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Ruff, S Emil; Ramette, Alban; Boetius, Antje (2016): Relative abundance of prokaryotes in sediments of the Håkon Mosby mud volcano (Z1-Z3, all habitats) [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.861872, In supplement to: Ruff, S Emil; Felden, Janine; Gruber-Vodicka, Harald R; Marcon, Yann; Knittel, Katrin; Ramette, Alban; Boetius, Antje (2018): In situ development of a methanotrophic microbiome in deep-sea sediments. The ISME Journal, https://doi.org/10.1038/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: MSM16/2 (LOOME) * Basis: Maria S. Merian * 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: MSM16/2 (LOOME) * Basis: Maria S. Merian * 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: MSM16/2 (LOOME) * Basis: Maria S. Merian * 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):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Event labelEventRuff, S Emil
2Date/Time of eventDate/TimeRuff, S Emil
3Latitude of eventLatitudeRuff, S Emil
4Longitude of eventLongitudeRuff, S Emil
5Sample code/labelSample labelRuff, S Emil
6HabitatHabitatRuff, S Emil
7DEPTH, sediment/rockDepth sedmRuff, S EmilGeocode
8Depth, top/minDepth topmRuff, S Emil
9Depth, bottom/maxDepth botmRuff, S Emil
10Bacteria, targed with EUB338(I-III) oligonucleotide FISH-probeEUB338 I-III%Ruff, S EmilCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
11Archaea, targed with ARCH915 oligonucleotide FISH-probeARCH915%Ruff, S EmilCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
12Desulfusarcina/Desulfococcus, targeted with DSS658 oligonucleotide FISH-probeDSS658%Ruff, S EmilCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
13Methylococcaceae, targeted with MTMC701 oligonucleotide FISH-probeMTMC701%Ruff, S EmilCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
14Anaerobic methanotrophic archaea-3, targeted with ANME-3-1249 oligonucleotide FISH-probeANME-3-1249%Ruff, S EmilCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
15Desulfobulbus, targeted with DBB660 oligonucleotide FISH-probeDBB660%Ruff, S EmilCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)
License:
Creative Commons Attribution 3.0 Unported (CC-BY-3.0)
Size:
290 data points

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