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Toy, Jason A; Kroeker, Kristy J; Logan, Cheryl A; Takeshita, Yuichiro; Longo, Gary C; Bernardi, Giacomo (2022): Seawater carbonate chemistry in experiment 1 and 2 [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.951362

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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):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1TypeTypeToy, Jason AStudy
2Species, unique identificationSpecies UIDToy, Jason A
3Species, unique identification (URI)Species UID (URI)Toy, Jason A
4Species, unique identification (Semantic URI)Species UID (Semantic URI)Toy, Jason A
5ExperimentExpToy, Jason A
6TreatmentTreatToy, Jason A
7pHpHToy, Jason Atotal scale
8pH, standard deviationpH std dev±Toy, Jason Atotal scale
9Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmToy, Jason A
10Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Toy, Jason A
11Aragonite saturation stateOmega ArgToy, Jason A
12Aragonite saturation state, standard deviationOmega Arg std dev±Toy, Jason A
13Alkalinity, totalATµmol/kgToy, Jason A
14Alkalinity, total, standard deviationAT std dev±Toy, Jason A
15Temperature, waterTemp°CToy, Jason A
16Temperature, water, standard deviationTemp std dev±Toy, Jason A
17SalinitySalToy, Jason A
18Salinity, standard deviationSal std dev±Toy, Jason A
19pHpHToy, Jason Atotal scale, from YSI readings
20pH, standard deviationpH std dev±Toy, Jason Atotal scale, from YSI readings
21Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
22Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
23Carbon dioxide, standard deviationCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
24Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
25Fugacity of carbon dioxide in seawater, standard deviationfCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
26Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
27Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
28Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
29Bicarbonate ion, standard deviation[HCO3]- std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
30Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
31Carbonate ion, standard deviation[CO3]2- std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
32Carbon, inorganic, dissolvedDICµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
33Carbon, inorganic, dissolved, standard deviationDIC std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
34Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
35Aragonite saturation state, standard deviationOmega Arg std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
36Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
37Calcite saturation state, standard deviationOmega Cal std dev±Yang, YanCalculated 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

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