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Fonseca, Filomena; Cerqueira, Ricardo; Fuentes, Juan (2019): Seawater carbonate chemistry and the diversity indexes of the microbiota of the intestinal fluid of Sparus aurata [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.910337, Supplement to: Fonseca, F et al. (2019): Impact of Ocean Acidification on the Intestinal Microbiota of the Marine Sea Bream (Sparus aurata L.). Frontiers in Physiology, 10, https://doi.org/10.3389/fphys.2019.01446

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Abstract:
Within a scenario of increasing atmospheric CO2 and ocean acidification (OA), it is highly relevant to investigate its impacts not only on fish performance but also on fish intestinal microbiome and how that reflects on host performance and health. The main objective of this study was to establish if the intestinal microbiota of the sea bream (Sparus aurata) was affected by high level of CO2 in line with the predictions for this century. The bacterial communities of the intestinal fluid were characterized in animals kept at the present-day level of CO2 (400 μatm) and in animals switched to high CO2 (1200 μatm) for 1 month. Bacterial taxa identification was based on molecular methods, using the DNA coding for the 16S ribosomal RNA and primers targeting the regions V1–V3. Amplicons obtained from DNA samples of animals in the same tank were combined, cloned to obtain a bacterial DNA library, and the clones were sequenced. No significant differences were found between the two treatments for alpha diversity. However, beta diversity analysis revealed distinct dysbiosis in response to hypercapnia, with phylum Firmicutes absent from the bacterial communities of fish exposed to 1200 μatm CO2, whereas Proteobacteria relative abundance was increased at elevated CO2, due to the presence of Gammaproteobacteria (Vibrionaceae and Alteromonadaceae), a class not present in the control samples. This study provides a first glimpse at the impact of OA in fish intestinal microbiota and highlights potential downstream effects to the general condition of fishes under hypercapnia.
Keyword(s):
Animalia; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Laboratory experiment; Mediterranean Sea; Nekton; Other studied parameter or process; Pelagos; Single species; Sparus aurata; Temperate
Further details:
Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James C; Gentili, Bernard; Hagens, Mathilde; Hofmann, Andreas; Mueller, Jens-Daniel; Proye, Aurélien; Rae, James; Soetaert, Karline (2019): seacarb: seawater carbonate chemistry with R. R package version 3.2.12. https://CRAN.R-project.org/package=seacarb
Comment:
In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2019) 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 2019-12-20.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1TypeTypeFonseca, Filomenastudy
2SpeciesSpeciesFonseca, Filomena
3Registration number of speciesReg spec noFonseca, Filomena
4Uniform resource locator/link to referenceURL refFonseca, FilomenaWoRMS Aphia ID
5Experiment durationExp durationdaysFonseca, Filomena
6TreatmentTreatFonseca, Filomena
7Sample IDSample IDFonseca, Filomena
8Shannon Diversity IndexH'Fonseca, FilomenaShannon-Weaver
9Simpson index of diversitySimpson IFonseca, FilomenaSimpson reciprocal
10Chao 1 richnessChao1 richFonseca, Filomena
11ReadsReads#Fonseca, Filomena
12Operational taxonomic unitOTU#Fonseca, FilomenaFamily level
13Accession numberAccess NoFonseca, Filomena
14pHpHFonseca, FilomenaPotentiometricNBS scale
15pH, standard deviationpH std dev±Fonseca, FilomenaPotentiometricNBS scale
16Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmFonseca, FilomenaCalculated using CO2calc
17Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Fonseca, FilomenaCalculated using CO2calc
18Alkalinity, totalATµmol/kgFonseca, FilomenaPotentiometric titration
19Alkalinity, total, standard deviationAT std dev±Fonseca, FilomenaPotentiometric titration
20SalinitySalFonseca, Filomena
21Salinity, standard deviationSal std dev±Fonseca, Filomena
22Temperature, waterTemp°CFonseca, Filomena
23Temperature, water, standard deviationTemp std dev±Fonseca, Filomena
24Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
25pHpHYang, YanCalculated using seacarb after Nisumaa et al. (2010)total scale
26Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
27Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
28Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
29Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
30Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
31Carbon, inorganic, dissolvedDICµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
32Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
33Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
198 data points

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