Citation:

PANGAEA.966769

Name: Seawater carbonate chemistry and physiological metrics and gene expression responses of transplants of three species of reef-building corals
Published: 2024-03-19
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Animalia; Benthic animals; Benthos; Biomass/Abundance/Elemental composition; Calcification/Dissolution; Cnidaria; Coast and continental shelf; Field experiment; Gene expression (incl. proteomics); Growth/Morphology; North Atlantic; Porites astreoides; Porites porites; Siderastrea siderea; Single species; Tropical

Always quote citation above when using data! You can download the citation in several formats below.

RIS Citation BibTeX Citation Text Citation Facebook TwitterShow Map Google Earth

Abstract:

We examined gene expression responses of >2-year coral transplant experiment to ambient and low pH common garden sites of three species of reef-building corals (Porites astreoides, Porites porites and Siderastrea siderea) and their algal endosymbiont communities (Symbiodiniaceae) originating from low pH (Ojo) and ambient pH native origins (Lagoon or Reef).

Keyword(s):

Animalia; Benthic animals; Benthos; Biomass/Abundance/Elemental composition; Calcification/Dissolution; Cnidaria; Coast and continental shelf; Field experiment; Gene expression (incl. proteomics); Growth/Morphology; North Atlantic; Porites astreoides; Porites porites; Siderastrea siderea; Single species; Tropical

Supplement to:

Radice, Veronica Z; Martinez, Ana; Paytan, Adina; Potts, Donald C; Barshis, Daniel J (2024): Complex dynamics of coral gene expression responses to low pH across species. Molecular Ecology, 33(1), e17186, https://doi.org/10.1111/mec.17186

Source:

Martinez, Ana; Crook, Elizabeth Derse; Barshis, Daniel J; Potts, Donald C; Rebolledo-Vieyra, Mario; Hernandez, Laura; Paytan, Adina (2019): Seawater carbonate chemistry and calcification, survival, concentrations of Symbiodiniaceae, chlorophyll a and protein of Caribbean corals. PANGAEA, https://doi.org/10.1594/PANGAEA.913183

Documentation:

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

Further details:

Gene expression of reef-building corals and algal symbionts (2022). https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA865460

Project(s):

Ocean Acidification International Coordination Centre (OA-ICC)

Coverage:

Median Latitude: 20.883000 * Median Longitude: -86.859000 * South-bound Latitude: 20.880000 * West-bound Longitude: -86.861000 * North-bound Latitude: 20.886000 * East-bound Longitude: -86.857000

Date/Time Start: 2012-12-12T00:00:00 * Date/Time End: 2012-12-15T00:00:00

Event(s):

Ojo_Norte * Latitude: 20.886000 * Longitude: -86.857000 * Date/Time Start: 2012-12-12T00:00:00 * Date/Time End: 2012-12-13T00:00:00 * Method/Device: Experiment (EXP)

Ojo_Pargos * Latitude: 20.880000 * Longitude: -86.861000 * Date/Time Start: 2012-12-14T00:00:00 * Date/Time End: 2012-12-15T00:00:00 * Method/Device: Experiment (EXP)

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 2020-03-06.

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Event label	Event		Aranda, Manuel
2	Type of study	Study type		Aranda, Manuel
3	Species, unique identification	Species UID		Aranda, Manuel
4	Species, unique identification (URI)	Species UID (URI)		Aranda, Manuel
5	Species, unique identification (Semantic URI)	Species UID (Semantic URI)		Aranda, Manuel
6	Site	Site		Aranda, Manuel		origin
7	Site	Site		Aranda, Manuel		transplant
8	Replicates	Repl	#	Aranda, Manuel
9	Linear extension	Lin ext	µm	Aranda, Manuel		Skeletal
10	Linear extension, standard error	Lin ext std e	±	Aranda, Manuel		Skeletal
11	Density	Density	g/cm³	Aranda, Manuel		Skeletal
12	Density, standard error	Density std e	±	Aranda, Manuel		Skeletal
13	Symbiont cell density	Symbiont	#/cm²	Aranda, Manuel
14	Symbiont cell density, standard error	Symbiont std e	±	Aranda, Manuel
15	Chlorophyll a	Chl a	µg/l	Aranda, Manuel
16	Chlorophyll a, standard error	Chl a std e	±	Aranda, Manuel
17	Chlorophyll a per cell	Chl a/cell	pg/#	Aranda, Manuel
18	Chlorophyll a, standard error	Chl a std e	±	Aranda, Manuel
19	Proteins	Protein	µg/cm²	Aranda, Manuel
20	Proteins, standard error	Protein std e	±	Aranda, Manuel
21	Alkalinity, total	AT	µmol/kg	Aranda, Manuel
22	Alkalinity, total, standard error	AT std e	±	Aranda, Manuel
23	Carbon, inorganic, dissolved	DIC	µmol/kg	Aranda, Manuel
24	Carbon, inorganic, dissolved, standard error	DIC std e	±	Aranda, Manuel
25	pH	pH		Aranda, Manuel		NBS scale
26	pH, standard error	pH std e	±	Aranda, Manuel		NBS scale
27	Aragonite saturation state	Omega Arg		Aranda, Manuel
28	Aragonite saturation state, standard error	Omega Arg std e	±	Aranda, Manuel
29	Temperature, water	Temp	°C	Aranda, Manuel
30	Temperature, water, standard error	T std e	±	Aranda, Manuel
31	Salinity	Sal		Aranda, Manuel
32	Salinity, standard error	Sal std e	±	Aranda, Manuel
33	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
34	pH	pH		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	total scale
35	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
36	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)
37	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)
38	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
39	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
40	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
41	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:

380 data points

Data

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

1 Event	2 Study type	3 Species UID	4 Species UID (URI)	5 Species UID (Semantic URI)	6 Site (origin)	7 Site (transplant)	8 Repl [#]	9 Lin ext [µm] (Skeletal)	10 Lin ext std e [±] (Skeletal)	11 Density [g/cm³] (Skeletal)	12 Density std e [±] (Skeletal)	13 Symbiont [#/cm²]	14 Symbiont std e [±]	15 Chl a [µg/l]	16 Chl a std e [±]	17 Chl a/cell [pg/#]	18 Chl a std e [±]	19 Protein [µg/cm²]	20 Protein std e [±]	21 AT [µmol/kg]	22 AT std e [±]	23 DIC [µmol/kg]	24 DIC std e [±]	25 pH (NBS scale)	26 pH std e [±] (NBS scale)	27 Omega Arg	28 Omega Arg std e [±]	29 Temp [°C]	30 T std e [±]	31 Sal	32 Sal std e [±]	33 CSC flag	34 pH (total scale)	35 CO2 [µmol/kg]	36 fCO2water_SST_wet [µatm]	37 pCO2water_SST_wet [µatm]	38 [HCO3]- [µmol/kg]	39 [CO3]2- [µmol/kg]	40 Omega Arg	41 Omega Cal
Ojo_Norte	field	Porites astreoides	marinespecies.org	urn:lsid:marinespecies.org:taxname:288889	Lagoon native	Ambient pH	9	8170	760	1.60	0.03	11300000	3980000	5910	2399	5.44	1.39	1330	210	2365	32	2019	12	8.17	0.07	3.53	0.43	26.9	0.3	35.6	0.1	15	8.07	10.04	371.96	373.12	1763.31	245.64	3.92	5.90
Ojo_Norte	field	Porites astreoides	marinespecies.org	urn:lsid:marinespecies.org:taxname:288889	Lagoon native	Low pH	5	9680	2040	1.11	0.03	29500000	8620000	26607	8684	8.30	0.89	3060	1040	2759	104	2621	93	7.70	0.14	2.10	0.35	27.1	0.2	33.2	0.5	15	7.67	36.17	1329.59	1333.74	2456.62	128.21	2.08	3.15
Ojo_Norte	field	Porites astreoides	marinespecies.org	urn:lsid:marinespecies.org:taxname:288889	Ojo native	Ambient pH	8	7810	390	1.58	0.02	10400000	2030000	4908	1112	4.43	0.47	1150	190	2365	32	2019	12	8.17	0.07	3.53	0.43	26.9	0.3	35.6	0.1	15	8.07	10.04	371.96	373.12	1763.31	245.64	3.92	5.90
Ojo_Norte	field	Porites astreoides	marinespecies.org	urn:lsid:marinespecies.org:taxname:288889	Ojo native	Low pH	7	13550	1170	1.13	0.04	29800000	12100000	20265	7241	7.84	1.10	1720	700	2759	104	2621	93	7.70	0.14	2.10	0.35	27.1	0.2	33.2	0.5	15	7.67	36.17	1329.59	1333.74	2456.62	128.21	2.08	3.15
Ojo_Pargos	field	Siderastrea siderea	marinespecies.org	urn:lsid:marinespecies.org:taxname:207516	Lagoon native	Ambient pH	6	2970	600	1.72	0.03	11600000	6620000	3264	1908	2.59	0.44	2230	1000	2365	32	2019	12	8.17	0.07	3.53	0.43	26.9	0.3	35.6	0.1	15	8.07	10.04	371.96	373.12	1763.31	245.64	3.92	5.90
Ojo_Pargos	field	Siderastrea siderea	marinespecies.org	urn:lsid:marinespecies.org:taxname:207516	Lagoon native	Low pH	5	4500	980	1.40	0.06	14800000	6170000	8365	4375	6.33	1.61	1370	460	2759	104	2621	93	7.70	0.14	2.10	0.35	27.1	0.2	33.2	0.5	15	7.67	36.17	1329.59	1333.74	2456.62	128.21	2.08	3.15
Ojo_Pargos	field	Siderastrea siderea	marinespecies.org	urn:lsid:marinespecies.org:taxname:207516	Ojo native	Ambient pH	5	2800	320	1.48	0.02	1370000	459000	512	165	3.82	0.34	360	210	2365	32	2019	12	8.17	0.07	3.53	0.43	26.9	0.3	35.6	0.1	15	8.07	10.04	371.96	373.12	1763.31	245.64	3.92	5.90
Ojo_Pargos	field	Siderastrea siderea	marinespecies.org	urn:lsid:marinespecies.org:taxname:207516	Ojo native	Low pH	6	3940	480	1.31	0.03	9470000	2200000	5915	1363	6.10	0.71	880	190	2759	104	2621	93	7.70	0.14	2.10	0.35	27.1	0.2	33.2	0.5	15	7.67	36.17	1329.59	1333.74	2456.62	128.21	2.08	3.15
Ojo_Pargos	field	Siderastrea siderea	marinespecies.org	urn:lsid:marinespecies.org:taxname:207516	Reef native	Ambient pH	7	6190	720	1.68	0.02	1990000	394000	680	164	3.09	0.27	320	80	2365	32	2019	12	8.17	0.07	3.53	0.43	26.9	0.3	35.6	0.1	15	8.07	10.04	371.96	373.12	1763.31	245.64	3.92	5.90
Ojo_Pargos	field	Siderastrea siderea	marinespecies.org	urn:lsid:marinespecies.org:taxname:207516	Reef native	Low pH	7	6430	910	1.42	0.07	23300000	9350000	8121	2681	4.23	0.51	1270	270	2759	104	2621	93	7.70	0.14	2.10	0.35	27.1	0.2	33.2	0.5	15	7.67	36.17	1329.59	1333.74	2456.62	128.21	2.08	3.15