Citation:

PANGAEA.995588

Name: Seawater carbonate chemistry and calcifying fluid chemistry of Crassostrea virginica
Published: 2026-06-18
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Acid-base regulation; Animalia; Benthic animals; Benthos; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Crassostrea virginica; Entire community; Laboratory experiment; Mollusca; North Atlantic; Ocean acidification; Single species; Temperate

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Published: 2026-06-18 • DOI registered: 2026-07-17

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Abstract:

To better understand oysters' molecular mechanisms and the role of their calcifying-fluid microbes, we conducted experiments that simulated a tidal cycle, measured calcifying fluid pH and total dissolved inorganic carbon, and characterized host and microbial gene expression via transcriptomics.

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 2026-06-18.

Keyword(s):

Acid-base regulation; Animalia; Benthic animals; Benthos; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Crassostrea virginica; Entire community; Laboratory experiment; Mollusca; North Atlantic; Ocean acidification; Single species; Temperate

Related to:

Unzueta-Martínez, Andrea; Delaney, Jennifer A; Morkeski, K; Ross, Abby; Wang, Zhaohui Aleck; Girguis, Peter R (2026): Coexpression among eastern oyster host and microbiome genes suggests coordinated regulation of calcifying fluid chemistry. Proceedings of the National Academy of Sciences of the United States of America, 123(11), e2521539123, https://doi.org/10.1073/pnas.2521539123

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

Further details:

GitHub - Andrea-Unzueta-Martinez/oyster-host-microbiome-transcriptomics: Count matrices and scripts for oyster host and microbiome transcriptomic analyses. · GitHub [webpage]. https://github.com/Andrea-Unzueta-Martinez/oyster-host-microbiome-transcriptomics

Project(s):

Ocean Acidification International Coordination Centre (OA-ICC)

Coverage:

Latitude: 41.710400 * Longitude: -70.305100

Event(s):

Barnstable_OA * Latitude: 41.710400 * Longitude: -70.305100 * Method/Device: Experiment (EXP)

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type of study	Study type		Unzueta-Martínez, Andrea
2	Species, unique identification	Species UID		Unzueta-Martínez, Andrea
3	Treatment	Treat		Unzueta-Martínez, Andrea
4	Local Time	Local time		Unzueta-Martínez, Andrea
5	Replicates	Repl	#	Unzueta-Martínez, Andrea
6	Salinity	Sal		Unzueta-Martínez, Andrea
7	Salinity, standard deviation	Sal std dev	±	Unzueta-Martínez, Andrea
8	Salinity	Sal		Unzueta-Martínez, Andrea		min
9	Salinity	Sal		Unzueta-Martínez, Andrea		max
10	Temperature, water	Temp	°C	Unzueta-Martínez, Andrea
11	Temperature, water, standard deviation	Temp std dev	±	Unzueta-Martínez, Andrea
12	Temperature, water	Temp	°C	Unzueta-Martínez, Andrea		min
13	Temperature, water	Temp	°C	Unzueta-Martínez, Andrea		max
14	pH, NBS scale	pH NBS		Unzueta-Martínez, Andrea	Potentiometric
15	pH, standard deviation	pH std dev	±	Unzueta-Martínez, Andrea	Potentiometric	NBS scale
16	pH, NBS scale	pH NBS		Unzueta-Martínez, Andrea	Potentiometric	min
17	pH, NBS scale	pH NBS		Unzueta-Martínez, Andrea	Potentiometric	max
18	Carbon, inorganic, dissolved	DIC	µmol/kg	Unzueta-Martínez, Andrea
19	Carbon, inorganic, dissolved, standard deviation	DIC std dev	±	Unzueta-Martínez, Andrea
20	Carbon, inorganic, dissolved	DIC	µmol/kg	Unzueta-Martínez, Andrea		min
21	Carbon, inorganic, dissolved	DIC	µmol/kg	Unzueta-Martínez, Andrea		max
22	Alkalinity, total	AT	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
23	Alkalinity, total, standard deviation	AT std dev	±	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
24	Alkalinity, total	AT	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	min
25	Alkalinity, total	AT	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	max
26	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	ppmv	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
27	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
28	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	ppmv	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	min
29	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	ppmv	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	max
30	Carbonate ion	[CO3]2-	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
31	Carbonate ion, standard deviation	[CO3]2- std dev	±	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
32	Carbonate ion	[CO3]2-	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	min
33	Carbonate ion	[CO3]2-	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	max
34	Bicarbonate ion	[HCO3]-	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
35	Bicarbonate ion, standard deviation	[HCO3]- std dev	±	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
36	Bicarbonate ion	[HCO3]-	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	min
37	Bicarbonate ion	[HCO3]-	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	max
38	Carbon dioxide	CO2	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
39	Carbon dioxide, standard deviation	CO2 std dev	±	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
40	Carbon dioxide	CO2	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	min
41	Carbon dioxide	CO2	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	max
42	Calcite saturation state	Omega Cal		Unzueta-Martínez, Andrea	Calculated with seacarb package in R
43	Calcite saturation state, standard deviation	Omega Cal std dev	±	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
44	Calcite saturation state	Omega Cal		Unzueta-Martínez, Andrea	Calculated with seacarb package in R	min
45	Calcite saturation state	Omega Cal		Unzueta-Martínez, Andrea	Calculated with seacarb package in R	max
46	Aragonite saturation state	Omega Arg		Unzueta-Martínez, Andrea	Calculated with seacarb package in R
47	Aragonite saturation state, standard deviation	Omega Arg std dev	±	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
48	Aragonite saturation state	Omega Arg		Unzueta-Martínez, Andrea	Calculated with seacarb package in R	min
49	Aragonite saturation state	Omega Arg		Unzueta-Martínez, Andrea	Calculated with seacarb package in R	max
50	Salinity	Sal		Unzueta-Martínez, Andrea		calcifying fluid
51	Salinity, standard deviation	Sal std dev	±	Unzueta-Martínez, Andrea		calcifying fluid
52	Salinity	Sal		Unzueta-Martínez, Andrea		min, calcifying fluid
53	Salinity	Sal		Unzueta-Martínez, Andrea		max, calcifying fluid
54	Temperature, water	Temp	°C	Unzueta-Martínez, Andrea		calcifying fluid
55	Temperature, water, standard deviation	Temp std dev	±	Unzueta-Martínez, Andrea		calcifying fluid
56	Temperature, water	Temp	°C	Unzueta-Martínez, Andrea		min, calcifying fluid
57	Temperature, water	Temp	°C	Unzueta-Martínez, Andrea		max, calcifying fluid
58	Calcifying fluid, pH	CF pH		Unzueta-Martínez, Andrea	Potentiometric	NBS scale
59	Calcifying fluid, pH, standard deviation	CF pH std dev	±	Unzueta-Martínez, Andrea	Potentiometric	NBS scale
60	Calcifying fluid, pH	CF pH		Unzueta-Martínez, Andrea	Potentiometric	min, NBS scale
61	Calcifying fluid, pH	CF pH		Unzueta-Martínez, Andrea	Potentiometric	max, NBS scale
62	Calcifying fluid, dissolved inorganic carbon	CF DIC	µmol/kg	Unzueta-Martínez, Andrea
63	Calcifying fluid, dissolved inorganic carbon, standard deviation	CF DIC std dev	±	Unzueta-Martínez, Andrea
64	Calcifying fluid, dissolved inorganic carbon	CF DIC	µmol/kg	Unzueta-Martínez, Andrea		min
65	Calcifying fluid, dissolved inorganic carbon	CF DIC	µmol/kg	Unzueta-Martínez, Andrea		max
66	Calcifying fluid, total alkalinity	CF AT	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
67	Calcifying fluid, total alkalinity, standard deviation	CF AT std dev	±	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
68	Calcifying fluid, total alkalinity	CF AT	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	min
69	Calcifying fluid, total alkalinity	CF AT	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	max
70	Calcifying fluid, partial pressure of carbon dioxide	CF pCO2	ppmv	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
71	Calcifying fluid, partial pressure of carbon dioxide, standard deviation	CF pCO2 std dev	±	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
72	Calcifying fluid, partial pressure of carbon dioxide	CF pCO2	ppmv	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	min
73	Calcifying fluid, partial pressure of carbon dioxide	CF pCO2	ppmv	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	max
74	Calcifying fluid, carbonate ion	CF [CO3]2-	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
75	Calcifying fluid, carbonate ion, standard deviation	CF [CO3]2- std dev	±	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
76	Calcifying fluid, carbonate ion	CF [CO3]2-	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	min
77	Calcifying fluid, carbonate ion	CF [CO3]2-	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	max
78	Calcifying fluid, bicarbonate ion	CF HCO3	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
79	Calcifying fluid, bicarbonate ion, standard deviation	CF HCO3 std dev	±	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
80	Calcifying fluid, bicarbonate ion	CF HCO3	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	min
81	Calcifying fluid, bicarbonate ion	CF HCO3	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	max
82	Calcifying fluid, carbon dioxide	CF CO2	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
83	Calcifying fluid, carbon dioxide, standard deviation	CF CO2 std dev	±	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
84	Calcifying fluid, carbon dioxide	CF CO2	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	min
85	Calcifying fluid, carbon dioxide	CF CO2	µmol/kg	Unzueta-Martínez, Andrea	Calculated with seacarb package in R	max
86	Calcifying fluid, calcite saturation state	CF Omega Cal		Unzueta-Martínez, Andrea	Calculated with seacarb package in R
87	Calcifying fluid, calcite saturation state, standard deviation	CF Omega Cal (cf) std dev	±	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
88	Calcifying fluid, calcite saturation state	CF Omega Cal		Unzueta-Martínez, Andrea	Calculated with seacarb package in R	min
89	Calcifying fluid, calcite saturation state	CF Omega Cal		Unzueta-Martínez, Andrea	Calculated with seacarb package in R	max
90	Calcifying fluid, aragonite saturation state	CF Omega Arg		Unzueta-Martínez, Andrea	Calculated with seacarb package in R
91	Calcifying fluid, aragonite saturation state, standard deviation	CF Omega Arg std dev	±	Unzueta-Martínez, Andrea	Calculated with seacarb package in R
92	Calcifying fluid, aragonite saturation state	CF Omega Arg		Unzueta-Martínez, Andrea	Calculated with seacarb package in R	min
93	Calcifying fluid, aragonite saturation state	CF Omega Arg		Unzueta-Martínez, Andrea	Calculated with seacarb package in R	max
94	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
95	pH, total scale	pHT		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
96	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
97	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)
98	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)
99	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
100	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
101	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
102	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
103	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:

1030 data points

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