Citation:

s41396-018-0263-1

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Abstract:

CARD-FISH was performed as previously described in Ruff et al., (2013; doi:10.1371/journal.pone.0072627) with the following modifications. 4-6 µl of 25-fold diluted sediment were used for filtration. Archaeal cell walls were permeabilized with 0.1M HCl for 2 min to detect ANME-3 cells, or Proteinase K solution (15 µg ml-1 (Merck, Darmstadt, Germany) in 0.05 M EDTA (pH 8), 0.1 M Tris-HCl (pH 8), 0.5 M NaCl) for 2-4 min at room temperature for all other archaea. Bacterial cell walls were permeabilized with lysozyme solution (1000kU/ml) for 60 min at 37°. Cells were stained with DAPI (1µg/ml), embedded in mounting medium and counted in 40-60 independent microscopic fields using an Axiophot II epifluorescence microscope (Carl Zeiss, Jena, Germany).

Further details:

Oligonucleotide probes and formamide concentration used in Ruff et al., 2016

Project(s):

European Seafloor Observatory Network (ESONET)

Hotspot Ecosystem Research and Mans Impact On European Seas (HERMIONE)

Funding:

Seventh Framework Programme (FP7), grant/award no. 226354 : Hotspot Ecosystem Research and Mans Impact On European Seas

Sixth Framework Programme (FP6), grant/award no. 36851 : European Seafloor Observatory Network

Coverage:

Median Latitude: 72.003918 * Median Longitude: 14.727823 * South-bound Latitude: 72.000300 * West-bound Longitude: 14.702167 * North-bound Latitude: 72.006660 * East-bound Longitude: 14.747660

Date/Time Start: 2003-07-02T00:00:00 * Date/Time End: 2010-10-04T13:01:00

Minimum DEPTH, sediment/rock: 0.01 m * Maximum DEPTH, sediment/rock: 4.65 m

Event(s):

MSM16/2_809-1 * Latitude: 72.006660 * Longitude: 14.747660 * Date/Time: 2010-09-26T08:23:00 * Elevation: -1257.4 m * Location: North Atlantic * Campaign: (LOOME) * Basis: * Method/Device: MultiCorer (MUC) * Comment: Action: at sea bottom; ship position

MSM16/2_823-1 * Latitude: 72.002700 * Longitude: 14.732467 * Date/Time: 2010-09-28T09:54:00 * Elevation: -1261.5 m * Location: Håkon Mosby Mud Volcano * Campaign: (LOOME) * Basis: * Method/Device: MultiCorer (MUC) * Comment: Action: at sea bottom; Position sensor: Gear-mounted USBL transponder (Ixsea Posidonia); Comment: rope length max. 1267 m

MSM16/2_838-1 * Latitude: 72.004796 * Longitude: 14.726150 * Date/Time: 2010-10-01T09:13:00 * Elevation: -1258.5 m * Location: Håkon Mosby Mud Volcano * Campaign: (LOOME) * Basis: * Method/Device: MultiCorer (MUC) * Comment: Action: at sea bottom; Position sensor: Gear-mounted USBL transponder (Ixsea Posidonia); Comment: rope length max. 1258 m

Comment:

ANME aggregates had been observed in various samples (#) but they had been NOT included in the relative abundance calculations here.

Parameter(s):

#	Name	Short Name	Unit	Principal Investigator	Method/Device	Comment
1	Event label	Event		Ruff, S Emil
2	Date/Time of event	Date/Time		Ruff, S Emil
3	Latitude of event	Latitude		Ruff, S Emil
4	Longitude of event	Longitude		Ruff, S Emil
5	Sample code/label	Sample label		Ruff, S Emil
6	Habitat	Habitat		Ruff, S Emil
7	DEPTH, sediment/rock	Depth sed	m	Ruff, S Emil		Geocode
8	Depth, top/min	Depth top	m	Ruff, S Emil
9	Depth, bottom/max	Depth bot	m	Ruff, S Emil
10	Bacteria, targed with EUB338(I-III) oligonucleotide FISH-probe	EUB338 I-III	%	Ruff, S Emil	Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
11	Archaea, targed with ARCH915 oligonucleotide FISH-probe	ARCH915	%	Ruff, S Emil	Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
12	Desulfusarcina/Desulfococcus, targeted with DSS658 oligonucleotide FISH-probe	DSS658	%	Ruff, S Emil	Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
13	Methylococcaceae, targeted with MTMC701 oligonucleotide FISH-probe	MTMC701	%	Ruff, S Emil	Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
14	Anaerobic methanotrophic archaea-3, targeted with ANME-3-1249 oligonucleotide FISH-probe	ANME-3-1249	%	Ruff, S Emil	Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
15	Desulfobulbus, targeted with DBB660 oligonucleotide FISH-probe	DBB660	%	Ruff, S Emil	Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)

License:

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

Size:

290 data points

Data

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

1 Event	2 Date/Time	3 Latitude	4 Longitude	5 Sample label	6 Habitat	7 Depth sed [m]	8 Depth top [m]	9 Depth bot [m]	10 EUB338 I-III [%]	11 ARCH915 [%]	12 DSS658 [%]	13 MTMC701 [%]	14 ANME-3-1249 [%]	15 DBB660 [%]
PS74/169-1_PUC-1	2009-07-23T18:24	72.0050	14.7264	1	new flow surface	0.01	0.00	0.02	12.5	24.2	0.0	0.0	0.0
PS74/169-1_PUC-1	2009-07-23T18:24	72.0050	14.7264	1	new flow surface	0.04	0.02	0.06	18.9	20.0	10.0	0.0	0.0
PS74/169-1_PUC-1	2009-07-23T18:24	72.0050	14.7264	1	new flow surface	0.08	0.06	0.10	25.6	19.2	7.1	0.0	0.0
PS74/168-1	2009-07-23T13:49	72.0047	14.7242	2	new flow surface	0.01	0.00	0.02	51.2	7.9	21.9	42.5	0.0
PS74/168-1	2009-07-23T13:49	72.0047	14.7242	2	new flow surface	0.04	0.02	0.06	13.2	33.3	3.2	2.9	0.0
PS74/168-1	2009-07-23T13:49	72.0047	14.7242	2	new flow surface	0.08	0.06	0.10	8.3	27.3	0.0	0.0	0.0
MSM16/2_838-1	2010-10-01T09:13	72.0048	14.7262	3	new flow surface	0.01	0.00	0.02	87.1	0.2	45.3	#19.5	0.0
MSM16/2_838-1	2010-10-01T09:13	72.0048	14.7262	3	new flow surface	0.04	0.02	0.06	39.0	5.4	3.8	21.2	0.0
MSM16/2_838-1	2010-10-01T09:13	72.0048	14.7262	3	new flow surface	0.08	0.06	0.10	3.8	17.1	2.6	0.0	0.0
MSM16/2_847-1	2010-10-02T16:29	72.0042	14.7270	5	aged flow surface	0.01	0.00	0.02	89.7	#1.8	36.0	#23.3	#0.0	#0.0
MSM16/2_847-1	2010-10-02T16:29	72.0042	14.7270	5	aged flow surface	0.04	0.02	0.06	69.7	4.2	26.6	25.2	0.0	#0.0
MSM16/2_847-1	2010-10-02T16:29	72.0042	14.7270	5	aged flow surface	0.08	0.06	0.10	14.6	25.0	0.0	0.0	0.0	0.0
MSM16/2_855-1	2010-10-04T13:01	72.0040	14.7298	6	aged flow surface	0.01	0.00	0.02	91.9	#0.9	56.3	50.9	#0.0	#0.0
MSM16/2_855-1	2010-10-04T13:01	72.0040	14.7298	6	aged flow surface	0.04	0.02	0.06	68.3	#2.0	37.3	#3.9	0.0	0.0
MSM16/2_855-1	2010-10-04T13:01	72.0040	14.7298	6	aged flow surface	0.08	0.06	0.10	16.0	0.0	18.2	0.0	0.0	0.0
PS74/172-1_PUC-131	2009-07-25T04:49	72.0052	14.7262	8	old flow surface	0.01	0.00	0.02	89.6	#3.1	17.5	#12.2	#1.9	#0.1
PS74/172-1_PUC-131	2009-07-25T04:49	72.0052	14.7262	8	old flow surface	0.04	0.02	0.06	72.0	#6.2	13.4	18.9	#7.5	#0.6
PS74/172-1_PUC-131	2009-07-25T04:49	72.0052	14.7262	8	old flow surface	0.08	0.06	0.10	52.9	#26.7	20.9	9.7	#19.8	#0.0
MSM16/2_823-1	2010-09-28T09:54	72.0027	14.7325	9	old flow surface	0.01	0.00	0.02	85.7	#5.1	#17.0	#8.5	#8.2	#0.1
MSM16/2_823-1	2010-09-28T09:54	72.0027	14.7325	9	old flow surface	0.04	0.02	0.06	83.1	#4.4	16.7	#3.9	#2.9	#0.0
MSM16/2_823-1	2010-09-28T09:54	72.0027	14.7325	9	old flow surface	0.08	0.06	0.10	30.1	#23.9	12.1	0.0	2.4	0.0
PS64/326_PUC-12	2003-07-02T16:19	72.0010	14.7022	10	hydrate zone surface	0.01	0.00	0.02	37.1	5.2	1.9	0.0	#0.0	0.0
PS64/326_PUC-12	2003-07-02T16:19	72.0010	14.7022	10	hydrate zone surface	0.04	0.02	0.06	32.0	3.3	1.0	0.0	0.0	0.4
PS64/326_PUC-12	2003-07-02T16:19	72.0010	14.7022	10	hydrate zone surface	0.08	0.06	0.10	31.2	#1.3	7.1	0.0	0.0	0.2
PS64/332-1	2003-07-02T16:37	72.0047	14.7262	11	new flow deep	4.25			5.7	#16.3	2.9	0.0	0.0	0.0
PS64/372-1	2003-07-11T12:52	72.0044	14.7266	12	aged flow deep	4.65			6.5	#2.8	0.0	0.0	0.0	0.0
PS64/371-1	2003-07-11T11:12	72.0033	14.7313	13	old flow deep	4.58			3.6	0.0	0.0	0.0	0.0	0.0
PS64/336-1	2003-07-05T08:23	72.0003	14.7355	15	hydrate zone deep	4.50			9.9	0.0	0.0	0.0	0.0	0.7
MSM16/2_809-1	2010-09-26T08:23	72.0067	14.7477	16	reference surface	0.01	0.00	0.02	63.3	2.9	1.0	0.2	#0.0
MSM16/2_809-1	2010-09-26T08:23	72.0067	14.7477	16	reference surface	0.04	0.02	0.06	66.9	1.9	0.6	0.0	0.0
MSM16/2_809-1	2010-09-26T08:23	72.0067	14.7477	16	reference surface	0.08	0.06	0.10	48.5	0.1	0.2	0.0	0.0