Citation:

fphys.2019.01446

Name: Seawater carbonate chemistry and the diversity indexes of the microbiota of the intestinal fluid of Sparus aurata
Published: 2019-12-24
License: https://creativecommons.org/licenses/by/4.0/
Keywords: 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

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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

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, 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):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type	Type		Fonseca, Filomena		study
2	Species	Species		Fonseca, Filomena
3	Registration number of species	Reg spec no		Fonseca, Filomena
4	Uniform resource locator/link to reference	URL ref		Fonseca, Filomena		WoRMS Aphia ID
5	Experiment duration	Exp duration	days	Fonseca, Filomena
6	Treatment	Treat		Fonseca, Filomena
7	Sample ID	Sample ID		Fonseca, Filomena
8	Shannon Diversity Index	H'		Fonseca, Filomena		Shannon-Weaver
9	Simpson index of diversity	Simpson I		Fonseca, Filomena		Simpson reciprocal
10	Chao 1 richness	Chao1 rich		Fonseca, Filomena
11	Reads	Reads	#	Fonseca, Filomena
12	Operational taxonomic unit	OTU	#	Fonseca, Filomena		Family level
13	Accession number	Access No		Fonseca, Filomena
14	pH	pH		Fonseca, Filomena	Potentiometric	NBS scale
15	pH, standard deviation	pH std dev	±	Fonseca, Filomena	Potentiometric	NBS scale
16	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Fonseca, Filomena	Calculated using CO2calc
17	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Fonseca, Filomena	Calculated using CO2calc
18	Alkalinity, total	AT	µmol/kg	Fonseca, Filomena	Potentiometric titration
19	Alkalinity, total, standard deviation	AT std dev	±	Fonseca, Filomena	Potentiometric titration
20	Salinity	Sal		Fonseca, Filomena
21	Salinity, standard deviation	Sal std dev	±	Fonseca, Filomena
22	Temperature, water	Temp	°C	Fonseca, Filomena
23	Temperature, water, standard deviation	Temp std dev	±	Fonseca, Filomena
24	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
25	pH	pH		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	total scale
26	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
27	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)
28	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)
29	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
30	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
31	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
32	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
33	Calcite saturation state	Omega Cal		Yang, Yan	Calculated 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:

198 data points

Data

Download dataset as tab-delimited text — use the following character encoding:

1 Type (study)	2 Species	3 Reg spec no	4 URL ref (WoRMS Aphia ID)	5 Exp duration [days]	6 Treat	7 Sample ID	8 H' (Shannon-Weaver)	9 Simpson I (Simpson reciprocal)	10 Chao1 rich	11 Reads [#]	12 OTU [#] (Family level)	13 Access No	14 pH (NBS scale, Potentiometric)	15 pH std dev [±] (NBS scale, Potentiometric)	16 pCO2water_SST_wet [µatm] (Calculated using CO2calc)	17 pCO2 std dev [±] (Calculated using CO2calc)	18 AT [µmol/kg] (Potentiometric titration)	19 AT std dev [±] (Potentiometric titration)	20 Sal	21 Sal std dev [±]	22 Temp [°C]	23 Temp std dev [±]	24 CSC flag (Calculated using seacarb afte...)	25 pH (total scale, Calculated using...)	26 CO2 [µmol/kg] (Calculated using seacarb afte...)	27 fCO2water_SST_wet [µatm] (Calculated using seacarb afte...)	28 pCO2water_SST_wet [µatm] (Calculated using seacarb afte...)	29 [HCO3]- [µmol/kg] (Calculated using seacarb afte...)	30 [CO3]2- [µmol/kg] (Calculated using seacarb afte...)	31 DIC [µmol/kg] (Calculated using seacarb afte...)	32 Omega Arg (Calculated using seacarb afte...)	33 Omega Cal (Calculated using seacarb afte...)
laboratory	Sparus aurata (fish)	151523	marinespecies.org	30	400	F1¨CF4	2.643	5.727	7	32	7	MN240895¨CMN240926	8.14	0.02	411	11	2526	29	34.8	0.1	24.7	0.07	26	8.00	14.07	491.46	493.04	2005.57	215.62	2235.27	3.42	5.20
laboratory	Sparus aurata (fish)	151523	marinespecies.org	30	400	F9¨CF12	2.844	6.080	10	33	9	MN240969¨CMN241001	8.14	0.02	411	11	2526	29	34.8	0.1	24.7	0.07	26	8.00	14.07	491.46	493.04	2005.57	215.62	2235.27	3.42	5.20
laboratory	Sparus aurata (fish)	151523	marinespecies.org	30	400	F17¨CF20	2.980	6.323	14	32	11	MN240937¨CMN240968	8.14	0.02	411	11	2526	29	34.8	0.1	24.7	0.07	26	8.00	14.07	491.46	493.04	2005.57	215.62	2235.27	3.42	5.20
laboratory	Sparus aurata (fish)	151523	marinespecies.org	30	1200	F5¨CF8	2.266	3.879	6	30	6	MN243925¨CMN243954	7.75	0.02	1130	55	2511	33	34.8	0.1	24.7	0.07	26	7.61	39.13	1366.31	1370.71	2271.18	99.46	2409.77	1.58	2.40
laboratory	Sparus aurata (fish)	151523	marinespecies.org	30	1200	F13¨CF16	2.777	5.631	10	30	9	MN241002¨CMN241031	7.75	0.02	1130	55	2511	33	34.8	0.1	24.7	0.07	26	7.61	39.13	1366.31	1370.71	2271.18	99.46	2409.77	1.58	2.40
laboratory	Sparus aurata (fish)	151523	marinespecies.org	30	1200	F21¨CF24	3.378	8.654	14	31	13	MN257910¨CMN257940	7.75	0.02	1130	55	2511	33	34.8	0.1	24.7	0.07	26	7.61	39.13	1366.31	1370.71	2271.18	99.46	2409.77	1.58	2.40