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Timmers, Molly A; Jury, Christopher P; Vicente, Jan; Bahr, Keisha D; Webb, M; Toonen, Robert J (2021): Seawater carbonate chemistry and biodiversity of coral reef cryptobiota [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.942812

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Abstract:
Ocean-warming and acidification are predicted to reduce coral reef biodiversity, but the combined effects of these stressors on overall biodiversity are largely unmeasured. Here, we examined the individual and combined effects of elevated temperature (+2 °C) and reduced pH (−0.2 units) on the biodiversity of coral reef communities that developed on standardized sampling units over a 2-y mesocosm experiment. Biodiversity and species composition were measured using amplicon sequencing libraries targeting the cytochrome oxidase I (COI) barcoding gene. Ocean-warming significantly increased species richness relative to present-day control conditions, whereas acidification significantly reduced richness. Contrary to expectations, species richness in the combined future ocean treatment with both warming and acidification was not significantly different from the present-day control treatment. Rather than the predicted collapse of biodiversity under the dual stressors, we find significant changes in the relative abundance but not in the occurrence of species, resulting in a shuffling of coral reef community structure among the highly species-rich cryptobenthic community. The ultimate outcome of altered community structure for coral reef ecosystems will depend on species-specific ecological functions and community interactions. Given that most species on coral reefs are members of the understudied cryptobenthos, holistic research on reef communities is needed to accurately predict diversity–function relationships and ecosystem responses to future climate conditions.
Keyword(s):
Benthos; Coast and continental shelf; Community composition and diversity; Containers and aquaria (20-1000 L or < 1 m**2); Entire community; Laboratory experiment; North Pacific; Rocky-shore community; Temperature; Tropical
Supplement to:
Timmers, Molly A; Jury, Christopher P; Vicente, Jan; Bahr, Keisha D; Webb, M; Toonen, Robert J (2021): Biodiversity of coral reef cryptobiota shuffles but does not decline under the combined stressors of ocean warming and acidification. Proceedings of the National Academy of Sciences, 118(39), https://doi.org/10.1073/pnas.2103275118
Further details:
Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James (2021): seacarb: seawater carbonate chemistry with R. R package version 3.2.16. https://cran.r-project.org/web/packages/seacarb/index.html
Comment:
In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) 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 2022-03-30.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
TypeTypeTimmers, Molly Astudy
TreatmentTreatTimmers, Molly A
IdentificationIDTimmers, Molly AARMS Unit
IdentificationIDTimmers, Molly AMesocosm Name
Number of sequencesSequence no#Timmers, Molly ARaw
Number of sequencesSequence no#Timmers, Molly APost Filtration
Number of sequencesSequence no#Timmers, Molly AMetazoa & Macroalgae
Number of sequencesSequence no#Timmers, Molly AClassified to Phylum
Number of sequencesSequence no#Timmers, Molly APost Rarefied
10 Operational taxonomic unitOTU#Timmers, Molly ARaw
11 Operational taxonomic unitOTU#Timmers, Molly APost Filtration
12 Operational taxonomic unitOTU#Timmers, Molly AMetazoa & Macroalgae
13 Operational taxonomic unitOTU#Timmers, Molly AClassified to Phylum
14 Species richnessSTimmers, Molly Atotal
15 PhylumPhylumTimmers, Molly A
16 ReadsReads#Timmers, Molly Aphlya
17 AbundanceAbundTimmers, Molly ARelative, phlya reads
18 ProportionPropTimmers, Molly APhlya reads relative to Control
19 Operational taxonomic unitOTU#Timmers, Molly A
20 AbundanceAbundTimmers, Molly ARelative, MOTUs
21 ProportionPropTimmers, Molly AMOTUs relative to Control
22 SalinitySalTimmers, Molly A
23 Salinity, standard deviationSal std dev±Timmers, Molly A
24 Temperature, waterTemp°CTimmers, Molly A
25 Temperature, water, standard deviationTemp std dev±Timmers, Molly A
26 pHpHTimmers, Molly ASpectrophotometrictotal scale
27 pH, standard deviationpH std dev±Timmers, Molly ASpectrophotometrictotal scale
28 Alkalinity, totalATµmol/kgTimmers, Molly APotentiometric titration
29 Alkalinity, total, standard deviationAT std dev±Timmers, Molly APotentiometric titration
30 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmTimmers, Molly ACalculated using CO2SYS
31 Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Timmers, Molly ACalculated using CO2SYS
32 Aragonite saturation stateOmega ArgTimmers, Molly ACalculated using CO2SYS
33 Aragonite saturation state, standard deviationOmega Arg std dev±Timmers, Molly ACalculated using CO2SYS
34 Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
35 Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
36 Carbon dioxide, standard deviationCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
37 Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
38 Fugacity of carbon dioxide in seawater, standard deviationfCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
39 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
40 Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
41 Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
42 Bicarbonate ion, standard deviation[HCO3]- std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
43 Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
44 Carbonate ion, standard deviation[CO3]2- std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
45 Carbon, inorganic, dissolvedDICµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
46 Carbon, inorganic, dissolved, standard deviationDIC std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
47 Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
48 Aragonite saturation state, standard deviationOmega Arg std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
49 Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
50 Calcite saturation state, standard deviationOmega Cal std dev±Yang, YanCalculated using seacarb after Orr et al. (2018)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
2010 data points

Data

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


Type
(study)

Treat

ID
(ARMS Unit)

ID
(Mesocosm Name)

Sequence no [#]
(Raw)

Sequence no [#]
(Post Filtration)

Sequence no [#]
(Metazoa & Macroalgae)

Sequence no [#]
(Classified to Phylum)

Sequence no [#]
(Post Rarefied)
10 
OTU [#]
(Raw)
11 
OTU [#]
(Post Filtration)
12 
OTU [#]
(Metazoa & Macroalgae)
13 
OTU [#]
(Classified to Phylum)
14 
S
(total)
15 
Phylum
16 
Reads [#]
(phlya)
17 
Abund
(Relative, phlya reads)
18 
Prop
(Phlya reads relative to Control)
19 
OTU [#]
20 
Abund
(Relative, MOTUs)
21 
Prop
(MOTUs relative to Control)
22 
Sal
23 
Sal std dev [±]
24 
Temp [°C]
25 
Temp std dev [±]
26 
pH
(total scale, Spectrophotometric)
27 
pH std dev [±]
(total scale, Spectrophotometric)
28 
AT [µmol/kg]
(Potentiometric titration)
29 
AT std dev [±]
(Potentiometric titration)
30 
pCO2water_SST_wet [µatm]
(Calculated using CO2SYS)
31 
pCO2 std dev [±]
(Calculated using CO2SYS)
32 
Omega Arg
(Calculated using CO2SYS)
33 
Omega Arg std dev [±]
(Calculated using CO2SYS)
34 
CSC flag
(Calculated using seacarb afte...)
35 
CO2 [µmol/kg]
(Calculated using seacarb afte...)
36 
CO2 std dev [±]
(Calculated using seacarb afte...)
37 
fCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)
38 
fCO2 std dev [±]
(Calculated using seacarb afte...)
39 
pCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)
40 
pCO2 std dev [±]
(Calculated using seacarb afte...)
41 
[HCO3]- [µmol/kg]
(Calculated using seacarb afte...)
42 
[HCO3]- std dev [±]
(Calculated using seacarb afte...)
43 
[CO3]2- [µmol/kg]
(Calculated using seacarb afte...)
44 
[CO3]2- std dev [±]
(Calculated using seacarb afte...)
45 
DIC [µmol/kg]
(Calculated using seacarb afte...)
46 
DIC std dev [±]
(Calculated using seacarb afte...)
47 
Omega Arg
(Calculated using seacarb afte...)
48 
Omega Arg std dev [±]
(Calculated using seacarb afte...)
49 
Omega Cal
(Calculated using seacarb afte...)
50 
Omega Cal std dev [±]
(Calculated using seacarb afte...)
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laboratoryControl2Control177925278290543904385716137613208119818134.240.3525.101.247.990.06217654447612.880.34812.502.15439.6974.14441.1074.381729.5568.36180.2821.341922.3359.642.880.354.370.52
laboratoryControl3Control234193941552345042053916133417154103656534.240.3525.101.247.990.06217654447612.880.34812.502.15439.6974.14441.1074.381729.5568.36180.2821.341922.3359.642.880.354.370.52
laboratoryControl4Control26133359131426875866935616133800217120828234.240.3525.101.247.990.06217654447612.880.34812.502.15439.6974.14441.1074.381729.5568.36180.2821.341922.3359.642.880.354.370.52
laboratoryControl5Control91885371860781218698438416131790183106636334.240.3525.101.247.990.06217654447612.880.34812.502.15439.6974.14441.1074.381729.5568.36180.2821.341922.3359.642.880.354.370.52
laboratoryAcidified6Acid1147690146290102861902111613359013874474734.240.3525.121.237.780.072184517981281.930.30822.084.14777.11143.69779.59144.151884.5762.58121.2117.742027.8757.071.930.292.940.43
laboratoryAcidified7Acid15589715845047430382231613342113072494934.240.3525.121.237.780.072184517981281.930.30822.084.14777.11143.69779.59144.151884.5762.58121.2117.742027.8757.071.930.292.940.43
laboratoryAcidified8Acid25230802281016867161321613237216189595934.240.3525.121.237.780.072184517981281.930.30822.084.14777.11143.69779.59144.151884.5762.58121.2117.742027.8757.071.930.292.940.43
laboratoryAcidified9Acid3613675013507496455619681613162914485565634.240.3525.121.237.780.072184517981281.930.30822.084.14777.11143.69779.59144.151884.5762.58121.2117.742027.8757.071.930.292.940.43
laboratoryAcidified10Acid39871378631174351510371613548913480545434.240.3525.121.237.780.072184517981281.930.30822.084.14777.11143.69779.59144.151884.5762.58121.2117.742027.8757.071.930.292.940.43
laboratoryAcidified11Acid7760797535159197545731613245312967434334.240.3525.121.237.780.072184517981281.930.30822.084.14777.11143.69779.59144.151884.5762.58121.2117.742027.8757.071.930.292.940.43
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laboratoryHeated13Heat22108989107753946828723216132637185123909034.270.3527.051.207.980.06218851455623.060.35812.272.12453.0676.79454.4877.031722.1967.77188.5121.961922.9757.743.040.364.580.54
laboratoryHeated14Heat3329916325855237876133258161351084226157979734.270.3527.051.207.980.06218851455623.060.35812.272.12453.0676.79454.4877.031722.1967.77188.5121.961922.9757.743.040.364.580.54
laboratoryHeated15Heat3148960648318542986234806616132116421614610110134.270.3527.051.207.980.06218851455623.060.35812.272.12453.0676.79454.4877.031722.1967.77188.5121.961922.9757.743.040.364.580.54
laboratoryHeated16Heat821738821445219715815314316133884223134939334.270.3527.051.207.980.06218851455623.060.35812.272.12453.0676.79454.4877.031722.1967.77188.5121.961922.9757.743.040.364.580.54
laboratoryAcidified-Heated17AcidHeat16864868558839209348501613050115977505034.270.3527.111.507.770.072197508191292.060.31821.744.11803.75149.31806.26149.781883.1963.56127.3818.812032.3056.912.050.313.100.46
laboratoryAcidified-Heated18AcidHeat206935368626480104312116137493199109787834.270.3527.111.507.770.072197508191292.060.31821.744.11803.75149.31806.26149.781883.1963.56127.3818.812032.3056.912.050.313.100.46
laboratoryAcidified-Heated19AcidHeat213595735738309172635816127307167109818134.270.3527.111.507.770.072197508191292.060.31821.744.11803.75149.31806.26149.781883.1963.56127.3818.812032.3056.912.050.313.100.46
laboratoryAcidified-Heated20AcidHeat24107760106702787065825716132541179115808034.270.3527.111.507.770.072197508191292.060.31821.744.11803.75149.31806.26149.781883.1963.56127.3818.812032.3056.912.050.313.100.46
laboratoryAcidified-Heated21AcidHeat33710967037466717351471613548014399636334.270.3527.111.507.770.072197508191292.060.31821.744.11803.75149.31806.26149.781883.1963.56127.3818.812032.3056.912.050.313.100.46
laboratoryAcidified-Heated22AcidHeat41762101742431401631280791613270116294575734.270.3527.111.507.770.072197508191292.060.31821.744.11803.75149.31806.26149.781883.1963.56127.3818.812032.3056.912.050.313.100.46
laboratoryControlAnnelida2616628.671.004764.381.0034.240.3525.101.247.990.06217654447612.880.34812.502.15439.6974.14441.1074.381729.5568.36180.2821.341922.3359.642.880.354.370.52
laboratoryAcidifiedAnnelida2675829.321.022838.360.6034.240.3525.121.237.780.072184517981281.930.30822.084.14777.11143.69779.59144.151884.5762.58121.2117.742027.8757.071.930.292.940.43
laboratoryHeatedAnnelida1841220.180.705676.711.1934.270.3527.051.207.980.06218851455623.060.35812.272.12453.0676.79454.4877.031722.1967.77188.5121.961922.9757.743.040.364.580.54
laboratoryAcidified-HeatedAnnelida1992521.830.764663.010.9834.270.3527.111.507.770.072197508191292.060.31821.744.11803.75149.31806.26149.781883.1963.56127.3818.812032.3056.912.050.313.100.46
laboratoryControlArthropoda354911.311.0033501.0034.240.3525.101.247.990.06217654447612.880.34812.502.15439.6974.14441.1074.381729.5568.36180.2821.341922.3359.642.880.354.370.52
laboratoryAcidifiedArthropoda1142736.423.223146.970.9434.240.3525.121.237.780.072184517981281.930.30822.084.14777.11143.69779.59144.151884.5762.58121.2117.742027.8757.071.930.292.940.43
laboratoryHeatedArthropoda673821.481.904162.121.2434.270.3527.051.207.980.06218851455623.060.35812.272.12453.0676.79454.4877.031722.1967.77188.5121.961922.9757.743.040.364.580.54
laboratoryAcidified-HeatedArthropoda965830.792.723857.581.1534.270.3527.111.507.770.072197508191292.060.31821.744.11803.75149.31806.26149.781883.1963.56127.3818.812032.3056.912.050.313.100.46
laboratoryControlCnidaria401128.851.001052.631.0034.240.3525.101.247.990.06217654447612.880.34812.502.15439.6974.14441.1074.381729.5568.36180.2821.341922.3359.642.880.354.370.52
laboratoryAcidifiedCnidaria339124.390.85631.580.6034.240.3525.121.237.780.072184517981281.930.30822.084.14777.11143.69779.59144.151884.5762.58121.2117.742027.8757.071.930.292.940.43
laboratoryHeatedCnidaria359725.870.901263.161.2034.270.3527.051.207.980.06218851455623.060.35812.272.12453.0676.79454.4877.031722.1967.77188.5121.961922.9757.743.040.364.580.54
laboratoryAcidified-HeatedCnidaria290320.880.72842.110.8034.270.3527.111.507.770.072197508191292.060.31821.744.11803.75149.31806.26149.781883.1963.56127.3818.812032.3056.912.050.313.100.46
laboratoryControlEchinodermata982218.041.001090.911.0034.240.3525.101.247.990.06217654447612.880.34812.502.15439.6974.14441.1074.381729.5568.36180.2821.341922.3359.642.880.354.370.52
laboratoryAcidifiedEchinodermata2073638.12.11111001.1034.240.3525.121.237.780.072184517981281.930.30822.084.14777.11143.69779.59144.151884.5762.58121.2117.742027.8757.071.930.292.940.43
laboratoryHeatedEchinodermata589410.830.60111001.1034.270.3527.051.207.980.06218851455623.060.35812.272.12453.0676.79454.4877.031722.1967.77188.5121.961922.9757.743.040.364.580.54
laboratoryAcidified-HeatedEchinodermata1797933.031.831090.911.0034.270.3527.111.507.770.072197508191292.060.31821.744.11803.75149.31806.26149.781883.1963.56127.3818.812032.3056.912.050.313.100.46
laboratoryControlMollusca1312022.861.001562.51.0034.240.3525.101.247.990.06217654447612.880.34812.502.15439.6974.14441.1074.381729.5568.36180.2821.341922.3359.642.880.354.370.52
laboratoryAcidifiedMollusca55269.630.421354.170.8734.240.3525.121.237.780.072184517981281.930.30822.084.14777.11143.69779.59144.151884.5762.58121.2117.742027.8757.071.930.292.940.43
laboratoryHeatedMollusca2592945.171.982291.671.4734.270.3527.051.207.980.06218851455623.060.35812.272.12453.0676.79454.4877.031722.1967.77188.5121.961922.9757.743.040.364.580.54
laboratoryAcidified-HeatedMollusca1282422.340.981354.170.8734.270.3527.111.507.770.072197508191292.060.31821.744.11803.75149.31806.26149.781883.1963.56127.3818.812032.3056.912.050.313.100.46
laboratoryControlPorifera1988634.261.001843.91.0034.240.3525.101.247.990.06217654447612.880.34812.502.15439.6974.14441.1074.381729.5568.36180.2821.341922.3359.642.880.354.370.52
laboratoryAcidifiedPorifera1258221.670.632048.781.1134.240.3525.121.237.780.072184517981281.930.30822.084.14777.11143.69779.59144.151884.5762.58121.2117.742027.8757.071.930.292.940.43
laboratoryHeatedPorifera1650828.440.832970.731.6134.270.3527.051.207.980.06218851455623.060.35812.272.12453.0676.79454.4877.031722.1967.77188.5121.961922.9757.743.040.364.580.54
laboratoryAcidified-HeatedPorifera907515.630.461946.341.0634.270.3527.111.507.770.072197508191292.060.31821.744.11803.75149.31806.26149.781883.1963.56127.3818.812032.3056.912.050.313.100.46
laboratoryControlRhodophyta382524.981.001753.131.0034.240.3525.101.247.990.06217654447612.880.34812.502.15439.6974.14441.1074.381729.5568.36180.2821.341922.3359.642.880.354.370.52
laboratoryAcidifiedRhodophyta1551.010.04515.630.2934.240.3525.121.237.780.072184517981281.930.30822.084.14777.11143.69779.59144.151884.5762.58121.2117.742027.8757.071.930.292.940.43
laboratoryHeatedRhodophyta354223.130.932578.131.4734.270.3527.051.207.980.06218851455623.060.35812.272.12453.0676.79454.4877.031722.1967.77188.5121.961922.9757.743.040.364.580.54
laboratoryAcidified-HeatedRhodophyta779250.882.041959.381.1234.270.3527.111.507.770.072197508191292.060.31821.744.11803.75149.31806.26149.781883.1963.56127.3818.812032.3056.912.050.313.100.46