Citation:

PANGAEA.967461

Name: Seawater carbonate chemistry and gene function and transposon activity of juvenile subarctic crustacean
Published: 2024-04-25
License: https://creativecommons.org/licenses/by/4.0/
Keywords: Animalia; Arthropoda; Benthic animals; Benthos; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Gene expression (incl. proteomics); Laboratory experiment; North Pacific; Paralithodes camtschaticus; Single species; Temperate

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Abstract:

In this study, we used functional genomics to examine the molecular response of OA exposed red king crab. We leveraged juveniles that were exposed to (and tolerated) three carbonate chemistry treatments from hatching to the first crab stage (C1), thus capturing transcriptional differences among crab that are reared in historically ambient conditions along the Bering Sea shelf (pH 8.0), and those acclimated to a moderately (pH 7.8) and severely (pH 7.5) acidified environments that are projected to occur in surface and bottom waters by the end of this century [15]. Using RNA-Seq, a high-throughput sequencing approach that measures gene-activity, our study provides a snap-shot of system-wide changes in energy allocation due to acidification exposure by identifying genes, their functions, and biological processes that differ in OA-reared crab [56]. Libraries were constructed from at least 13 individuals per treatment, rather than pools of individuals which can obscure genotypedependent variation. Importantly, since the crab used in this experiment were quite tolerant of OA conditions, the molecular mechanisms and pathways described here may be potentially critical to survival in an acidified environment.

Keyword(s):

Animalia; Arthropoda; Benthic animals; Benthos; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Gene expression (incl. proteomics); Laboratory experiment; North Pacific; Paralithodes camtschaticus; Single species; Temperate

Related to:

Spencer, Laura H; Long, William Christopher; Spies, Ingrid B; Nichols, Krista M; Foy, Robert J (2024): Narrowed gene functions and enhanced transposon activity are associated with high tolerance to ocean acidification in a juvenile subarctic crustacean. PLOS Climate, 3(3), e0000319, https://doi.org/10.1371/journal.pclm.0000319

Source:

laurahspencer/red-king_RNASeq-2022: Release for Zenodo (2024). Zenodo, https://doi.org/10.5281/ZENODO.10547911

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)

Comment:

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 2024-04-25.

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type of study	Study type		Spies, Ingrid B
2	Species, unique identification	Species UID		Spies, Ingrid B
3	Species, unique identification (URI)	Species UID (URI)		Spies, Ingrid B
4	Species, unique identification (Semantic URI)	Species UID (Semantic URI)		Spies, Ingrid B
5	Treatment	Treat		Spies, Ingrid B
6	Identification	ID		Spies, Ingrid B
7	Alkalinity, total	AT	µmol/kg	Spies, Ingrid B
8	Alkalinity, total, standard deviation	AT std dev	±	Spies, Ingrid B
9	Carbonate ion	[CO3]2-	µmol/kg	Spies, Ingrid B
10	Carbonate ion, standard deviation	[CO3]2- std dev	±	Spies, Ingrid B
11	Carbon, inorganic, dissolved	DIC	µmol/kg	Spies, Ingrid B
12	Carbon, inorganic, dissolved, standard deviation	DIC std dev	±	Spies, Ingrid B
13	Bicarbonate ion	[HCO3]-	µmol/kg	Spies, Ingrid B
14	Bicarbonate ion, standard deviation	[HCO3]- std dev	±	Spies, Ingrid B
15	Aragonite saturation state	Omega Arg		Spies, Ingrid B
16	Aragonite saturation state, standard deviation	Omega Arg std dev	±	Spies, Ingrid B
17	Calcite saturation state	Omega Cal		Spies, Ingrid B
18	Calcite saturation state, standard deviation	Omega Cal std dev	±	Spies, Ingrid B
19	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Spies, Ingrid B
20	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Spies, Ingrid B
21	pH	pH		Spies, Ingrid B		total scale
22	pH, standard deviation	pH std dev	±	Spies, Ingrid B		total scale
23	Salinity	Sal		Spies, Ingrid B
24	Salinity, standard deviation	Sal std dev	±	Spies, Ingrid B
25	Temperature, water	Temp	°C	Spies, Ingrid B
26	Temperature, water, standard deviation	Temp std dev	±	Spies, Ingrid B
27	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
28	pH	pH		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	total scale
29	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
30	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)
31	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)
32	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
33	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
34	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
35	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:

495 data points

Data

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

1 Study type	2 Species UID	3 Species UID (URI)	4 Species UID (Semantic URI)	5 Treat	6 ID	7 AT [µmol/kg]	8 AT std dev [±]	9 [CO3]2- [µmol/kg]	10 [CO3]2- std dev [±]	11 DIC [µmol/kg]	12 DIC std dev [±]	13 [HCO3]- [µmol/kg]	14 [HCO3]- std dev [±]	15 Omega Arg	16 Omega Arg std dev [±]	17 Omega Cal	18 Omega Cal std dev [±]	19 pCO2water_SST_wet [µatm]	20 pCO2 std dev [±]	21 pH (total scale)	22 pH std dev [±] (total scale)	23 Sal	24 Sal std dev [±]	25 Temp [°C]	26 Temp std dev [±]	27 CSC flag	28 pH (total scale)	29 CO2 [µmol/kg]	30 fCO2water_SST_wet [µatm]	31 pCO2water_SST_wet [µatm]	32 [HCO3]- [µmol/kg]	33 [CO3]2- [µmol/kg]	34 Omega Arg	35 Omega Cal
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	Ambient	1	2090	75.0	111.0	4.88	2020	84.3	1890	81.2	1.690	0.0734	2.690	0.118	364	20.3	8.06	0.0201	31.3	0.126	7.39	1.09	15	7.83	30.75	627.93	630.45	1923.02	66.23	1.01	1.61
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	Ambient	2	2090	81.6	107.0	3.59	2010	82.6	1890	80.9	1.630	0.0554	2.600	0.087	375	20.0	8.05	0.0137	31.2	0.202	7.28	1.07	15	7.87	28.17	572.76	575.06	1910.67	71.16	1.09	1.73
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	Ambient	3	2080	83.4	107.0	6.16	2020	80.1	1890	76.0	1.640	0.0930	2.600	0.149	378	24.6	8.05	0.0274	31.3	0.129	7.39	1.13	15	7.80	33.34	680.78	683.51	1925.42	61.24	0.94	1.49
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	Ambient	9	2090	79.4	110.0	6.49	2010	79.8	1880	75.7	1.680	0.0970	2.670	0.157	368	30.7	8.06	0.0335	31.3	0.119	7.46	1.13	15	7.87	28.26	578.49	580.80	1910.54	71.20	1.09	1.73
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	Ambient	14	2090	79.6	110.0	8.46	2010	83.1	1880	78.7	1.680	0.1270	2.670	0.205	368	36.6	8.06	0.0400	31.3	0.143	7.48	1.13	15	7.87	28.26	578.98	581.29	1910.53	71.20	1.09	1.73
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	pH 7.8	5	2100	59.9	63.8	13.60	2060	53.1	1960	48.8	0.976	0.2070	1.550	0.329	700	126.0	7.80	0.0825	31.2	0.176	7.39	1.15	15	7.73	40.25	821.54	824.83	1966.90	52.85	0.81	1.29
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	pH 7.8	10	2100	49.6	62.2	8.02	2060	47.6	1960	48.1	0.952	0.1240	1.510	0.196	714	114.0	7.79	0.0578	31.3	0.123	7.51	1.14	15	7.72	40.34	827.26	830.57	1966.77	52.89	0.81	1.29
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	pH 7.8	11	2100	66.1	61.2	4.68	2060	50.7	1970	49.0	0.936	0.0718	1.490	0.114	717	60.4	7.79	0.0348	31.3	0.200	7.38	1.19	15	7.73	40.31	822.86	826.16	1966.85	52.85	0.81	1.29
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	pH 7.8	12	2100	52.8	62.7	2.59	2060	59.9	1960	58.8	0.960	0.0405	1.530	0.063	697	38.1	7.80	0.0192	31.3	0.134	7.54	1.18	15	7.72	40.35	828.28	831.59	1966.76	52.90	0.81	1.29
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	pH 7.8	15	2100	56.5	64.1	11.10	2060	52.1	1960	48.2	0.980	0.1690	1.560	0.269	693	96.1	7.81	0.0682	31.3	0.119	7.44	1.13	15	7.73	40.32	824.89	828.19	1966.81	52.86	0.81	1.29
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	pH 7.5	4	2110	51.1	37.4	18.70	2100	41.5	2000	37.7	0.571	0.2850	0.909	0.455	1350	304.0	7.54	0.1490	31.3	0.124	7.45	1.11	15	7.61	53.20	1088.78	1093.13	2005.15	41.65	0.64	1.01
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	pH 7.5	6	2100	52.9	36.4	20.20	2090	79.3	1980	72.5	0.556	0.3070	0.885	0.490	1400	403.0	7.52	0.1670	31.3	0.193	7.43	1.21	15	7.61	52.97	1083.24	1087.58	1995.61	41.42	0.63	1.01
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	pH 7.5	7	2110	38.4	31.7	4.87	2110	15.1	2010	14.2	0.485	0.0750	0.771	0.119	1460	171.0	7.49	0.0557	31.3	0.119	7.44	1.13	15	7.58	58.23	1191.17	1195.94	2013.41	38.36	0.59	0.93
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	pH 7.5	8	2120	20.6	32.6	7.60	2110	15.5	2010	19.9	0.499	0.1160	0.794	0.185	1480	373.0	7.49	0.1030	31.3	0.110	7.57	1.09	15	7.61	53.47	1098.68	1103.07	2014.63	41.90	0.64	1.02
laboratory	Paralithodes camtschaticus	marinespecies.org	urn:lsid:marinespecies.org:taxname:233889	pH 7.5	13	2130	25.3	31.8	2.02	2100	60.1	2000	56.2	0.487	0.0315	0.774	0.049	1430	84.2	7.50	0.0191	31.4	0.235	7.44	1.14	15	7.69	44.87	918.47	922.15	2005.65	49.47	0.76	1.20