Citation:

fmars.2017.00073

Name: Measurements of microbial processes, dissolution, water and porewater chemistry during experiments on two coral reef sediments: Davies Reef MPB growth and chamber fluxes
Creator: Artur Fink
Published: 2017-03-22
License: https://creativecommons.org/licenses/by/3.0/
Keywords: Benthos; Biomass/Abundance/Elemental composition; Bottles or small containers/Aquaria (<20 L); Coast and continental shelf; Entire community; Laboratory experiment; Soft-bottom community; Tropical

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Keyword(s):

Benthos; Biomass/Abundance/Elemental composition; Bottles or small containers/Aquaria (<20 L); Coast and continental shelf; Entire community; Laboratory experiment; Soft-bottom community; Tropical

Further details:

Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James C; Gentili, Bernard; Proye, Aurélien; Soetaert, Karline; Rae, James (2016): seacarb: seawater carbonate chemistry with R. R package version 3.1. https://cran.r-project.org/package=seacarb

Project(s):

Biological Impacts of Ocean Acidification (BIOACID)

Coverage:

Date/Time Start: 2015-05-23T00:00:00 * Date/Time End: 2015-05-31T00:00:00

Comment:

In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2016) 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 is 2017-03-22.

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	DATE/TIME	Date/Time		Fink, Artur		Geocode
2	Origin	Origin		Fink, Artur		sediment
3	Treatment	Treat		Fink, Artur
4	Sample code/label	Sample label		Fink, Artur		timepoint
5	Treatment	Treat		Fink, Artur
6	Sample code/label	Sample label		Fink, Artur		chamber
7	Ratio	Ratio		Fink, Artur		chl signal
8	Chlorophyll a	Chl a	µg/g	Fink, Artur
9	Replicate	Repl		Fink, Artur
10	Local Time	Local time		Fink, Artur
11	Oxygen saturation	O2 sat	%	Fink, Artur
12	Temperature, water	Temp	°C	Fink, Artur
13	Volume	Vol	l	Fink, Artur		water
14	pH	pH		Fink, Artur		total scale
15	pH, standard error	pH std e	±	Fink, Artur		total scale
16	Alkalinity, total	AT	µmol/kg	Fink, Artur
17	Standard error	Std e	±	Fink, Artur
18	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Fink, Artur
19	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Fink, Artur
20	Carbon, inorganic, dissolved	DIC	µmol/l	Fink, Artur
21	Carbon, inorganic, dissolved, standard deviation	DIC std dev	±	Fink, Artur
22	Calcite saturation state	Omega Cal		Fink, Artur
23	Standard error	Std e	±	Fink, Artur
24	Aragonite saturation state	Omega Arg		Fink, Artur
25	Standard error	Std e	±	Fink, Artur
26	High magnesium calcite saturation state	Omega HMC		Fink, Artur
27	Standard error	Std e	±	Fink, Artur
28	Temperature, water	Temp	°C	Fink, Artur
29	Standard error	Std e	±	Fink, Artur
30	Salinity	Sal		Fink, Artur
31	Standard error	Std e	±	Fink, Artur
32	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
33	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
34	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)
35	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)
36	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
37	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
38	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
39	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
40	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
41	Carbon, organic, dissolved	DOC	µmol/l	Fink, Artur
42	Phosphate	[PO4]3-	µmol/l	Fink, Artur
43	Nitrate and Nitrite	[NO3]- + [NO2]-	µmol/l	Fink, Artur
44	Nitrite	[NO2]-	µmol/l	Fink, Artur
45	Silicate	Si(OH)4	µmol/l	Fink, Artur

License:

Creative Commons Attribution 3.0 Unported (CC-BY-3.0)

Size:

1814 data points

Data

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

1 Date/Time	2 Origin (sediment)	3 Treat	4 Sample label (timepoint)	5 Treat	6 Sample label (chamber)	7 Ratio (chl signal)	8 Chl a [µg/g]	9 Repl	10 Local time	11 O2 sat [%]	12 Temp [°C]	13 Vol [l] (water)	14 pH (total scale)	15 pH std e [±] (total scale)	16 AT [µmol/kg]	17 Std e [±]	18 pCO2water_SST_wet [µatm]	19 pCO2 std dev [±]	20 DIC [µmol/l]	21 DIC std dev [±]	22 Omega Cal	23 Std e [±]	24 Omega Arg	25 Std e [±]	26 Omega HMC	27 Std e [±]	28 Temp [°C]	29 Std e [±]	30 Sal	31 Std e [±]	32 CSC flag	33 CO2 [µmol/kg]	34 fCO2water_SST_wet [µatm]	35 pCO2water_SST_wet [µatm]	36 [HCO3]- [µmol/kg]	37 [CO3]2- [µmol/kg]	38 DIC [µmol/kg]	39 Omega Arg	40 Omega Cal	41 DOC [µmol/l]	42 [PO4]3- [µmol/l]	43 [NO3]- + [NO2]- [µmol/l]	44 [NO2]- [µmol/l]	45 Si(OH)4 [µmol/l]
2015-05-23	Davies Reef		1	high	1	0.004329465	0.187788749	1					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-23	Davies Reef		1	control	2	-0.002809912	0.080291156	1					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-23	Davies Reef		1	high	4	-0.007310689	0.012522960	3					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-23	Davies Reef		1	control	5	0.000283964	0.126875643	2					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-23	Davies Reef		1	control	6	-0.010606659	-0.037104464	3					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-25	Davies Reef		3	high	1	-0.006132099	0.030268979	1					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-25	Davies Reef		3	control	2	0.002313640	0.157436475	1					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-25	Davies Reef		3	high	3	0.003854767	0.180641220	2					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-25	Davies Reef		3	high	4	0.003728939	0.178746634	3					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-25	Davies Reef		3	control	5	0.010615297	0.282434530	2					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-25	Davies Reef		3	control	6	0.005086234	0.199183426	3					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-26	Davies Reef		4	high	1	0.018316045	0.398384688	1					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-26	Davies Reef		4	control	2	0.014208339	0.336534959	1					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-26	Davies Reef		4	high	3	0.017286898	0.382888827	2					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-26	Davies Reef		4	high	4	0.011341423	0.293367799	3					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-26	Davies Reef		4	control	5	0.017276417	0.382731004	2					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-26	Davies Reef		4	control	6	0.014009053	0.333534305	3					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-27	Davies Reef		5	high	1	0.046238415	0.818811814	1					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-27	Davies Reef		5	control	2	0.053951437	0.934946782	1					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-27	Davies Reef		5	high	3	0.047216207	0.833534429	2					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-27	Davies Reef		5	high	4	0.038371124	0.700354011	3					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-27	Davies Reef		5	control	5	0.051619776	0.899838963	2					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-27	Davies Reef		5	control	6	0.034911880	0.648268171	3					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-29	Davies Reef		7	high	1	0.064834563	1.098814021	1					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-29	Davies Reef		7	control	2	0.057226695	0.984262341	1					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-29	Davies Reef		7	high	3	0.068748619	1.157747951	2					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-29	Davies Reef		7	high	4	0.038696078	0.705246849	3					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-29	Davies Reef		7	control	5	0.068145678	1.148669480	2					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-29	Davies Reef		7	control	6	0.060422663	1.032384043	3					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-31	Davies Reef		9	high	1	0.071847554	1.204408626	1					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-31	Davies Reef		9	control	2	0.059376705	1.016635045	1					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-31	Davies Reef		9	high	3	0.076029809	1.267380838	2					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-31	Davies Reef		9	high	4	0.066366522	1.121880718	3					7.61	0	2363.000000	0	1338	18	2270	4	2.22	0	1.46	0	0.54	0	25.5	0	34	0	8	36.82	1306.45	1311	2135.56	93.64	2266.02	1.50	2.28
2015-05-31	Davies Reef		9	control	5	0.083433103	1.378852229	2					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-31	Davies Reef		9	control	6	0.062271536	1.060222514	3					8.01	0	2360.000000	0	441	4	2075	4	4.99	0	3.29	0	1.20	0	25.5	0	34	0	8	12.77	453.20	455	1860.83	204.95	2078.55	3.28	4.98
2015-05-30	Davies Reef	dark	Start	high				1	02:44	96.02	25.5	4.35	7.99		2365.565251														34		8	13.54	480.28	482	1883.26	198.08	2094.88	3.17	4.81	0.828214757	0.043305383	0.359888473	0.05650	2.595456125
2015-05-30	Davies Reef	dark	Start	control				1	02:44	95.90	25.6	4.35	8.43		2364.391163														34		8	3.60	127.92	128	1380.67	401.44	1785.70	6.43	9.76	0.874704340	0.058387500	0.361984902	0.05550	2.695049168
2015-05-30	Davies Reef	dark	Start	high				2	02:44	95.90	25.3	4.35	8.00		2364.620656														34		8	13.23	467.07	469	1876.31	200.48	2090.02	3.21	4.87	0.897160040	0.074480646	0.365085130	0.06350	2.691547110
2015-05-30	Davies Reef	dark	Start	high				3	02:44	95.60	25.6	4.35	8.00		2366.069628														34		8	13.13	467.14	469	1873.31	202.37	2088.81	3.24	4.92	0.970369080	0.059415058	0.384161386	0.05950	2.750040907
2015-05-30	Davies Reef	dark	Start	control				2	02:44	95.50	25.5	4.35	8.41		2361.983932														34		8	3.85	136.50	137	1407.80	389.48	1801.12	6.24	9.46	0.871708462	0.067471091	0.399261182	0.07250	2.780169453
2015-05-30	Davies Reef	dark	Start	control				3	02:44	95.90	25.5	4.35	8.44		2362.501358														34		8	3.49	123.80	124	1368.21	405.60	1777.29	6.49	9.86	0.846701208	0.073519256	0.378421675	0.06050	2.756463502
2015-05-30	Davies Reef	light	Start	high				1	12:06	113.00	25.4	4.35	8.08		2349.222737														34		8	10.46	370.21	371	1786.97	230.39	2027.82	3.69	5.60	0.965620121	0.077076768	0.385451800	0.05750	2.865067318
2015-05-30	Davies Reef	light	Start	control				1	12:11	111.80	25.4	4.35	8.51		2347.490278														34		8	2.75	97.50	98	1266.69	439.56	1709.01	7.03	10.68	0.931204143	0.082335360	0.392385345	0.05950	3.079381656
2015-05-30	Davies Reef	light	Start	high				2	12:16	112.90	25.6	4.35	8.09		2352.086874														34		8	10.12	360.01	361	1776.16	236.06	2022.34	3.78	5.74	0.963951063	0.075257664	0.327568241	0.05550	2.334154871
2015-05-30	Davies Reef	light	Start	high				3	12:20	111.00	25.4	4.35	8.06		2352.401880														34		8	11.09	392.45	394	1809.07	222.74	2042.90	3.56	5.41	0.905674379	0.055982660	0.395047730	0.06650	3.153897468
2015-05-30	Davies Reef	light	Start	control				2	12:26	111.20	25.4	4.35	8.51		2348.587146														34		8	2.76	97.55	98	1267.37	439.80	1709.93	7.04	10.68	0.974555870	0.049289039	0.364138540	0.05288	2.961322320
2015-05-30	Davies Reef	light	Start	control				3	12:32	112.60	25.4	4.35	8.52		2345.540137														34		8	2.66	94.17	94	1251.99	444.58	1699.24	7.11	10.80	0.895287624	0.057912928	0.365356691	0.06688	2.810363099
2015-05-30	Davies Reef	dark	End	high				1	05:05	86.20	24.6	4.35	7.94		2394.269943														34		8	16.10	558.42	560	1961.94	177.94	2155.98	2.84	4.32	0.928837467	0.029273023	0.087819674	0.02150	1.140145546
2015-05-30	Davies Reef	dark	End	control				1	05:10	85.20	24.8	4.35	8.40		2376.991425														34		8	4.10	142.82	143	1445.47	380.89	1830.45	6.08	9.24	0.923541538	0.041353247	0.085852609	0.02450	1.146544905
2015-05-30	Davies Reef	dark	End	high				2	05:17	84.60	24.7	4.35	7.96		2396.024097														34		8	15.22	529.13	531	1945.50	185.45	2146.16	2.96	4.50	0.930591962	0.022241068	0.085884884	0.02050	1.181431979
2015-05-30	Davies Reef	dark	End	high				3	05:25	83.20	24.5	4.35	7.96		2398.021925														34		8	15.31	529.68	531	1949.81	184.50	2149.62	2.94	4.47	0.938742408	0.028285743	0.090919396	0.02850	0.899754942
2015-05-30	Davies Reef	dark	End	control				2	05:30	81.45	24.4	4.35	8.41		2373.226847														34		8	4.01	138.54	139	1438.21	382.14	1824.37	6.09	9.27	0.981995883	0.039367542	0.106965891	0.03550	0.976920614
2015-05-30	Davies Reef	dark	End	control				3	05:37	83.40	25.6	4.35	8.43		2375.263719														34		8	3.61	128.56	129	1387.66	403.47	1794.74	6.46	9.81	0.966140244	0.033334363	0.128032129	0.03650	1.221731431
2015-05-30	Davies Reef	light	End	high				1	15:36	169.00	25.3	4.35	8.44		2344.151510														34		8	3.48	123.02	123	1361.10	400.54	1765.13	6.41	9.73	0.970269463	<0.020000000	0.048207291	<0.02000	0.560112276
2015-05-30	Davies Reef	light	End	control				1	15:43	168.00	25.3	4.35	8.77		2309.302210														34		8	1.08	38.04	38	899.96	566.21	1467.25	9.06	13.75	1.048141509	<0.020000000	0.078383032	0.05188	0.918545008
2015-05-30	Davies Reef	light	End	high				2	15:48	171.00	25.4	4.35	8.43		2346.505617														34		8	3.59	127.12	128	1373.70	396.50	1773.79	6.35	9.63	1.148035752	<0.020000000	0.094517325	<0.02000	1.160842626
2015-05-30	Davies Reef	light	End	high				3	15:53	161.50	25.6	4.35	8.39		2343.109347														34		8	4.05	144.24	145	1419.83	376.50	1800.38	6.03	9.15	1.273981516	<0.020000000	0.105640179	0.02488	1.517348434
2015-05-30	Davies Reef	light	End	control				2	15:58	172.40	25.6	4.35	8.75		2311.710125														34		8	1.15	40.83	41	920.65	559.27	1481.07	8.96	13.59	1.086620675	<0.020000000	0.063421542	<0.02000	0.911757910
2015-05-30	Davies Reef	light	End	control				3	16:00	169.00	25.4	4.35	8.76		2305.176199														34		8	1.11	39.34	39	908.93	560.89	1470.93	8.98	13.63	1.007709194	<0.020000000	0.107779606	0.02688	1.060174239