Citation:

PANGAEA.951362

Name: Seawater carbonate chemistry in experiment 1 and 2
Published: 2022-11-30
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Animalia; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Embiotoca jacksoni; Gene expression (incl. proteomics); Laboratory experiment; Nekton; North Pacific; Other; Pelagos; Single species; Temperate

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Abstract:

Acidification-induced changes in neurological function have been documented in several tropical marine fishes. Here, we investigate whether similar patterns of neurological impacts are observed in a temperate Pacific fish that naturally experiences regular and often large shifts in environmental pH/pCO2. In two laboratory experiments, we tested the effect of acidification, as well as pH/pCO2 variability, on gene expression in the brain tissue of a common temperate kelp forest/estuarine fish, Embiotoca jacksoni. Experiment 1 employed static pH treatments (target pH = 7.85/7.30), while Experiment 2 incorporated two variable treatments that oscillated around corresponding static treatments with the same mean (target pH = 7.85/7.70) in an eight-day cycle (amplitude ± 0.15). We found that patterns of global gene expression differed across pH level treatments. Additionally, we identified differential expression of specific genes and enrichment of specific gene sets (GSEA) in comparisons of static pH treatments and in comparisons of static and variable pH treatments of the same mean pH. Importantly, we found that pH/pCO2 variability decreased the number of differentially expressed genes detected between high and low pH treatments, and that inter-individual variability in gene expression was greater in variable treatments than static treatments. These results provide important confirmation of neurological impacts of acidification in a temperate fish species and, critically, that natural environmental variability may mediate the impacts of ocean acidification.

Keyword(s):

Animalia; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Embiotoca jacksoni; Gene expression (incl. proteomics); Laboratory experiment; Nekton; North Pacific; Other; Pelagos; Single species; Temperate

Supplement to:

Toy, Jason A; Kroeker, Kristy J; Logan, Cheryl A; Takeshita, Yuichiro; Longo, Gary C; Bernardi, Giacomo (2022): Upwelling‐level acidification and pH/ pCO 2 variability moderate effects of ocean acidification on brain gene expression in the temperate surfperch, Embiotoca jacksoni. Molecular Ecology, 31(18), 4707-4725, https://doi.org/10.1111/mec.16611

Source:

Toy, Jason A (2021): Environmental data and annotated transcriptome for Black Perch brain differential gene expression experiments (2015 & 2017). Dryad, https://doi.org/10.7291/D19H5G

Further details:

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 2022-11-30.

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type	Type		Toy, Jason A		Study
2	Species, unique identification	Species UID		Toy, Jason A
3	Species, unique identification (URI)	Species UID (URI)		Toy, Jason A
4	Species, unique identification (Semantic URI)	Species UID (Semantic URI)		Toy, Jason A
5	Experiment	Exp		Toy, Jason A
6	Treatment	Treat		Toy, Jason A
7	pH	pH		Toy, Jason A		total scale
8	pH, standard deviation	pH std dev	±	Toy, Jason A		total scale
9	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Toy, Jason A
10	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Toy, Jason A
11	Aragonite saturation state	Omega Arg		Toy, Jason A
12	Aragonite saturation state, standard deviation	Omega Arg std dev	±	Toy, Jason A
13	Alkalinity, total	AT	µmol/kg	Toy, Jason A
14	Alkalinity, total, standard deviation	AT std dev	±	Toy, Jason A
15	Temperature, water	Temp	°C	Toy, Jason A
16	Temperature, water, standard deviation	Temp std dev	±	Toy, Jason A
17	Salinity	Sal		Toy, Jason A
18	Salinity, standard deviation	Sal std dev	±	Toy, Jason A
19	pH	pH		Toy, Jason A		total scale, from YSI readings
20	pH, standard deviation	pH std dev	±	Toy, Jason A		total scale, from YSI readings
21	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
22	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
23	Carbon dioxide, standard deviation	CO2 std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
24	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)
25	Fugacity of carbon dioxide in seawater, standard deviation	fCO2 std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
26	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)
27	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
28	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
29	Bicarbonate ion, standard deviation	[HCO3]- std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
30	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
31	Carbonate ion, standard deviation	[CO3]2- std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
32	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
33	Carbon, inorganic, dissolved, standard deviation	DIC std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
34	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
35	Aragonite saturation state, standard deviation	Omega Arg std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)
36	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
37	Calcite saturation state, standard deviation	Omega Cal std dev	±	Yang, Yan	Calculated using seacarb after Orr et al. (2018)

License:

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

Status:

Curation Level: Enhanced curation (CurationLevelC)

Size:

245 data points

Data

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

1 Type (Study)	2 Species UID	3 Species UID (URI)	4 Species UID (Semantic URI)	5 Exp	6 Treat	7 pH (total scale)	8 pH std dev [±] (total scale)	9 pCO2water_SST_wet [µatm]	10 pCO2 std dev [±]	11 Omega Arg	12 Omega Arg std dev [±]	13 AT [µmol/kg]	14 AT std dev [±]	15 Temp [°C]	16 Temp std dev [±]	17 Sal	18 Sal std dev [±]	19 pH (total scale, from YSI readings)	20 pH std dev [±] (total scale, from YSI readings)	21 CSC flag (Calculated using seacarb afte...)	22 CO2 [µmol/kg] (Calculated using seacarb afte...)	23 CO2 std dev [±] (Calculated using seacarb afte...)	24 fCO2water_SST_wet [µatm] (Calculated using seacarb afte...)	25 fCO2 std dev [±] (Calculated using seacarb afte...)	26 pCO2water_SST_wet [µatm] (Calculated using seacarb afte...)	27 pCO2 std dev [±] (Calculated using seacarb afte...)	28 [HCO3]- [µmol/kg] (Calculated using seacarb afte...)	29 [HCO3]- std dev [±] (Calculated using seacarb afte...)	30 [CO3]2- [µmol/kg] (Calculated using seacarb afte...)	31 [CO3]2- std dev [±] (Calculated using seacarb afte...)	32 DIC [µmol/kg] (Calculated using seacarb afte...)	33 DIC std dev [±] (Calculated using seacarb afte...)	34 Omega Arg (Calculated using seacarb afte...)	35 Omega Arg std dev [±] (Calculated using seacarb afte...)	36 Omega Cal (Calculated using seacarb afte...)	37 Omega Cal std dev [±] (Calculated using seacarb afte...)
laboratory	Embiotoca jacksoni	marinespecies.org	urn:lsid:marinespecies.org:taxname:240746	1	Target pH 7.85	7.88	0.02	599	36	1.50	0.08	2193	59	13.0	0.50	33.8	0.1	7.89	0.04	8	23.67	1.48	590.14	35.97	592.34	36.10	1946.13	55.03	98.75	6.02	2068.56	57.56	1.51	0.12	2.37	0.18
laboratory	Embiotoca jacksoni	marinespecies.org	urn:lsid:marinespecies.org:taxname:240746	1	Target pH 7.30	7.35	0.06	2204	333	0.48	0.07	2212	20	12.2	0.80	33.8	0.1	7.36	0.14	8	89.72	13.08	2180.83	315.08	2189.04	316.27	2134.58	22.23	30.99	4.37	2255.29	28.25	0.47	0.07	0.74	0.11
laboratory	Embiotoca jacksoni	marinespecies.org	urn:lsid:marinespecies.org:taxname:240746	2	Ambient	8.00	0.04	452	55	2.36	0.23	2266	3	17.5	0.06	34.3	0.1	8.01	0.08	8	15.63	1.70	447.68	48.80	449.25	48.97	1889.92	30.47	152.01	12.53	2057.57	19.76	2.35	0.22	3.65	0.34
laboratory	Embiotoca jacksoni	marinespecies.org	urn:lsid:marinespecies.org:taxname:240746	2	Target pH 7.85-Static	7.90	0.01	586	14	1.94	0.07	2268	3	17.6	0.06	34.3	0.1	7.90	0.05	8	20.34	0.64	584.15	18.68	586.20	18.75	1957.55	10.35	125.55	4.60	2103.43	6.64	1.94	0.11	3.01	0.18
laboratory	Embiotoca jacksoni	marinespecies.org	urn:lsid:marinespecies.org:taxname:240746	2	Target pH 7.85-Variable	7.89	0.08	614	136	1.93	0.34	2268	4	17.5	0.06	34.3	0.1	7.88	0.11	8	20.94	4.39	599.52	125.70	601.63	126.14	1964.64	49.18	122.67	19.94	2108.24	33.72	1.90	0.32	2.94	0.50
laboratory	Embiotoca jacksoni	marinespecies.org	urn:lsid:marinespecies.org:taxname:240746	2	Target pH 7.70-Static	7.76	0.04	848	64	1.46	0.17	2268	5	17.6	0.06	34.3	0.1	7.75	0.08	8	29.18	3.01	837.98	86.50	840.92	86.81	2034.32	20.77	94.52	8.37	2158.01	15.63	1.46	0.15	2.27	0.23
laboratory	Embiotoca jacksoni	marinespecies.org	urn:lsid:marinespecies.org:taxname:240746	2	Target pH 7.70-Variable	7.76	0.09	870	199	1.47	0.30	2267	4	17.6	0.06	34.3	0.1	7.74	0.10	8	29.16	6.69	837.60	192.08	840.54	192.76	2033.40	44.03	94.47	17.81	2157.04	32.96	1.46	0.28	2.27	0.44