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Spencer, Laura H; Long, William Christopher; Spies, Ingrid B; Nichols, Krista M; Foy, Robert J (2024): Seawater carbonate chemistry and gene function and transposon activity of juvenile subarctic crustacean [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.967461

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Abstract:
In this study, we used functional genomics to examine the molecular response of OA exposed red king crab. We leveraged juveniles that were exposed to (and tolerated) three carbonate chemistry treatments from hatching to the first crab stage (C1), thus capturing transcriptional differences among crab that are reared in historically ambient conditions along the Bering Sea shelf (pH 8.0), and those acclimated to a moderately (pH 7.8) and severely (pH 7.5) acidified environments that are projected to occur in surface and bottom waters by the end of this century [15]. Using RNA-Seq, a high-throughput sequencing approach that measures gene-activity, our study provides a snap-shot of system-wide changes in energy allocation due to acidification exposure by identifying genes, their functions, and biological processes that differ in OA-reared crab [56]. Libraries were constructed from at least 13 individuals per treatment, rather than pools of individuals which can obscure genotypedependent variation. Importantly, since the crab used in this experiment were quite tolerant of OA conditions, the molecular mechanisms and pathways described here may be potentially critical to survival in an acidified environment.
Keyword(s):
Animalia; Arthropoda; Benthic animals; Benthos; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Gene expression (incl. proteomics); Laboratory experiment; North Pacific; Paralithodes camtschaticus; Single species; Temperate
Related to:
Spencer, Laura H; Long, William Christopher; Spies, Ingrid B; Nichols, Krista M; Foy, Robert J (2024): Narrowed gene functions and enhanced transposon activity are associated with high tolerance to ocean acidification in a juvenile subarctic crustacean. PLOS Climate, 3(3), e0000319, https://doi.org/10.1371/journal.pclm.0000319
Source:
laurahspencer/red-king_RNASeq-2022: Release for Zenodo (2024). Zenodo, https://doi.org/10.5281/ZENODO.10547911
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)
Comment:
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 2024-04-25.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Type of studyStudy typeSpies, Ingrid B
2Species, unique identificationSpecies UIDSpies, Ingrid B
3Species, unique identification (URI)Species UID (URI)Spies, Ingrid B
4Species, unique identification (Semantic URI)Species UID (Semantic URI)Spies, Ingrid B
5TreatmentTreatSpies, Ingrid B
6IdentificationIDSpies, Ingrid B
7Alkalinity, totalATµmol/kgSpies, Ingrid B
8Alkalinity, total, standard deviationAT std dev±Spies, Ingrid B
9Carbonate ion[CO3]2-µmol/kgSpies, Ingrid B
10Carbonate ion, standard deviation[CO3]2- std dev±Spies, Ingrid B
11Carbon, inorganic, dissolvedDICµmol/kgSpies, Ingrid B
12Carbon, inorganic, dissolved, standard deviationDIC std dev±Spies, Ingrid B
13Bicarbonate ion[HCO3]-µmol/kgSpies, Ingrid B
14Bicarbonate ion, standard deviation[HCO3]- std dev±Spies, Ingrid B
15Aragonite saturation stateOmega ArgSpies, Ingrid B
16Aragonite saturation state, standard deviationOmega Arg std dev±Spies, Ingrid B
17Calcite saturation stateOmega CalSpies, Ingrid B
18Calcite saturation state, standard deviationOmega Cal std dev±Spies, Ingrid B
19Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmSpies, Ingrid B
20Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Spies, Ingrid B
21pHpHSpies, Ingrid Btotal scale
22pH, standard deviationpH std dev±Spies, Ingrid Btotal scale
23SalinitySalSpies, Ingrid B
24Salinity, standard deviationSal std dev±Spies, Ingrid B
25Temperature, waterTemp°CSpies, Ingrid B
26Temperature, water, standard deviationTemp std dev±Spies, Ingrid B
27Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
28pHpHYang, YanCalculated using seacarb after Nisumaa et al. (2010)total scale
29Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
30Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
31Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
32Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
33Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
34Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
35Calcite saturation stateOmega CalYang, YanCalculated 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:
495 data points

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