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Kerfahi, Dorsaf; Harvey, Ben P; Agostini, Sylvain; Kon, Koetsu; Huang, Ruiping; Adams, Jonathan M; Hall-Spencer, Jason M (2020): Seawater carbonate chemistry and bacterial diversity of intertidal bacterial biofilm communities [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.930400

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Abstract:
The effects of ocean acidification on ecosystems remain poorly understood, because it is difficult to simulate the effects of elevated CO2 on entire marine communities. Natural systems enriched in CO2 are being used to help understand the long-term effects of ocean acidification in situ. Here, we compared biofilm bacterial communities on intertidal cobbles/boulders and bedrock along a seawater CO2 gradient off Japan. Samples sequenced for 16S rRNA showed differences in bacterial communities with different pCO2 and between habitat types. In both habitats, bacterial diversity increased in the acidified conditions. Differences in pCO2 were associated with differences in the relative abundance of the dominant phyla. However, despite the differences in community composition, there was no indication that these changes would be significant for nutrient cycling and ecosystem function. As well as direct effects of seawater chemistry on the biofilm, increased microalgal growth and decreased grazing may contribute to the shift in bacterial composition at high CO2, as documented by other studies. Thus, the effects of changes in bacterial community composition due to globally increasing pCO2 levels require further investigation to assess the implications for marine ecosystem function. However, the apparent lack of functional shifts in biofilms along the pCO2 gradient is a reassuring indicator of stability of their ecosystem functions in shallow ocean margins.
Keyword(s):
Benthos; CO2 vent; Coast and continental shelf; Community composition and diversity; Entire community; Field observation; North Pacific; Rocky-shore community; Temperate
Related to:
Kerfahi, Dorsaf; Harvey, Ben P; Agostini, Sylvain; Kon, Koetsu; Huang, Ruiping; Adams, Jonathan M; Hall-Spencer, Jason M (2020): Responses of Intertidal Bacterial Biofilm Communities to Increasing pCO2. Marine Biotechnology, 22(6), 727-738, https://doi.org/10.1007/s10126-020-09958-3
Further details:
Taxonomy and OTUs of bacterial biofilm communities
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
Project(s):
Ocean Acidification International Coordination Centre (OA-ICC)
Coverage:
Median Latitude: 34.320565 * Median Longitude: 139.213528 * South-bound Latitude: 34.317639 * West-bound Longitude: 139.204722 * North-bound Latitude: 34.322278 * East-bound Longitude: 139.221778
Event(s):
Shikine_Island * Latitude: 34.533300 * Longitude: 139.333300 * Method/Device: Experiment (EXP)
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 2021-04-07.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1 TypeTypeKerfahi, Dorsafstudy
2 SiteSiteKerfahi, Dorsaf
3 SiteSiteKerfahi, Dorsaf
4 LATITUDELatitudeKerfahi, DorsafGeocode
5 LONGITUDELongitudeKerfahi, DorsafGeocode
6 GroupGroupKerfahi, Dorsaf
7 Species richnessSKerfahi, Dorsaf
8 Shannon Diversity IndexH'Kerfahi, Dorsaf
9 Simpson index of diversitySimpson IKerfahi, Dorsaf
10 Chao 1 richnessChao1 richKerfahi, Dorsaf
11 ACE richnessACE richKerfahi, Dorsaf
12 pHpHKerfahi, DorsafPotentiometricNBS scale
13 Temperature, waterTemp°CKerfahi, Dorsaf
14 Oxygen, dissolvedDOmg/lKerfahi, Dorsaf
15 Alkalinity, totalATµmol/kgKerfahi, DorsafPotentiometric titration
16 SalinitySalKerfahi, Dorsaf
17 Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
18 pHpHYang, YanCalculated using seacarb after Nisumaa et al. (2010)total scale
19 Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
20 Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
21 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
22 Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
23 Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
24 Carbon, inorganic, dissolvedDICµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
25 Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
26 Calcite saturation stateOmega CalYang, YanCalculated 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:
864 data points

Data

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

1 
Type
(study)		2 
Site		3 
Site		4 
Latitude		5 
Longitude		6 
Group		7 
S		8 
H'		9 
Simpson I		10 
Chao1 rich		11 
ACE rich		12 
pH
(NBS scale, Potentiometric)		13 
Temp [°C]		14 
DO [mg/l]		15 
AT [µmol/kg]
(Potentiometric titration)		16 
Sal		17 
CSC flag
(Calculated using seacarb afte...)		18 
pH
(total scale, Calculated using...)		19 
CO2 [µmol/kg]
(Calculated using seacarb afte...)		20 
fCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)		21 
pCO2water_SST_wet [µatm]
(Calculated using seacarb afte...)		22 
[HCO3]- [µmol/kg]
(Calculated using seacarb afte...)		23 
[CO3]2- [µmol/kg]
(Calculated using seacarb afte...)		24 
DIC [µmol/kg]
(Calculated using seacarb afte...)		25 
Omega Arg
(Calculated using seacarb afte...)		26 
Omega Cal
(Calculated using seacarb afte...)
fieldBoulderAmbient34.32227778139.2217778KE15563.3949600.123899817.6037741132.1663948.4622.44.492156.39397934268.335.00163.86164.401428.02292.281725.304.617.07
fieldBoulderAmbient34.32227778139.2217778KE26954.2847300.039841962.5342471358.4568148.4722.54.532235.81837534268.345.03165.15165.691471.15309.121785.304.887.47
fieldBoulderAmbient34.32227778139.2217778KE33672.8252120.221231422.942857444.0862838.4422.94.472094.03895034268.315.09168.95169.511398.07277.641680.804.396.72
fieldBoulderAmbient34.32227778139.2217778KE45893.7391900.095688734.933333811.9544998.4123.24.422239.22665234268.285.95199.01199.661531.44286.511823.904.546.93
fieldBoulderAmbient34.32227778139.2217778KE54173.0369050.140204597.621622761.6676318.4422.64.682240.85096834268.315.51181.53182.131507.73296.661809.904.697.17
fieldBoulderAmbient34.32227778139.2217778KE65493.4033960.122803794.780220970.6930418.4421.14.602223.42200534268.315.68179.71180.321518.23284.691808.604.476.87
fieldBoulderLow34.32163889139.2198056KW17084.3311610.0469561078.6410261441.7792867.3426.75.102196.12685034267.2091.513345.063355.592104.4237.362233.300.600.91
fieldBoulderLow34.32163889139.2198056KW29344.7663020.0380481287.1147541637.3880857.6426.25.502178.78624934267.5044.011588.911593.932006.3970.012120.401.121.70
fieldBoulderLow34.32163889139.2198056KW36574.0264140.069784982.7889911244.5073447.6726.35.492192.07641734267.5341.021484.641489.322006.9075.282123.201.211.83
fieldBoulderLow34.32163889139.2198056KW48724.6657650.0337421171.3617021576.0702667.7426.05.452175.42328934267.6034.321232.921236.821964.0685.722084.101.382.08
fieldBoulderLow34.32163889139.2198056KW57014.2233740.052371970.0227271044.8754597.8326.05.522217.30965234267.6927.82999.471002.631958.80105.182091.801.692.56
fieldBoulderLow34.32163889139.2198056KW66584.3111110.043413937.6315791210.4990927.5326.55.032101.13384434267.3955.392014.762021.101967.8253.792077.000.871.31
fieldBoulderVery_low34.31880556139.2175556ASH111795.3996150.0133681550.4615381688.5788666.5027.94.632161.62349834266.36635.5923917.5923993.512148.285.732789.600.090.14
fieldBoulderVery_low34.31880556139.2175556ASH210185.0752730.0202191325.4395161530.6561576.3029.33.702127.50814934266.15976.0937965.7838086.132119.583.723099.400.060.09
fieldBoulderVery_low34.31880556139.2175556ASH39084.7176830.0426071191.0631071347.2855996.3728.73.792152.14037734266.22846.2832456.9832559.992142.484.342993.100.070.11
fieldBoulderVery_low34.31880556139.2175556ASH47003.6038910.1637241057.0252101317.6233626.4328.44.202149.62235934266.28738.4928122.6328211.782138.394.932881.800.080.12
fieldBoulderVery_low34.31880556139.2175556ASH59534.7185380.0369381272.7064681394.1235766.5028.04.322163.44204534266.36635.3223964.5524040.532150.045.752791.100.090.14
fieldBoulderVery_low34.31880556139.2175556ASH610085.1208420.0195661300.9828331471.0488136.7026.75.842221.95448034266.56417.3215254.1115302.762200.538.962626.800.140.22
fieldCliffAmbient34.31763889139.2111389C16914.3774510.036672868.377358963.7243348.2920.36.062236.97615634268.169.07280.72281.671694.82219.311923.203.435.29
fieldCliffAmbient34.31763889139.2111389C25904.1890420.040480865.2192981160.3863568.2920.36.062238.54003434268.169.08280.98281.941696.09219.431924.603.435.29
fieldCliffAmbient34.31763889139.2111389C34543.9400530.051554687.833333871.3763768.2820.36.732236.47521534268.159.33288.88289.861703.95215.421928.703.375.19
fieldCliffAmbient34.31763889139.2111389C47814.5442420.0320521028.9585801146.6225088.2920.37.072238.01126834268.169.08280.85281.801695.61219.411924.103.435.29
fieldCliffAmbient34.31763889139.2111389C56424.3254550.038143788.447853905.3496558.2820.37.402238.11729334268.159.34289.03290.011705.15215.611930.103.385.20
fieldCliffAmbient34.31763889139.2111389C68993.1455050.240287949.3286121023.5482628.2820.27.632236.17746534268.159.35288.59289.571704.84214.911929.103.365.18
fieldCliffMedium34.32136111139.2061667IM17123.9589040.066166935.6125001039.2123747.8520.35.732270.29501534267.7230.02928.90932.052035.1295.562160.701.502.30
fieldCliffMedium34.32136111139.2061667IM26244.0325070.052665936.3389831280.4769457.8720.66.072272.43347134267.7428.39885.70888.692025.07100.552154.001.582.42
fieldCliffMedium34.32136111139.2061667IM35053.3967050.094841690.981308902.5853657.9620.16.842272.22713334267.8322.73699.54701.921979.29118.982121.001.862.87
fieldCliffMedium34.32136111139.2061667IM44152.8392300.170462616.452055787.3147637.9519.96.852270.59698934267.8223.40716.20718.651985.21115.892124.501.812.79
fieldCliffMedium34.32136111139.2061667IM56233.2474930.152636969.2589291254.9961767.9419.86.812270.12345934267.8124.07734.67737.181991.35113.172128.601.772.73
fieldCliffMedium34.32136111139.2061667IM69004.0939270.0874081089.1153851209.1574487.9219.96.742272.99767334267.7925.32774.82777.462004.21109.182138.701.712.63
fieldCliffLow34.32166667139.2047222IH18584.7368600.0255131147.1894741293.6140957.0820.87.052269.61834334266.95191.996023.546043.982225.5018.012435.500.280.43
fieldCliffLow34.32166667139.2047222IH212884.4260790.1184141571.2258061724.6465887.1020.67.072266.65427334266.97183.445723.935743.392220.8418.712423.000.290.45
fieldCliffLow34.32166667139.2047222IH310994.5667070.0512931435.8115381587.8918687.0020.77.082273.25640634266.87232.287267.527292.242236.6115.012483.900.240.36
fieldCliffLow34.32166667139.2047222IH49934.9079740.0240941267.9026551394.5649736.9920.77.022276.33248334266.86238.197452.607477.952240.4214.692493.300.230.35
fieldCliffLow34.32166667139.2047222IH510505.0194150.0237251390.8486241518.5609306.9820.66.832271.93345334266.85243.727604.737630.642236.9914.292495.000.220.34
fieldCliffLow34.32166667139.2047222IH611395.0718990.0241041431.5520831611.3627347.0520.56.752273.16212834266.92207.286449.866471.842232.3216.702456.300.260.40