Citation:

fix013

Name: Seawater carbonate chemistry and the microbiome of the octocoral Lobophytum pauciflorum
Published: 2017
License: https://creativecommons.org/licenses/by/3.0/
Keywords: Animalia; Benthic animals; Benthos; Cnidaria; Coast and continental shelf; Community composition and diversity; Containers and aquaria (20-1000 L or < 1 m**2); Laboratory experiment; Lobophytum pauciflorum; Single species; South Pacific; Temperature; Tropical

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Abstract:

Bacteria associated with marine invertebrates are thought to have a range of important roles that benefit the host including production of compounds that may exclude pathogenic microorganisms and recycling of essential nutrients. This study characterised the microbiome of a gonochoric octocoral, Lobophytum pauciflorum, and investigated whether either sex or environmental stresses influenced the diversity of the associated microbiome through amplicon profiling of the bacterial 16S rRNA gene. Sequences affiliated to Spirochaetaceae and Endozoicimonaceae dominated the microbiome of L. pauciflorum, representing 43% and 21% of the community, respectively. Among the dominant class affiliations, no sex-specific differences were detected, though unassigned sequences were at a 2-fold higher relative abundance in samples from female individuals than from males. These potentially novel sequences contributed to observed differences between sexes as detected by a multivariate analysis at the OTU level. Exposing L. pauciflorum fragments to increased temperature (31°C), decreased pH (7.9) or both stressors simultaneously for 12 days did not significantly alter the microbial community, indicating that the soft coral microbiome is relatively resilient to short-term environmental stress.

Keyword(s):

Animalia; Benthic animals; Benthos; Cnidaria; Coast and continental shelf; Community composition and diversity; Containers and aquaria (20-1000 L or < 1 m**2); Laboratory experiment; Lobophytum pauciflorum; Single species; South Pacific; Temperature; 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):

Ocean Acidification International Coordination Centre (OA-ICC)

Coverage:

Latitude: -18.560000 * Longitude: 146.480000

Date/Time Start: 2013-08-01T00:00:00 * Date/Time End: 2014-10-30T00:00:00

Event(s):

Orpheus_Pelorus_Island * Latitude: -18.560000 * Longitude: 146.480000 * Date/Time Start: 2013-08-01T00:00:00 * Date/Time End: 2014-10-30T00:00:00 * Method/Device: Experiment (EXP)

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 by seacarb is 2018-09-04.

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Type	Type		Bourne, David G		study
2	Species	Species		Bourne, David G
3	Registration number of species	Reg spec no		Bourne, David G
4	Uniform resource locator/link to reference	URL ref		Bourne, David G		WoRMS Aphia ID
5	Experiment duration	Exp duration	days	Bourne, David G
6	Experiment	Exp		Bourne, David G
7	Treatment	Treat		Bourne, David G
8	Operational taxonomic unit	OTU		Bourne, David G		Observed
9	Operational taxonomic unit, standard deviation	OTU std dev	±	Bourne, David G		Observed
10	Operational taxonomic unit	OTU		Bourne, David G		Unique
11	Alpha diversity	alpha		Bourne, David G
12	Alpha diversity, standard deviation	alpha std dev	±	Bourne, David G
13	Operational taxonomic unit	OTU		Bourne, David G		Chao 1 estimate
14	Operational taxonomic unit, standard deviation	OTU std dev	±	Bourne, David G		Chao 1 estimate
15	Shannon Diversity Index	H'		Bourne, David G
16	Shannon Diversity Index, standard deviation	H' std dev	±	Bourne, David G
17	Simpson index of diversity	Simpson I		Bourne, David G
18	Simpson index of diversity, standard deviation	Simpsons I std dev	±	Bourne, David G
19	Class	Class		Bourne, David G
20	Family	Family		Bourne, David G
21	Sequence abundance	Sequence abund	%	Bourne, David G
22	Sequence abundance, standard error	Sequence abund std e	±	Bourne, David G
23	Salinity	Sal		Bourne, David G
24	Salinity, standard deviation	Sal std dev	±	Bourne, David G
25	Temperature, water	Temp	°C	Bourne, David G
26	Temperature, water, standard deviation	Temp std dev	±	Bourne, David G
27	pH	pH		Bourne, David G		NBS scale
28	pH, standard deviation	pH std dev	±	Bourne, David G		NBS scale
29	Alkalinity, total	AT	µmol/kg	Bourne, David G
30	Alkalinity, total, standard deviation	AT std dev	±	Bourne, David G
31	Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)	pCO2water_SST_wet	µatm	Bourne, David G
32	Partial pressure of carbon dioxide, standard deviation	pCO2 std dev	±	Bourne, David G
33	Carbonate system computation flag	CSC flag		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
34	pH	pH		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)	total scale
35	Carbon dioxide	CO2	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
36	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)
37	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)
38	Bicarbonate ion	[HCO3]-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
39	Carbonate ion	[CO3]2-	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
40	Carbon, inorganic, dissolved	DIC	µmol/kg	Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
41	Aragonite saturation state	Omega Arg		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)
42	Calcite saturation state	Omega Cal		Yang, Yan	Calculated using seacarb after Nisumaa et al. (2010)

License:

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

Status:

Curation Level: Enhanced curation (CurationLevelC)

Size:

1036 data points

Data

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

1 Type (study)	2 Species	3 Reg spec no	4 URL ref (WoRMS Aphia ID)	5 Exp duration [days]	6 Exp	7 Treat	8 OTU (Observed)	9 OTU std dev [±] (Observed)	10 OTU (Unique)	11 alpha	12 alpha std dev [±]	13 OTU (Chao 1 estimate)	14 OTU std dev [±] (Chao 1 estimate)	15 H'	16 H' std dev [±]	17 Simpson I	18 Simpsons I std dev [±]	19 Class	20 Family	21 Sequence abund [%]	22 Sequence abund std e [±]	23 Sal	24 Sal std dev [±]	25 Temp [°C]	26 Temp std dev [±]	27 pH (NBS scale)	28 pH std dev [±] (NBS scale)	29 AT [µmol/kg]	30 AT std dev [±]	31 pCO2water_SST_wet [µatm]	32 pCO2 std dev [±]	33 CSC flag	34 pH (total scale)	35 CO2 [µmol/kg]	36 fCO2water_SST_wet [µatm]	37 pCO2water_SST_wet [µatm]	38 [HCO3]- [µmol/kg]	39 [CO3]2- [µmol/kg]	40 DIC [µmol/kg]	41 Omega Arg	42 Omega Cal
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Overal	575.29	73.66	832	79.10	10.65	679.64	85.17	3.50	0.40	0.75	0.08
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Female	567.63	48.55	66	79.00	6.30	683.95	60.00	3.56	0.33	0.77	0.05
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Male	582.11	89.74	257	79.19	13.38	675.81	102.33	3.45	0.44	0.73	0.09
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	Overal	161.83	50.84	249	24.05	8.19	173.99	49.09	3.92	1.51	0.79	0.19
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	1 day	185.79	36.30	105	27.04	6.17	197.8	34.37	4.17	1.43	0.82	0.14
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	12 day	136.83	51.79	27	20.93	8.85	149.15	49.83	3.66	1.54	0.76	0.22
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	Control	182.17	42.62	11	27.59	7.35	192.52	37.50	4.39	1.49	0.83	0.15					35.51	0.4	27.5	0.24	8.11	0.02	2319	10.2	502.8	41.41	26	7.97	13.11	492.25	493.8	1821.50	202.75	2037.35	3.25	4.88
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	Temperature	154.58	57.21	5	23.03	9.20	166.4	57.10	4.12	1.41	0.83	0.20					35.51	0.4	30.9	0.15	8.08	0.02	2323	4.5	542.3	32.45	26	7.93	13.43	545.92	547.5	1812.56	208.44	2034.43	3.40	5.05
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	CO2	153.92	43.07	4	22.51	6.94	167.83	43.50	3.54	1.32	0.77	0.14					35.51	0.4	27.4	0.28	7.94	0.01	2323	13.8	779.7	24.70	26	7.80	20.91	783.50	785.9	1962.46	147.24	2130.61	2.36	3.54
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	Temperature+CO2	156.18	53.47	5	22.97	8.04	168.79	51.33	3.59	1.65	0.74	0.24					35.51	0.4	31.1	0.17	7.91	0.02	2325	7.3	869.9	38.34	26	7.76	21.34	871.48	874.1	1952.06	152.69	2126.09	2.49	3.70
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment													Bacteroidia	Marinilabiaceae	0.00	0.00
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment													Flavobacteria	Flavobacteriaceae	0.01	0.00
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment													Alphaproteobacteria	Rhodobacteraceae	1.13	0.41
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment														Rickettsiaceae	4.19	2.04
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment													Gammaproteobacteria	Alteromonadaceae	0.14	0.03
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment														Endozoicimonaceae	22.70	6.70
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment														Enterobacteriaceae	0.02	0.01
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment														Francisellaceae	1.50	0.55
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment														Pseudoalteromonadaceae	0.68	0.37
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment														Vibrionaceae	0.44	0.20
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment													Spirochaetes	Spirochaetaceae	42.51	6.00
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment													Others		4.49	1.00
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment													Unassigned		22.21	4.20
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Female												Bacteroidia	Marinilabiaceae	0.00	0.00
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Female												Flavobacteria	Flavobacteriaceae	0.01	0.00
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Female												Alphaproteobacteria	Rhodobacteraceae	0.45	0.18
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Female													Rickettsiaceae	5.86	3.35
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Female												Gammaproteobacteria	Alteromonadaceae	0.17	0.05
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Female													Endozoicimonaceae	23.13	10.01
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Female													Enterobacteriaceae	0.03	0.02
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Female													Francisellaceae	1.57	0.68
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Female													Pseudoalteromonadaceae	0.18	0.10
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Female													Vibrionaceae	0.25	0.12
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Female												Spirochaetes	Spirochaetaceae	35.05	8.81
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Female												Others		3.94	0.92
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Female												Unassigned		29.34	7.13
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Male												Bacteroidia	Marinilabiaceae	0.00	0.00
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Male												Flavobacteria	Flavobacteriaceae	0.01	0.01
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Male												Alphaproteobacteria	Rhodobacteraceae	1.72	0.71
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Male													Rickettsiaceae	2.71	2.52
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Male												Gammaproteobacteria	Alteromonadaceae	0.11	0.02
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Male													Endozoicimonaceae	22.31	9.57
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Male													Enterobacteriaceae	0.01	0.01
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Male													Francisellaceae	1.43	0.88
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Male													Pseudoalteromonadaceae	1.08	0.69
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Male													Vibrionaceae	0.62	0.37
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Male												Spirochaetes	Spirochaetaceae	49.15	8.00
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Male												Others		4.99	1.74
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Sex experiment	Male												Unassigned		15.85	4.05
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment													Bacteroidia	Marinilabiaceae	2.35	1.10
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment													Flavobacteria	Flavobacteriaceae	4.92	1.07
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment													Alphaproteobacteria	Rhodobacteraceae	9.96	1.62
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment														Rickettsiaceae	0.00	0.00
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment													Gammaproteobacteria	Alteromonadaceae	5.54	1.02
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment														Endozoicimonaceae	4.15	1.43
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment														Enterobacteriaceae	4.53	1.71
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment														Francisellaceae	0.24	0.10
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment														Pseudoalteromonadaceae	0.00	0.00
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment														Vibrionaceae	1.89	0.54
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment													Spirochaetes	Spirochaetaceae	34.04	5.22
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment													Others		17.23	1.90
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment													Unassigned		15.15	2.90
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	1 day												Bacteroidia	Marinilabiaceae	0.28	0.15
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	1 day												Flavobacteria	Flavobacteriaceae	7.33	1.78
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	1 day												Alphaproteobacteria	Rhodobacteraceae	10.26	2.11
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	1 day													Rickettsiaceae
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	1 day												Gammaproteobacteria	Alteromonadaceae	7.20	1.78
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	1 day													Endozoicimonaceae	1.97	0.75
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	1 day													Enterobacteriaceae	5.82	3.10
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	1 day													Francisellaceae	0.23	0.16
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	1 day													Pseudoalteromonadaceae
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	1 day													Vibrionaceae	0.80	0.36
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	1 day												Spirochaetes	Spirochaetaceae	31.83	6.79
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	1 day												Others		16.83	2.46
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	1 day												Unassigned		17.45	4.62
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	12 day												Bacteroidia	Marinilabiaceae	4.51	2.17
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	12 day												Flavobacteria	Flavobacteriaceae	2.41	0.90
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	12 day												Alphaproteobacteria	Rhodobacteraceae	9.66	2.54
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	12 day													Rickettsiaceae
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	12 day												Gammaproteobacteria	Alteromonadaceae	3.80	0.85
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	12 day													Endozoicimonaceae	6.42	2.76
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	12 day													Enterobacteriaceae	3.19	1.40
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	12 day													Francisellaceae	0.25	0.11
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	12 day													Pseudoalteromonadaceae
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	12 day													Vibrionaceae	3.03	1.01
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	12 day												Spirochaetes	Spirochaetaceae	36.34	8.10
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	12 day												Others		17.66	2.96
laboratory	Lobophytum pauciflorum (coral)	209963	marinespecies.org	12	Stess experiment	12 day												Unassigned		12.75	3.49