Citation:

PANGAEA.987144

Name: Seawater carbonate chemistry and olfactory behaviour of the yellow shore crab, Hemigrapsus oregonensis
Published: 2025-10-31
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Animalia; Arthropoda; Behaviour; Benthic animals; Benthos; Bottles or small containers/Aquaria (<20 L); Coast and continental shelf; Hemigrapsus oregonensis; Laboratory experiment; North Pacific; Other studied parameter or process; Single species; Temperate

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Published: 2025-10-31 • DOI registered: 2025-11-29

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Abstract:

The acute, static, and fluctuating effects of acidification on the olfactory system were investigated in the coastal yellow shore crab (Hemigrapsus oregonensis (Dana, 1851)).

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 downloaded from the PANGAEA dataset (see Source). 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 2025-10-31.

Keyword(s):

Animalia; Arthropoda; Behaviour; Benthic animals; Benthos; Bottles or small containers/Aquaria (<20 L); Coast and continental shelf; Hemigrapsus oregonensis; Laboratory experiment; North Pacific; Other studied parameter or process; Single species; Temperate

Related to:

Khodikian, Elissa; Roggatz, Christina C; Yoon, Gwangseok R; Porteus, Cosima S (2025): Acute, static, and fluctuating ocean acidification effects on the olfactory system of the yellow shore crab, Hemigrapsus oregonensis. Canadian Journal of Zoology-Revue Canadienne de Zoologie, cjz-2025-0001, https://doi.org/10.1139/cjz-2025-0001

Source:

Khodikian, Elissa; Roggatz, Christina C; Yoon, Gwangseok R; Porteus, Cosima S (2025): Seawater carbonate chemistry and the effect of ocean acidification on olfactory behaviour and physiology of Hemigrapsus oregonensis [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.986452

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: 48.833722 * Longitude: -125.146222

Date/Time Start: 2022-08-04T16:00:00 * Date/Time End: 2023-07-19T16:00:00

Event(s):

Eagle_Bay_2022 (Collection 2022) * Latitude: 48.833722 * Longitude: -125.146222 * Date/Time: 2022-08-04T16:00:00 * Location: Eagle Bay, British Columbia, Canada * Method/Device: Hand net (HN)

Eagle_Bay_2023 (Collection 2023) * Latitude: 48.833722 * Longitude: -125.146222 * Date/Time: 2023-07-19T16:00:00 * Location: Eagle Bay, British Columbia, Canada * Method/Device: Hand net (HN)

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Event label	Event		Khodikian, Elissa
2	Latitude of event 2	Latitude 2		Khodikian, Elissa
3	Longitude of event 2	Longitude 2		Khodikian, Elissa
4	Date/Time of event	Date/Time		Khodikian, Elissa
5	Type of study	Study type		Khodikian, Elissa
6	Species, unique identification	Species UID		Khodikian, Elissa
7	Species, unique identification (URI)	Species UID (URI)		Khodikian, Elissa
8	Species, unique identification (Semantic URI)	Species UID (Semantic URI)		Khodikian, Elissa
9	Experiment	Exp		Khodikian, Elissa
10	Date/time analysis, experiment	Date/time analysis exp		Khodikian, Elissa
11	Experimental treatment	Exp treat		Khodikian, Elissa
12	Exposure time	Exp time	days	Khodikian, Elissa
13	Percent of time	Perc time	%	Khodikian, Elissa		Spent on odorant side (trial 1)
14	Percent of time	Perc time	%	Khodikian, Elissa		Spent on odorant side (trial 2)
15	Percent of time	Perc time	%	Khodikian, Elissa		Spent on odorant side (trial 3)
16	Time in seconds	Time sec	s	Khodikian, Elissa		to reach odorant (trial 1)
17	Time in seconds	Time sec	s	Khodikian, Elissa		to reach odorant (trial 2)
18	Time in seconds	Time sec	s	Khodikian, Elissa		to reach odorant (trial 3)
19	Percent of time	Perc time	%	Khodikian, Elissa		Spent on odorant side
20	Time in seconds	Time sec	s	Khodikian, Elissa		to reach odorant
21	Fluorescence intensity	Fluorescence		Khodikian, Elissa	ImageJ software	IR25a (integrated density)
22	Volume	Vol	µm³	Khodikian, Elissa	ImageJ software	of olfactory sensory neuron body
23	Percent of time	Perc time	%	Khodikian, Elissa		Spent on odorant side (in treatment)
24	Percent of time	Perc time	%	Khodikian, Elissa		Spent on odorant side (in recovery)
25	Time in seconds	Time sec	s	Khodikian, Elissa		to reach odorant (in treatment)
26	Time in seconds	Time sec	s	Khodikian, Elissa		to reach odorant (in recovery)
27	Cell surface area	Cell surface area	µm²	Khodikian, Elissa	ImageJ software	BrdU labelled
28	Proportion	Prop		Khodikian, Elissa	ImageJ software	of olfactory sensory neurons proliferating
29	Salinity	Sal		Khodikian, Elissa	Salinity meter, HANNA Instruments, Quebec, Canada, HI98319	in control trial (8.0)
30	Temperature, water	Temp	°C	Khodikian, Elissa	Temperature probe, HANNA Instruments, Quebec, Canada, HI1230B	in control trial (8.0)
31	pH, NBS scale	pH NBS		Khodikian, Elissa	pH meter, HANNA Instruments, Quebec, Canada, HI8424	in control trial (8.0)
32	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Khodikian, Elissa	CO2 analyzer, QUBIT Systems, Ontario, Canada), S157-P	in control trial (8.0)
33	Fugacity of carbon dioxide (water) at sea surface temperature (wet air)	fCO2water_SST_wet	µatm	Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (8.0)
34	Bicarbonate ion	[HCO3]-	µmol/kg	Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (8.0)
35	Carbonate ion	[CO3]2-	µmol/kg	Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (8.0)
36	Carbon, inorganic, dissolved	DIC	µmol/kg	Khodikian, Elissa	Dissolved Inorganic Analyzer, LI-COR Inc, Lincoln, NE, USA, LI-5350	in control trial (8.0)
37	Alkalinity, total	AT	µmol/kg	Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (8.0)
38	Aragonite saturation state	Omega Arg		Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (8.0)
39	Calcite saturation state	Omega Cal		Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (8.0)
40	Salinity	Sal		Khodikian, Elissa	Salinity meter, HANNA Instruments, Quebec, Canada, HI98319	in control trial (7.7)
41	Temperature, water	Temp	°C	Khodikian, Elissa	Temperature probe, HANNA Instruments, Quebec, Canada, HI1230B	in control trial (7.7)
42	pH, NBS scale	pH NBS		Khodikian, Elissa	pH meter, HANNA Instruments, Quebec, Canada, HI8424	in control trial (7.7)
43	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Khodikian, Elissa	CO2 analyzer, QUBIT Systems, Ontario, Canada), S157-P	in control trial (7.7)
44	Fugacity of carbon dioxide (water) at sea surface temperature (wet air)	fCO2water_SST_wet	µatm	Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (7.7)
45	Bicarbonate ion	[HCO3]-	µmol/kg	Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (7.7)
46	Carbonate ion	[CO3]2-	µmol/kg	Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (7.7)
47	Carbon, inorganic, dissolved	DIC	µmol/kg	Khodikian, Elissa	Dissolved Inorganic Analyzer, LI-COR Inc, Lincoln, NE, USA, LI-5350	in control trial (7.7)
48	Alkalinity, total	AT	µmol/kg	Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (7.7)
49	Aragonite saturation state	Omega Arg		Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (7.7)
50	Calcite saturation state	Omega Cal		Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (7.7)
51	Salinity	Sal		Khodikian, Elissa	Salinity meter, HANNA Instruments, Quebec, Canada, HI98319	in exposure
52	Temperature, water	Temp	°C	Khodikian, Elissa	Temperature probe, HANNA Instruments, Quebec, Canada, HI1230B	in exposure
53	pH, NBS scale	pH NBS		Khodikian, Elissa	pH meter, HANNA Instruments, Quebec, Canada, HI8424	in exposure
54	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Khodikian, Elissa	CO2 analyzer, QUBIT Systems, Ontario, Canada), S157-P	in exposure
55	Fugacity of carbon dioxide (water) at sea surface temperature (wet air)	fCO2water_SST_wet	µatm	Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in exposure
56	Bicarbonate ion	[HCO3]-	µmol/kg	Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in exposure
57	Carbonate ion	[CO3]2-	µmol/kg	Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in exposure
58	Carbon, inorganic, dissolved	DIC	µmol/kg	Khodikian, Elissa	Dissolved Inorganic Analyzer, LI-COR Inc, Lincoln, NE, USA, LI-5350	in exposure
59	Alkalinity, total	AT	µmol/kg	Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in exposure
60	Aragonite saturation state	Omega Arg		Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in exposure
61	Calcite saturation state	Omega Cal		Khodikian, Elissa	Calculated using seacarb after Nisumaa et al. (2010)	in exposure
62	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
63	pH, total scale	pHT		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (8.0)
64	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (8.0)
65	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)	in control trial (8.0)
66	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)	in control trial (8.0)
67	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (8.0)
68	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (8.0)
69	Alkalinity, total	AT	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (8.0)
70	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (8.0)
71	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (8.0)
72	pH, total scale	pHT		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (7.7)
73	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (7.7)
74	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)	in control trial (7.7)
75	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)	in control trial (7.7)
76	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (7.7)
77	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (7.7)
78	Alkalinity, total	AT	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (7.7)
79	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (7.7)
80	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in control trial (7.7)
81	pH, total scale	pHT		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in exposure
82	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in exposure
83	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)	in exposure
84	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)	in exposure
85	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in exposure
86	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in exposure
87	Alkalinity, total	AT	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in exposure
88	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in exposure
89	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	in exposure

License:

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

Status:

Curation Level: Enhanced curation (CurationLevelC)

Size:

5144 data points

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