Timmins-Schiffman, Emma; Root, Larken; Crim, Ryan N; Middleton, Mollie A; Ewing, Megan M; Winnikoff, Jacob; Ham, Gracelyn; Goetz, Giles; Roberts, Steven B; Gavery, Mackenzie R (2025): Seawater carbonate chemistry and the impacts of low-pH priming on Manila clam broodstock and its impacts on broodstock physiology and larval outcomes [dataset]. PANGAEA, https://doi.pangaea.de/10.1594/PANGAEA.987945 (DOI registration in progress)
Always quote citation above when using data! You can download the citation in several formats below.
Published: 2025-12-05
Abstract:
Here, we examined the impacts of low-pH priming on Manila clam broodstock and its impacts on broodstock physiology and larval outcomes. Measures of broodstock and larval phenotype were selected that would reveal how low pH impacts both generations and the transmission of environmental information between generations. In broodstock, we assessed energy metabolism and reproductive conditioning. Larval clams were reared in both ambient and low pH conditions to determine the impacts of priming on survival, growth, and shell formation. Based on different larval phenotypes resulting from the two broodstock pH conditions, we investigated the impact of maternal effects via egg lipidomes and maternal RNA.
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 github (see Source) by the OA-ICC data curator. 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 2025-12-05.
Keyword(s):
Benthic animals; Benthos; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Development; Gene expression (incl. proteomics); Growth/Morphology; Laboratory experiment; Mortality/Survival; North Pacific; Other studied parameter or process; Pelagos; Reproduction; Ruditapes philippinarum; Single species; Temperate; Zooplankton
Related to:
Timmins-Schiffman, Emma; Root, Larken; Crim, Ryan N; Middleton, Mollie A; Ewing, Megan M; Winnikoff, Jacob; Ham, Gracelyn; Goetz, Giles; Roberts, Steven B; Gavery, Mackenzie R (2026): Mothers know best: Maternal signaling boosts larval resilience under ocean acidification conditions. Aquaculture, 613, 743388, https://doi.org/10.1016/j.aquaculture.2025.743388
Source:
GitHub - emmats/Clam-OA-priming: Code for analysis and figures from Timmins-Schiffman & Root et al. paper on ocean acidification reproductive priming in Manila clams (2025). https://github.com/emmats/Clam-OA-priming
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):
Coverage:
Latitude: 47.720600 * Longitude: -122.630100
Date/Time Start: 2023-01-18T00:00:00 * Date/Time End: 2023-01-18T00:00:00
Event(s):
Parameter(s):
| # | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
|---|---|---|---|---|---|---|
| 1 | Type of study | Study type | Gavery, Mackenzie R | |||
| 2 | Species, unique identification | Species UID | Gavery, Mackenzie R | |||
| 3 | Species, unique identification (URI) | Species UID (URI) | Gavery, Mackenzie R | |||
| 4 | Species, unique identification (Semantic URI) | Species UID (Semantic URI) | Gavery, Mackenzie R | |||
| 5 | Identification | ID | Gavery, Mackenzie R | |||
| 6 | Time point, descriptive | Time point | Gavery, Mackenzie R | |||
| 7 | Sampling date | Sampling date | Gavery, Mackenzie R | |||
| 8 | Identification | ID | Gavery, Mackenzie R | Tank (OG) | ||
| 9 | Identification | ID | Gavery, Mackenzie R | Tank (new) | ||
| 10 | Sex | Sex | Gavery, Mackenzie R | |||
| 11 | Treatment | Treat | Gavery, Mackenzie R | |||
| 12 | Sodium/Potassium adenosine triphosphatase activity, per protein mass | Na/K-ATPase act/prot | µmol/mg/h | Gavery, Mackenzie R | ||
| 13 | Identification | ID | Gavery, Mackenzie R | clam | ||
| 14 | Mass | Mass | g | Gavery, Mackenzie R | foil | |
| 15 | Mass | Mass | g | Gavery, Mackenzie R | wet | |
| 16 | Mass | Mass | g | Gavery, Mackenzie R | dry | |
| 17 | Mass | Mass | g | Gavery, Mackenzie R | shell | |
| 18 | Mass | Mass | g | Gavery, Mackenzie R | wet_shell | |
| 19 | Sex | Sex | Gavery, Mackenzie R | Corr | ||
| 20 | Individuals | Ind | # | Gavery, Mackenzie R | spawn | |
| 21 | Comment | Comment | Gavery, Mackenzie R | Spawn | ||
| 22 | Identification | ID | Gavery, Mackenzie R | Egg_Num | ||
| 23 | Identification | ID | Gavery, Mackenzie R | Label | ||
| 24 | Area | Area | µm2 | Gavery, Mackenzie R | egg | |
| 25 | Identification | ID | Gavery, Mackenzie R | Image_Num | ||
| 26 | Eggs | Eggs | # | Gavery, Mackenzie R | ||
| 27 | Identification | ID | Gavery, Mackenzie R | |||
| 28 | Treatment | Treat | Gavery, Mackenzie R | Larval | ||
| 29 | Time in days | Time d | days | Gavery, Mackenzie R | ||
| 30 | Identification | ID | Gavery, Mackenzie R | silo | ||
| 31 | Identification | ID | Gavery, Mackenzie R | container | ||
| 32 | Length | l | µm | Gavery, Mackenzie R | Shell | |
| 33 | Comment | Comment | Gavery, Mackenzie R | normality | ||
| 34 | Larvae | Larvae | # | Gavery, Mackenzie R | 48h_in | |
| 35 | Larvae | Larvae | # | Gavery, Mackenzie R | 48h_out | |
| 36 | Larvae | Larvae | # | Gavery, Mackenzie R | 7d_in | |
| 37 | Larvae | Larvae | # | Gavery, Mackenzie R | 7d_out | |
| 38 | Larvae | Larvae | # | Gavery, Mackenzie R | 14d_in | |
| 39 | Larvae | Larvae | # | Gavery, Mackenzie R | 14_out | |
| 40 | Temperature, water | Temp | °C | Gavery, Mackenzie R | broodstock tanks | |
| 41 | Salinity | Sal | Gavery, Mackenzie R | broodstock tanks | ||
| 42 | pH, total scale | pHT | Gavery, Mackenzie R | broodstock tanks | ||
| 43 | Partial pressure of carbon dioxide (water) at sea surface temperature (wet air) | pCO2water_SST_wet | µatm | Gavery, Mackenzie R | broodstock tanks | |
| 44 | Aragonite saturation state | Omega Arg | Gavery, Mackenzie R | broodstock tanks | ||
| 45 | Carbon, inorganic, dissolved | DIC | µmol/kg | Gavery, Mackenzie R | broodstock tanks | |
| 46 | Alkalinity, total | AT | µmol/kg | Gavery, Mackenzie R | broodstock tanks | |
| 47 | Carbonate system computation flag | CSC flag | Yang, Yan | Calculated using seacarb after Nisumaa et al. (2010) | ||
| 48 | Carbon dioxide | CO2 | µmol/kg | Yang, Yan | Calculated using seacarb after Nisumaa et al. (2010) | |
| 49 | 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) | |
| 50 | 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) | |
| 51 | Bicarbonate ion | [HCO3]- | µmol/kg | Yang, Yan | Calculated using seacarb after Nisumaa et al. (2010) | |
| 52 | Carbonate ion | [CO3]2- | µmol/kg | Yang, Yan | Calculated using seacarb after Nisumaa et al. (2010) | |
| 53 | Carbon, inorganic, dissolved | DIC | µmol/kg | Yang, Yan | Calculated using seacarb after Nisumaa et al. (2010) | |
| 54 | Aragonite saturation state | Omega Arg | Yang, Yan | Calculated using seacarb after Nisumaa et al. (2010) | ||
| 55 | Calcite saturation state | Omega Cal | Yang, Yan | Calculated using seacarb after Nisumaa et al. (2010) | ||
| 56 | Temperature, water | Temp | °C | Gavery, Mackenzie R | larval tanks | |
| 57 | Salinity | Sal | Gavery, Mackenzie R | larval tanks | ||
| 58 | pH, total scale | pHT | Gavery, Mackenzie R | larval tanks | ||
| 59 | Partial pressure of carbon dioxide (water) at sea surface temperature (wet air) | pCO2water_SST_wet | µatm | Gavery, Mackenzie R | larval tanks | |
| 60 | Aragonite saturation state | Omega Arg | Gavery, Mackenzie R | larval tanks | ||
| 61 | Carbon, inorganic, dissolved | DIC | µmol/kg | Gavery, Mackenzie R | larval tanks |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
72014 data points
Download Data
View dataset as HTML (shows only first 2000 rows)