Citation:

PANGAEA.956107

Name: Seawater carbonate chemistry and disease susceptibility in the eastern oyster Crassostrea virginica
Published: 2015
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Animalia; Benthic animals; Benthos; Containers and aquaria (20-1000 L or < 1 m**2); Crassostrea virginica; Growth/Morphology; Laboratory experiment; Laboratory strains; Mollusca; Not applicable; Other; Other studied parameter or process; Oxygen; Single species

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Published: 2015 (exact date unknown) • DOI registered: 2023-03-30

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Keyword(s):

Animalia; Benthic animals; Benthos; Containers and aquaria (20-1000 L or < 1 m**2); Crassostrea virginica; Growth/Morphology; Laboratory experiment; Laboratory strains; Mollusca; Not applicable; Other; Other studied parameter or process; Oxygen; Single species

Supplement to:

Keppel, Andrew G; Breitburg, Denise; Wikfors, Gary H; Burrell, Rebecca B; Clark, Virginia M (2015): Effects of co-varying diel-cycling hypoxia and pH on disease susceptibility in the eastern oyster Crassostrea virginica. Marine Ecology Progress Series, 538, 169-183, https://doi.org/10.3354/meps11479

Documentation:

Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James (2021): seacarb: seawater carbonate chemistry with R. R package version 3.2.16. https://cran.r-project.org/web/packages/seacarb/index.html

Project(s):

Ocean Acidification International Coordination Centre (OA-ICC)

Comment:

In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) 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 2023-02-28.

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type	Type		Keppel, Andrew G		Study
2	Species, unique identification	Species UID		Keppel, Andrew G
3	Species, unique identification (URI)	Species UID (URI)		Keppel, Andrew G
4	Species, unique identification (Semantic URI)	Species UID (Semantic URI)		Keppel, Andrew G
5	Time point, descriptive	Time point		Keppel, Andrew G
6	Treatment	Treat		Keppel, Andrew G
7	Prevalence	Prevalence		Keppel, Andrew G		infection
8	Prevalence, standard error	Preval std e	±	Keppel, Andrew G		infection
9	Prevalence	Prevalence		Keppel, Andrew G		infections scoring 2 or higher on the Mackin scale
10	Prevalence, standard error	Preval std e	±	Keppel, Andrew G		infections scoring 2 or higher on the Mackin scale
11	Infection intensity	Infection int		Keppel, Andrew G		mackin scale intensity of all individuals with detectable infections
12	Infection intensity, standard error	Infection int std e	±	Keppel, Andrew G		mackin scale intensity of all individuals with detectable infections
13	Shell height	Shell h	mm	Keppel, Andrew G
14	Shell height, standard error	Shell h std e		Keppel, Andrew G
15	Hemocytes	Hemocytes	%	Keppel, Andrew G		Granular
16	Hemocytes, standard error	Hemocytes std e	±	Keppel, Andrew G		Granular
17	Hemocytes	Hemocytes	%	Keppel, Andrew G		Dead granular
18	Hemocytes, standard error	Hemocytes std e	±	Keppel, Andrew G		Dead granular
19	Hemocytes	Hemocytes	%	Keppel, Andrew G		Agranular
20	Hemocytes, standard error	Hemocytes std e	±	Keppel, Andrew G		Agranular
21	Hemocytes	Hemocytes	%	Keppel, Andrew G		Dead agranular
22	Hemocytes, standard error	Hemocytes std e	±	Keppel, Andrew G		Dead agranular
23	Hemocytes	Hemocytes	%	Keppel, Andrew G		Phagocytic granular
24	Hemocytes, standard error	Hemocytes std e	±	Keppel, Andrew G		Phagocytic granular
25	Hemocytes	Hemocytes	%	Keppel, Andrew G		Phagocytic
26	Hemocytes, standard error	Hemocytes std e	±	Keppel, Andrew G		Phagocytic
27	Reactive oxygen species production	ROS prod		Keppel, Andrew G		granular population 1
28	Reactive oxygen species production, standard error	ROS prod std e	±	Keppel, Andrew G		granular population 1
29	Reactive oxygen species production	ROS prod		Keppel, Andrew G		granular population 2
30	Reactive oxygen species production, standard error	ROS prod std e	±	Keppel, Andrew G		granular population 2
31	Hemocytes	Hemocytes	%	Keppel, Andrew G		Apoptotic dead cells
32	Hemocytes, standard error	Hemocytes std e	±	Keppel, Andrew G		Apoptotic dead cells
33	Hemocytes	Hemocytes	%	Keppel, Andrew G		Apoptotic live cells
34	Hemocytes, standard error	Hemocytes std e	±	Keppel, Andrew G		Apoptotic live cells
35	Salinity	Sal		Keppel, Andrew G
36	Salinity, standard error	Sal std e	±	Keppel, Andrew G
37	Temperature, water	Temp	°C	Keppel, Andrew G
38	Temperature, water, standard error	T std e	±	Keppel, Andrew G
39	Alkalinity, total	AT	µmol/kg	Keppel, Andrew G
40	Alkalinity, total, standard error	AT std e	±	Keppel, Andrew G
41	Oxygen, dissolved	DO	mg/l	Keppel, Andrew G		Normoxia
42	Oxygen, dissolved, standard error	DO std e	±	Keppel, Andrew G		Normoxia
43	Oxygen, dissolved	DO	mg/l	Keppel, Andrew G		Low-plateau
44	Oxygen, dissolved, standard error	DO std e	±	Keppel, Andrew G		Low-plateau
45	Oxygen, dissolved	DO	mg/l	Keppel, Andrew G		Supersat
46	Oxygen, dissolved, standard error	DO std e	±	Keppel, Andrew G		Supersat
47	pH, NBS scale	pH NBS		Keppel, Andrew G		Normoxia, NBS scale
48	pH, standard error	pH std e	±	Keppel, Andrew G		Normoxia, NBS scale
49	pH, NBS scale	pH NBS		Keppel, Andrew G		Low-plateau, NBS scale
50	pH, standard error	pH std e	±	Keppel, Andrew G		Low-plateau, NBS scale
51	pH, NBS scale	pH NBS		Keppel, Andrew G		Supersat, NBS scale
52	pH, standard error	pH std e	±	Keppel, Andrew G		Supersat, NBS scale
53	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	ppmv	Keppel, Andrew G		Low-Plateau
54	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air), standard error	pCO2water_SST_wet std e	±	Keppel, Andrew G		Low-Plateau
55	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
56	pH, total scale	pHT		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Normoxia, total scale
57	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Normoxia
58	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)	Normoxia
59	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)	Normoxia
60	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Normoxia
61	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Normoxia
62	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Normoxia
63	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Normoxia
64	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Normoxia
65	pH, total scale	pHT		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Low-plateau, total scale
66	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Low-plateau
67	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)	Low-plateau
68	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)	Low-plateau
69	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Low-plateau
70	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Low-plateau
71	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Low-plateau
72	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Low-plateau
73	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Low-plateau
74	pH, total scale	pHT		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Supersat, total scale
75	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Supersat
76	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)	Supersat
77	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)	Supersat
78	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Supersat
79	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Supersat
80	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Supersat
81	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Supersat
82	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	Supersat

License:

Creative Commons Attribution 4.0 International (CC-BY-4.0)

Status:

Curation Level: Enhanced curation (CurationLevelC)

Size:

1244 data points

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