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Shan, Encui; Yu, Zhenglin; Cong, Xiao; Hou, Chaowei; Guo, Xueying; Pang, Lei; Zhao, Jianmin; Wang, Qing; Yuan, Xiutang (2025): Seawater carbonate chemistry and gut microbiomeg, metabolomic profiling, metabolic plasticity of Apostichopus japonicus [dataset]. PANGAEA, https://doi.pangaea.de/10.1594/PANGAEA.987868 (DOI registration in progress)

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Published: 2025-12-03

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Abstract:
Herein, a mesocosm experiment was constructed and analyzed by using integrated gut microbiome and metabolomics approaches to investigate the responses of sea cucumbers Apostichopus japonicus to ocean acidification and ocean warming.
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 extracted from tables in the related paper (see Related to) 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 2025-12-03.
Keyword(s):
Animalia; Apostichopus japonicus; Benthic animals; Benthos; Coast and continental shelf; Community composition and diversity; Containers and aquaria (20-1000 L or < 1 m**2); Echinodermata; Entire community; Laboratory experiment; North Pacific; Other studied parameter or process; Single species; Temperate; Temperature
Related to:
Shan, Encui; Yu, Zhenglin; Cong, Xiao; Hou, Chaowei; Guo, Xueying; Pang, Lei; Zhao, Jianmin; Wang, Qing; Yuan, Xiutang (2025): Gut microbial community plasticity as a climate shield mediating sea cucumber resilience to ocean acidification and warming. ISME Communications, 5(1), ycaf188, https://doi.org/10.1093/ismeco/ycaf188
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)
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Type of studyStudy typeYuan, Xiutang
2Species, unique identificationSpecies UIDYuan, Xiutang
3Species, unique identification (URI)Species UID (URI)Yuan, Xiutang
4Species, unique identification (Semantic URI)Species UID (Semantic URI)Yuan, Xiutang
5TreatmentTreatYuan, Xiutang
6PhylumPhylumYuan, Xiutang
7AbundanceAbund%Yuan, XiutangRelative abundance of taxonomic of microbial communities
8FamilyFamilyYuan, Xiutang
9AbundanceAbund%Yuan, XiutangRelative abundance of taxonomic of microbial communities
10GroupGroupYuan, Xiutang
11Chao 1 richnessChao1 richYuan, Xiutang
12Species diversitySpecies divYuan, Xiutangpielou_e
13Shannon Diversity IndexH'Yuan, Xiutang
14Simpson index of diversitySimpson IYuan, Xiutang
15MetaboliteMetabolYuan, Xiutang
16Metabolite concentrationMetabolAUYuan, Xiutang
17ReplicatesRepl#Yuan, XiutangCarbonate chemistry data
18pH, NBS scalepH NBSYuan, Xiutang
19pH, standard deviationpH std dev±Yuan, Xiutang
20Temperature, waterTemp°CYuan, Xiutang
21Temperature, water, standard deviationTemp std dev±Yuan, Xiutang
22SalinitySalYuan, Xiutang
23Salinity, standard deviationSal std dev±Yuan, Xiutang
24Carbon, inorganic, dissolvedDICµmol/kgYuan, Xiutang
25Carbon, inorganic, dissolved, standard deviationDIC std dev±Yuan, Xiutang
26Alkalinity, totalATµmol/kgYuan, XiutangCalculated using CO2SYS
27Alkalinity, total, standard deviationAT std dev±Yuan, XiutangCalculated using CO2SYS
28Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYuan, XiutangCalculated using CO2SYS
29Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Yuan, XiutangCalculated using CO2SYS
30Calcite saturation stateOmega CalYuan, XiutangCalculated using CO2SYS
31Calcite saturation state, standard deviationOmega Cal std dev±Yuan, XiutangCalculated using CO2SYS
32Aragonite saturation stateOmega ArgYuan, XiutangCalculated using CO2SYS
33Aragonite saturation state, standard deviationOmega Arg std dev±Yuan, XiutangCalculated using CO2SYS
34Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
35pH, total scalepHTYang, YanCalculated using seacarb after Nisumaa et al. (2010)
36Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
37Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
38Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
39Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
40Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
41Alkalinity, totalATµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
42Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
43Calcite 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:
14744 data points

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