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Hoffmann, Katy; Bienhold, Christina; Buttigieg, Pier Luigi; Laso-Pérez, Rafael; Fadeev, Eduard; Rapp, Josephine Z; Boetius, Antje; Offre, Pierre (2017): Abundance of Prokaryotes in deep-sea sediments analyzed by CARD-FISH. PANGAEA, https://doi.org/10.1594/PANGAEA.874860, In supplement to: Hoffmann, Katy; Bienhold, Christina; Buttigieg, Pier Luigi; Knittel, Katrin; Laso-Pérez, Rafael; Rapp, Josephine Z; Boetius, Antje; Offre, Pierre (2020): Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities. The ISME Journal, 14(4), 1042-1056, https://doi.org/10.1038/s41396-020-0588-4

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Abstract:
We fixed 0.5 g aliquots of sediment with a 4% formaldehyde solution for 2-4 h, washed the fixed sediments three times with 1x phosphate-buffered saline (PBS), before storing them in 50% ethanol/PBS at -20°C. For water samples, we fixed 10 ml (for samples from the deep chlorophyll maximum and 100 m water depth) and 30 ml (for meso- and bathypelagic samples) with formaldehyde to a final concentration of 2-4% for 2-4 h, then filtered over a 0.22 µm polycarbonate filter, and stored samples at -20°C. We performed total cell counts as described by Schauer et al. (2011, doi:10.1111/j.1462-2920.2011.02530.x) using the nucleic acid dye 4'-6-diamidino-2-phenylindole (DAPI). A minimum of 1,000 cells in 20 independent grids were counted using a Zeiss Axio Imager M1 epifluorescence microscope equipped with a 100x/1.25 oil plan-apochromat objective. We used Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization (CARD-FISH) according to Ishii et al. (2004) to count Gammaproteobacteria and JTB255 cells. We used the GAM42a oligonucleotide probe and the BET42a competitor probe to target members of the Gammaproteobacteria (Manz et al., 1992, doi:10.1016/S0723-2020(11)80121-9). We designed the JTB819a and JTB897 probes to target 16S rRNA gene sequences assigned to JTB255 in SILVA release 128 and the cJTB897 competitor probe to target all non-JTB255 16S sequences in SILVA release 128 that have a single mismatch to JTB819a and JTB897 probes. We obtained total gammaproteobacterial and JTB255 cell counts from duplicate filters derived from each sampling site.
Related to:
Ruff, S Emil; Felden, Janine; Gruber-Vodicka, Harald R; Marcon, Yann; Knittel, Katrin; Ramette, Alban; Boetius, Antje (2014): Metagenom sequences of Archaea and Bacteria from sediment samples of the Haakon Mosby mud volcano. European Nucleotide Archive (ENA), insdc:PRJNA248084
Schauer, Regina; Røy, Hans; Augustin, Nico; Gennerich, Hans-Hermann; Peters, Marc; Wenzhöfer, Frank; Amann, Rudolf; Meyerdierks, Anke (2011): Bacterial sulfur cycling shapes microbial communities in surface sediments of an ultramafic hydrothermal vent field. Environmental Microbiology, 13(10), 2633-2648, https://doi.org/10.1111/j.1462-2920.2011.02530.x
Sokoll, Sarah; Holtappels, Moritz; Lam, Phyllis; Collins, Gavin; Schlüter, Michael; Lavik, Gaute; Kuypers, Marcel MM (2012): Benthic nitrogen loss in the Arabian Sea off Pakistan. Frontiers in Microbiology, 3, https://doi.org/10.3389/fmicb.2012.00395
Thiele, Stefan; Fuchs, Bernhard M; Amann, Rudolf; Iversen, Morten Hvitfeldt; Wommack, K Eric (2015): Colonization in the Photic Zone and Subsequent Changes during Sinking Determine Bacterial Community Composition in Marine Snow. Applied and Environmental Microbiology, 81(4), 1463-1471, https://doi.org/10.1128/AEM.02570-14
Coverage:
Median Latitude: 22.542717 * Median Longitude: -15.804435 * South-bound Latitude: -53.808830 * West-bound Longitude: -104.266667 * North-bound Latitude: 87.933380 * East-bound Longitude: 63.166680
Date/Time Start: 2007-01-29T13:17:24 * Date/Time End: 2015-09-15T02:36:11
Minimum DEPTH, sediment/rock: 0.005 m * Maximum DEPTH, sediment/rock: 0.110 m
Event(s):
AT26-23-05 * Latitude: 9.900000 * Longitude: -104.266667 * Elevation: -2600.0 m * Method/Device: Piston corer (PC)
AT26-23-12 * Latitude: 9.883333 * Longitude: -104.233333 * Elevation: -2800.0 m * Method/Device: Piston corer (PC)
GeoB12202-1 (M74/2_962-1) * Latitude Start: 24.700000 * Longitude Start: 63.166660 * Latitude End: 24.700000 * Longitude End: 63.166680 * Date/Time Start: 2007-10-09T02:15:00 * Date/Time End: 2007-10-09T03:50:00 * Elevation: -1527.0 m * Campaign: M74/2 * Basis: Meteor (1986) * Method/Device: MultiCorer (MUC)
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Event labelEventHoffmann, Katy
2Latitude of eventLatitudeHoffmann, Katy
3Longitude of eventLongitudeHoffmann, Katy
4Date/Time of eventDate/TimeHoffmann, Katy
5Elevation of eventElevationmHoffmann, Katy
6Sample IDSample IDHoffmann, Katy
7Depth, top/minDepth topmHoffmann, Katy
8Depth, bottom/maxDepth botmHoffmann, Katy
9DEPTH, sediment/rockDepthmHoffmann, KatyGeocode
10Environmental featureEnv featureHoffmann, Katybiome
11Environmental featureEnv featureHoffmann, Katymaterial
12Environmental featureEnv featureHoffmann, Katyfeature
13Sample typeSamp typeHoffmann, Katy
14Analytical methodMethodHoffmann, Katy
15Reference/sourceReferenceHoffmann, Katy
16CommentCommentHoffmann, Katy
17ProkaryotesProkaryotes#/mlHoffmann, KatyEpifluorescence microscopy after DAPI stainingminimum
18ProkaryotesProkaryotes#/mlHoffmann, KatyEpifluorescence microscopy after DAPI stainingmaximum
19Gammaproteobacteria, cellsGammaproteob103 #/mlHoffmann, KatyCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)minimum
20Gammaproteobacteria, cellsGammaproteob103 #/mlHoffmann, KatyCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)maximum
21GammaproteobacteriaGammaproteobacteria%Hoffmann, KatyCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)minimum
22GammaproteobacteriaGammaproteobacteria%Hoffmann, KatyCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)maximum
23Japan Trench Bacteria clone 255 marine benthic groupJTB255#/mlHoffmann, KatyCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)minimum
24Japan Trench Bacteria clone 255 marine benthic groupJTB255#/mlHoffmann, KatyCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)maximum
25Japan Trench Bacteria clone 255 marine benthic groupJTB255%Hoffmann, KatyCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)minimum
26Japan Trench Bacteria clone 255 marine benthic groupJTB255%Hoffmann, KatyCatalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH)maximum
27ReplicatesRepl#Hoffmann, Katy
Size:
648 data points

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