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Fujii, Masahiko; Ono, Tsuneo; Yamada, M; Ooue, Manabu; Ito, Takeru; Yang, Jen‑Han; Horiuchi, Yu; Oiwane, Hisashi; Wakita, Masahide; Wada, Shigeki (2025): Seawater carbonate chemistry and biodiversity of shallow-water CO2 seeps on Himeshima Island and Showa Iwojima Island, Japan [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.988343

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

Published: 2025-12-29DOI registered: 2026-01-27

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Abstract:
This study is the first to investigate two shallow-water CO2 seeps near Japan from the perspective of ocean acidification. Seawater chemical properties and composition of benthic communities were investigated.
This dataset is included in the OA-ICC data compilation maintained in the framework of the IAEA Ocean Acidification International Coordination Centre (see https://oa-icc.ipsl.fr). Original data were provided by the author of the related paper (see Related to) to the OA-ICC data curator. 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 2025-12-29.
Keyword(s):
Benthos; CO2 vent; Coast and continental shelf; Community composition and diversity; Entire community; Field experiment; North Pacific; Rocky-shore community; Temperate
Related to:
Fujii, Masahiko; Ono, Tsuneo; Yamada, M; Ooue, Manabu; Ito, Takeru; Yang, Jen‑Han; Horiuchi, Yu; Oiwane, Hisashi; Wakita, Masahide; Wada, Shigeki (2025): Biogeochemical properties of shallow-water CO2 seeps on Himeshima Island and Showa Iwojima Island, Japan. Progress in Earth and Planetary Science, 12(1), 101, https://doi.org/10.1186/s40645-025-00772-w
References:
Nisumaa, Anne-Marin; Pesant, Stephane; Bellerby, Richard G J; Delille, Bruno; Middelburg, Jack J; Orr, James C; Riebesell, Ulf; Tyrrell, Toby; Wolf-Gladrow, Dieter A; Gattuso, Jean-Pierre (2010): EPOCA/EUR-OCEANS data compilation on the biological and biogeochemical responses to ocean acidification. Earth System Science Data, 2(2), 167-175, https://doi.org/10.5194/essd-2-167-2010
Yang, Yan; Brockmann, Patrick; Galdino, Carolina; Schindler, Uwe; Gazeau, Frédéric (2024): An update of data compilation on the biological response to ocean acidification and overview of the OA-ICC data portal. Earth System Science Data, 16(8), 3771-3780, https://doi.org/10.5194/essd-16-3771-2024
Yang, Yan; Hansson, L; Gattuso, Jean-Pierre (2016): Data compilation on the biological response to ocean acidification: an update. Earth System Science Data, 8(1), 79-87, https://doi.org/10.5194/essd-8-79-2016
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
Funding:
Japan Society for the Promotion of Science (JSPS), grant/award no. 22H00555: Kakenhi
Japan Society for the Promotion of Science (JSPS), grant/award no. JPJSCCA20210006: International CO2 Natural Analogues Network (ICONA)
Coverage:
Median Latitude: 32.266210 * Median Longitude: 130.990610 * South-bound Latitude: 30.803420 * West-bound Longitude: 130.340390 * North-bound Latitude: 33.729000 * East-bound Longitude: 131.640830
Date/Time Start: 2024-08-20T00:00:00 * Date/Time End: 2024-12-02T00:00:00
Event(s):
Himeshima_CO2_seep * Latitude: 33.729000 * Longitude: 131.640830 * Date/Time Start: 2024-08-20T00:00:00 * Date/Time End: 2024-08-20T00:00:00
Showa_Iwojima_CO2_seep * Latitude: 30.803420 * Longitude: 130.340390 * Date/Time Start: 2024-12-01T00:00:00 * Date/Time End: 2024-12-02T00:00:00
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
Type of studyStudy typeFujii, Masahiko
DateDateFujii, Masahiko
SiteSiteFujii, Masahiko
DistanceDistancemFujii, Masahikofrom CO2 seep
CoverageCov%Fujii, MasahikoS. macrocarpum
CoverageCov%Fujii, MasahikoM. myagroides
CoverageCov%Fujii, MasahikoBare rock
CoverageCov%Fujii, MasahikoCrustose coralline algae
CoverageCov%Fujii, MasahikoS. micracanthum
10 CoverageCov%Fujii, MasahikoS. ringgoldianum
11 CoverageCov%Fujii, MasahikoP. arborescens
12 CoverageCov%Fujii, MasahikoUnidentified algae
13 CoverageCov%Fujii, MasahikoOthers
14 CoverageCov%Fujii, MasahikoTurf algae
15 CoverageCov%Fujii, MasahikoCorals
16 CoverageCov%Fujii, MasahikoLow-profile algae
17 CoverageCov%Fujii, MasahikoUrchin
18 CoverageCov%Fujii, MasahikoWhite mat
19 CoverageCov%Fujii, MasahikoSponge
20 CoverageCov%Fujii, MasahikoSand
21 SalinitySalFujii, Masahiko
22 Temperature, waterTemp°CFujii, Masahiko
23 pH, total scalepHTFujii, Masahiko
24 Dry air column-averaged mole fraction of carbon dioxideXCO2ppmvFujii, Masahikodry at 1 atm
25 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmFujii, MasahikoCalculated using CO2SYS
26 Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmFujii, MasahikoCalculated using CO2SYS
27 Bicarbonate ion[HCO3]-µmol/kgFujii, MasahikoCalculated using CO2SYS
28 Carbonate ion[CO3]2-µmol/kgFujii, MasahikoCalculated using CO2SYS
29 Carbon, inorganic, dissolvedDICµmol/kgFujii, MasahikoCalculated using CO2SYS
30 Alkalinity, totalATµmol/kgFujii, Masahiko
31 Aragonite saturation stateOmega ArgFujii, MasahikoCalculated using CO2SYS
32 Calcite saturation stateOmega CalFujii, MasahikoCalculated using CO2SYS
33 Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
34 Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
35 Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
36 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
37 Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
38 Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
39 Carbon, inorganic, dissolvedDICµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
40 Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
41 Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
1999 data points

Data

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


Study type

Date

Site

Distance [m]
(from CO2 seep)

Cov [%]
(S. macrocarpum)

Cov [%]
(M. myagroides)

Cov [%]
(Bare rock)

Cov [%]
(Crustose coralline algae)

Cov [%]
(S. micracanthum)
10 
Cov [%]
(S. ringgoldianum)
11 
Cov [%]
(P. arborescens)
12 
Cov [%]
(Unidentified algae)
13 
Cov [%]
(Others)
14 
Cov [%]
(Turf algae)
15 
Cov [%]
(Corals)
16 
Cov [%]
(Low-profile algae)
17 
Cov [%]
(Urchin)
18 
Cov [%]
(White mat)
19 
Cov [%]
(Sponge)
20 
Cov [%]
(Sand)
21 
Sal
22 
Temp [°C]
23 
pHT
24 
XCO2 [ppmv]
(dry at 1 atm)
25 
pCO2water_SST_wet [µatm]
(Calculated using CO2SYS)
26 
fCO2water_SST_wet [µatm]
(Calculated using CO2SYS)
27 
[HCO3]- [µmol/kg]
(Calculated using CO2SYS)
28 
[CO3]2- [µmol/kg]
(Calculated using CO2SYS)
29 
DIC [µmol/kg]
(Calculated using CO2SYS)
30 
AT [µmol/kg]
31 
Omega Arg
(Calculated using CO2SYS)
32 
Omega Cal
(Calculated using CO2SYS)
33 
CSC flag
(Calculated using seacarb afte...)
34 
CO2 [µmol/kg]
(Calculated using seacarb afte...)
35 
fCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)
36 
pCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)
37 
[HCO3]- [µmol/kg]
(Calculated using seacarb afte...)
38 
[CO3]2- [µmol/kg]
(Calculated using seacarb afte...)
39 
DIC [µmol/kg]
(Calculated using seacarb afte...)
40 
Omega Arg
(Calculated using seacarb afte...)
41 
Omega Cal
(Calculated using seacarb afte...)
field2024-08-20Himeshima Island0.01.21251.85924.8600.0007.9180.0006.1140.0000.1417.89632.42822.9927.89596.76580.53578.631816.03133.041966.612146.842.123.26817.53578.28580.171817.75133.381968.652.133.27
field2024-08-20Himeshima Island1.032.44523.0037.89594.66578.47576.581815.61133.561966.642147.712.133.27817.52578.44580.341818.26133.531969.312.133.27
field2024-08-20Himeshima Island2.032.42723.0017.91572.16556.58554.761805.56137.221959.592146.792.193.36816.61548.27550.071804.56138.691959.862.213.40
field2024-08-20Himeshima Island3.032.42623.0077.90584.57568.65566.791810.76135.121963.052146.742.163.31817.06563.08564.931811.05136.051964.152.173.33
field2024-08-20Himeshima Island4.032.42422.9877.93530.93516.49514.801786.73144.711947.042146.632.313.54815.75519.66521.361791.11144.061950.922.303.53
field2024-08-20Himeshima Island5.032.42522.9967.94519.56505.42503.771781.06147.001943.332146.682.353.60815.33505.88507.541784.14146.901946.372.353.60
field2024-08-20Himeshima Island5.832.42522.9887.94524.00509.75508.081783.36146.081944.842146.682.333.58815.33505.88507.541784.23146.861946.422.343.60
field2024-08-20Himeshima Island10.08.71024.19249.9660.0000.0000.0007.0870.1710.0009.87432.42622.9687.96490.39477.06475.501766.21152.971933.602146.742.443.75814.54479.30480.871770.38152.481937.392.433.73
field2024-08-20Himeshima Island12.032.42522.9667.97486.95473.72472.171764.32153.711932.352146.682.453.76814.15466.47468.001763.14155.381932.672.483.81
field2024-08-20Himeshima Island14.032.42322.9697.97482.02468.92467.391761.50154.801930.472146.582.473.79814.15466.46467.991763.04155.381932.562.483.81
field2024-08-20Himeshima Island16.032.42422.9667.97479.39466.37464.851760.10155.381929.582146.632.483.80814.15466.46467.991763.11155.371932.632.483.80
field2024-08-20Himeshima Island18.032.42422.9697.98473.81460.93459.431756.90156.661927.492146.632.503.84813.77453.95455.441755.75158.341927.862.533.88
field2024-08-20Himeshima Island20.032.42022.9717.98472.30459.46457.961755.89156.981926.762146.432.513.84813.77453.92455.411755.59158.331927.682.533.88
field2024-08-20Himeshima Island22.032.42222.9757.98469.73456.97455.471754.43157.611925.852146.532.523.86813.76453.94455.431755.61158.361927.732.533.88
field2024-08-20Himeshima Island24.032.42422.9647.98467.54454.84453.351753.35158.091925.182146.632.523.87813.77453.95455.441755.81158.321927.892.533.88
field2024-08-20Himeshima Island26.032.42222.9707.98462.79450.21448.741750.43159.211923.252146.532.543.90813.77453.94455.431755.67158.331927.772.533.88
field2024-08-20Himeshima Island28.032.42022.9737.98462.05449.49448.021749.90159.391922.872146.432.543.90813.76453.92455.411755.57158.341927.672.533.88
field2024-08-20Himeshima Island30.011.57330.78428.2910.10214.7270.4426.9430.2650.0006.87132.41722.9777.98461.67449.12447.651749.53159.471922.582146.282.553.90813.76453.90455.391755.42158.331927.522.533.88
field2024-08-20Himeshima Island32.032.42022.9657.98462.04449.49448.021749.99159.351922.932146.432.543.90813.77453.92455.411755.66158.301927.732.533.88
field2024-08-20Himeshima Island34.032.42022.9637.98462.41449.85448.381750.23159.251923.082146.432.543.90813.77453.92455.411755.68158.291927.742.533.88
field2024-08-20Himeshima Island36.032.42122.9607.98463.14450.56449.091750.72159.071923.422146.482.543.89813.77453.93455.421755.75158.281927.802.533.88
field2024-08-20Himeshima Island38.032.42022.9517.99459.15446.68445.221748.43159.971921.912146.432.553.92813.40441.72443.171748.39161.231923.022.573.95
field2024-08-20Himeshima Island40.032.42122.9437.99459.43446.96445.501748.73159.871922.122146.482.553.91813.40441.73443.181748.52161.201923.122.573.95
field2024-08-20Himeshima Island42.032.41922.9367.99458.33445.90444.441748.10160.081921.672146.382.553.92813.41441.71443.161748.54161.151923.092.573.95
field2024-08-20Himeshima Island45.032.42422.9257.99456.92444.54443.081747.53160.411921.392146.632.563.93813.41441.75443.201748.83161.131923.372.573.95
field2024-08-20Himeshima Island48.032.42422.9057.99457.99445.59444.131748.41160.051921.962146.632.553.92813.42441.75443.211749.06161.031923.522.573.94
field2024-08-20Himeshima Island49.032.42822.8957.99460.90448.43446.961750.39159.341923.312146.842.543.90813.42441.78443.241749.32161.011923.762.573.94
field2024-08-20Himeshima Island50.032.42022.9127.99456.32443.97442.511747.21160.451921.102146.432.563.93813.42441.73443.181748.85161.041923.312.573.94
field2024-08-20Himeshima Island50.027.28630.0581.3330.00014.5530.15424.0360.0000.0002.58132.42322.9137.99455.63443.29441.841746.87160.651920.942146.582.563.93813.42441.75443.201748.94161.071923.422.573.94
field2024-08-20Himeshima Island50.032.42522.9177.99455.28442.95441.501746.67160.771920.852146.682.573.94813.41441.76443.211748.96161.101923.472.573.94
field2024-08-20Himeshima Island51.032.42122.9097.99456.33443.97442.521747.28160.441921.172146.482.563.93813.42441.73443.181748.92161.031923.372.573.94
field2024-08-20Himeshima Island52.032.41722.9147.99457.74445.34443.881747.95160.101921.522146.282.553.92813.41441.71443.161748.73161.031923.172.573.94
field2024-08-20Himeshima Island53.032.41622.9157.99456.65444.29442.831747.26160.351921.062146.222.563.93813.41441.70443.151748.67161.031923.112.573.94
field2024-08-20Himeshima Island54.032.42122.9077.99455.25442.93441.481746.66160.691920.762146.482.563.93813.42441.73443.191748.94161.021923.382.573.94
field2024-08-20Himeshima Island55.032.42122.9087.99455.61443.28441.831746.86160.611920.892146.482.563.93813.42441.73443.181748.93161.031923.382.573.94
field2024-08-20Himeshima Island56.032.42022.9087.99455.60443.27441.821746.83160.611920.852146.432.563.93813.42441.73443.181748.90161.021923.342.573.94
field2024-08-20Himeshima Island57.032.42422.9017.99454.47442.17440.731746.35160.881920.622146.632.573.94813.42441.76443.211749.11161.011923.552.573.94
field2024-08-20Himeshima Island58.032.42622.8997.99454.48442.19440.741746.44160.881920.712146.742.573.94813.42441.77443.221749.21161.021923.652.573.94
field2024-08-20Himeshima Island59.032.41622.9087.99457.64445.26443.801747.93160.081921.492146.222.553.92813.42441.70443.151748.76160.991923.172.573.94
field2024-08-20Himeshima Island60.032.42222.8977.99454.46442.16440.711746.33160.851920.562146.532.573.94813.42441.74443.191749.09160.981923.492.573.94
field2024-08-20Himeshima Island62.032.42222.8977.99455.89443.55442.101747.19160.501921.122146.532.563.93813.42441.74443.191749.09160.981923.492.573.94
field2024-08-20Himeshima Island63.032.42122.8967.99453.74441.46440.021745.87161.011920.252146.482.573.94813.42441.74443.191749.07160.971923.462.573.94
field2024-08-20Himeshima Island64.032.42322.8977.99454.11441.82440.381746.14160.941920.462146.582.573.94813.42441.75443.201749.13160.991923.532.573.94
field2024-08-20Himeshima Island65.032.42322.8977.99452.68440.43438.991745.28161.291919.902146.582.573.95813.42441.75443.201749.13160.991923.532.573.94
field2024-08-20Himeshima Island66.032.42422.8947.99453.04440.79439.351745.56161.191920.112146.632.573.95813.42441.76443.211749.19160.981923.602.573.94
field2024-08-20Himeshima Island67.032.42322.8957.99455.53443.21441.761747.03160.581921.042146.582.563.93813.42441.75443.201749.15160.981923.552.573.94
field2024-08-20Himeshima Island68.032.42422.8927.99454.11441.83440.381746.24160.921920.542146.632.573.94813.42441.76443.211749.22160.971923.612.573.94
field2024-08-20Himeshima Island69.032.42422.8907.99454.47442.18440.731746.48160.831920.702146.632.573.94813.42441.76443.211749.24160.961923.632.573.94
field2024-08-20Himeshima Island70.032.42422.8847.99454.11441.83440.391746.33160.881920.602146.632.573.94813.43441.76443.211749.31160.931923.672.573.94
field2024-08-20Himeshima Island71.032.42822.8857.99454.85442.55441.101746.89160.741921.042146.842.563.93813.43441.79443.241749.44160.961923.832.573.94
field2024-08-20Himeshima Island76.032.42722.8817.99455.79443.47442.021747.47160.491921.402146.792.563.93813.43441.78443.231749.45160.941923.822.573.94
field2024-08-20Himeshima Island77.032.43022.8737.99455.81443.49442.041747.67160.471921.582146.942.563.93813.43441.80443.261749.65160.921924.002.573.94
field2024-08-20Himeshima Island78.032.43722.8627.99455.85443.54442.091748.04160.461921.942147.302.563.93813.44441.85443.311750.02160.911924.372.573.94
field2024-08-20Himeshima Island79.032.43322.8547.99454.75442.48441.031747.35160.661921.422147.092.563.93813.44441.83443.281749.97160.851924.262.573.94
field2024-08-20Himeshima Island80.032.42922.8537.99454.72442.45441.001747.22160.621921.262146.892.563.93813.44441.80443.251749.85160.811924.102.573.94
field2024-08-20Himeshima Island80.632.43222.8567.99456.53444.21442.761748.37160.231922.062147.042.563.92813.44441.82443.271749.91160.851924.202.573.94
field2024-08-20Himeshima Island82.032.42522.8577.99456.84444.51443.061748.33160.101921.912146.682.553.92813.44441.77443.221749.66160.811923.902.573.94
field2024-08-20Himeshima Island84.032.42622.8467.99457.20444.87443.411748.71159.961922.172146.742.553.92813.44441.78443.241749.83160.761924.032.563.94
field2024-08-20Himeshima Island85.032.42822.8467.99457.21444.88443.431748.78159.981922.252146.842.553.92813.44441.80443.251749.90160.771924.112.563.94
field2024-08-20Himeshima Island86.032.43122.8397.99457.15444.82443.371748.91159.991922.392146.992.553.92813.44441.82443.271750.08160.761924.282.563.94
field2024-08-20Himeshima Island88.032.42722.8347.99457.56445.23443.771749.10159.831922.432146.792.553.91813.45441.79443.251750.01160.711924.162.563.93
field2024-08-20Himeshima Island90.032.42722.8377.99457.12444.80443.341748.80159.951922.242146.792.553.92813.44441.79443.241749.97160.721924.142.563.93
field2024-08-20Himeshima Island91.032.42622.8417.99458.19445.84444.381749.37159.701922.592146.742.553.91813.44441.78443.241749.89160.741924.072.563.94
field2024-08-20Himeshima Island92.032.44022.8277.99457.21444.89443.431749.36159.991922.852147.452.553.92813.45441.88443.331750.53160.761924.742.563.94
field2024-08-20Himeshima Island93.032.43022.8207.99457.13444.82443.371749.10159.891922.492146.942.553.91813.45441.82443.271750.27160.661924.382.563.93
field2024-08-20Himeshima Island95.032.42822.8217.99458.92446.56445.101750.10159.451923.102146.842.543.90813.45441.80443.261750.19160.651924.292.563.93
field2024-08-20Himeshima Island97.032.42922.8127.99458.92446.57445.101750.24159.411923.202146.892.543.90813.45441.81443.261750.33160.611924.402.563.93
field2024-08-20Himeshima Island100.032.43422.7797.98463.28450.83449.361753.36158.261925.312147.142.523.87813.84454.06455.551758.29157.501929.622.513.86
field2024-08-20Himeshima Island100.032.43422.7807.98462.92450.48449.001753.14158.351925.172147.142.523.88813.84454.06455.551758.27157.501929.612.513.86
field2024-08-20Himeshima Island100.032.43222.7847.98461.82449.41447.931752.38158.611924.642147.042.533.88813.84454.04455.531758.16157.511929.512.513.86
field2024-08-20Himeshima Island100.041.9596.20020.8381.05123.4012.0301.4713.0490.0000.00032.43522.7807.98462.56450.13448.661752.96158.441925.072147.202.533.88813.84454.06455.561758.32157.511929.662.513.86
field2024-08-20Himeshima Island100.032.43522.7827.99461.11448.72447.251752.08158.791924.502147.202.533.89813.47441.86443.311750.89160.511924.862.563.93
field2024-08-20Himeshima Island100.032.43322.7907.99460.02447.65446.191751.28159.071923.942147.092.543.89813.46441.84443.301750.72160.541924.722.563.93
field2024-08-20Himeshima Island100.032.43422.7777.98462.19449.77448.301752.75158.501924.912147.142.533.88813.84454.06455.551758.31157.491929.642.513.86
field2024-12-01Showa Iwojima Island_Control0.55624.45657.20915.1452.5180.116000.00034.40022.0008.00457.74446.03444.551824.05174.152011.892256.852.744.19813.71445.21446.691826.75174.412014.872.744.20
field2024-12-02Showa Iwojima Island_Transition0.00012.87360.8830.00025.2610.000000.98234.40022.3007.90600.34584.69582.761895.85145.392059.042256.852.293.50817.82583.48585.411898.17145.572061.572.293.51
field2024-12-02Showa Iwojima Island_Seep5.3990.33193.8720.0000.3970.000000.00035.00023.1006.3029590.3128781.0228687.062336.884.703196.822347.950.070.118855.3828691.8728788.882337.274.703197.360.070.11