.orgdark6.8dead foraminifera000004711017.20.727.10.16.800.0425101002.980.140.200.02266.67468.7112787.7512833.462444.397.592920.682462.190.120.19
laboratoryAmmonia confertitestaurn:lsid:marinespecies.org:taxname:850208marinespecies.orgdark6.8dead foraminifera0000038521017.20.727.10.16.800.0425101002.980.140.200.02266.67468.7112787.7512833.462444.397.592920.682462.190.120.19