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 [dataset]. 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
Always quote citation above when using data! You can download the citation in several formats below.
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
Project(s):
Funding:
Seventh Framework Programme (FP7), grant/award no. 294757: Assessment of bacterial life and matter cycling in deep-sea surface sediments
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):
License:
Creative Commons Attribution 3.0 Unported (CC-BY-3.0)
Size:
648 data points
Data
| 1 Event | 2 Latitude | 3 Longitude | 4 Date/Time | 5 Elevation [m] | 6 Sample ID | 7 Depth top [m] | 8 Depth bot [m] | 9 Depth sed [m] | 10 Env feature (biome) | 11 Env feature (material) | 12 Env feature (feature) | 13 Samp type | 14 Method | 15 Reference | 16 Comment | 17 Prokaryotes [#/ml] (minimum, Epifluorescence micr...) | 18 Prokaryotes [#/ml] (maximum, Epifluorescence micr...) | 19 Gammaproteob [103 #/ml] (minimum, Catalysed reporter d...) | 20 Gammaproteob [103 #/ml] (maximum, Catalysed reporter d...) | 21 Gammaproteobacteria [%] (minimum, Catalysed reporter d...) | 22 Gammaproteobacteria [%] (maximum, Catalysed reporter d...) | 23 JTB255 [#/ml] (minimum, Catalysed reporter d...) | 24 JTB255 [#/ml] (maximum, Catalysed reporter d...) | 25 JTB255 [%] (minimum, Catalysed reporter d...) | 26 JTB255 [%] (maximum, Catalysed reporter d...) | 27 Repl [#] |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PS80/350-1 | 87.9334 | 61.1696 | 2012-09-18T11:25 | -4381 | AO.1a | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | this study | below multi-year ice | 618E6 | 658E6 | 3.26E3 | 3.47E3 | 500E-3 | 500E-3 | 6.42E6 | 6.94E6 | 1.0E0 | 1.1E0 | 2 |
| PS80/350-1 | 87.9334 | 61.1696 | 2012-09-18T11:25 | -4381 | AO.1b | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | this study | below multi-year ice; sediment with algal aggregate on top | 807E6 | 848E6 | 50.3E3 | 84.3E3 | 6.2E0 | 9.9E0 | 4.84E6 | 5.24E6 | 600E-3 | 600E-3 | 2 |
| PS80/225-1 | 84.0473 | 31.1926 | 2012-08-09T10:35 | -4019 | AO.2 | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | this study | ice edge | 1.05E9 | 1.09E9 | 1.38E3 | 1.91E3 | 100E-3 | 200E-3 | 26.6E6 | 30.6E6 | 2.5E0 | 2.7E0 | 2 |
| PS85/470-3 | 79.1335 | 6.1065 | 2014-06-24T23:34 | -1244 | AO.3a | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | this study | HGI | 1.34E9 | 1.94E9 | 83.9E3 | 140E3 | 6.3E0 | 7.2E0 | 105E6 | 166E6 | 7.8E0 | 8.6E0 | 18 |
| PS85/470-3 | 79.1335 | 6.1065 | 2014-06-24T23:34 | -1244 | AO.3b | 0.02 | 0.03 | 0.025 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | subsurface sediment | CARD-FISH | this study | HGI | 2.25E9 | 2.47E9 | 67.8E3 | 77.9E3 | 3.0E0 | 3.2E0 | 122E6 | 164E6 | 5.4E0 | 6.6E0 | 2 |
| PS85/470-3 | 79.1335 | 6.1065 | 2014-06-24T23:34 | -1244 | AO.3c | 0.04 | 0.05 | 0.045 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | subsurface sediment | CARD-FISH | this study | HGI | 2.05E9 | 2.07E9 | 37.3E3 | 48.5E3 | 1.8E0 | 2.3E0 | 58.3E6 | 59.8E6 | 2.8E0 | 2.9E0 | 2 |
| PS85/460-4 | 79.0652 | 4.1830 | 2014-06-22T18:47 | -2403 | AO.4a | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | this study | HGIV | 1.29E9 | 1.61E9 | 32.4E3 | 62.5E3 | 2.5E0 | 3.9E0 | 52.4E6 | 112E6 | 4.1E0 | 7.0E0 | 12 |
| PS85/464-1 | 79.0592 | 3.5728 | 2014-06-23T16:31 | -3531 | AO.5 | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | this study | HGVI | 765E6 | 796E6 | 11.8E3 | 21.9E3 | 1.5E0 | 2.8E0 | 56.8E6 | 59.8E6 | 7.4E0 | 7.5E0 | 2 |
| PS85/465-4 | 79.1583 | 2.8828 | 2014-06-24T02:48 | -5525 | AO.6 | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | this study | HGIX | 753E6 | 1.19E9 | 15.1E3 | 36E3 | 2.0E0 | 3.0E0 | 39E6 | 91.7E6 | 5.2E0 | 7.7E0 | 4 |
| PS85/436-1 | 78.9733 | -5.2905 | 2014-06-17T14:30 | -1056 | AO.7 | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | this study | EGI | 1.03E9 | 1.06E9 | 44.2E3 | 54.6E3 | 4.3E0 | 5.2E0 | 85.2E6 | 88.2E6 | 8.3E0 | 8.3E0 | 2 |
| PS85/454-3 | 78.5057 | -2.8177 | 2014-06-20T17:59 | -2558 | AO.8 | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | this study | EGIV | 937E6 | 1.05E9 | 25.3E3 | 55.7E3 | 2.7E0 | 5.3E0 | 28.3E6 | 48.9E6 | 3.0E0 | 4.7E0 | 4 |
| MSM04/3_251-ROV | 14.6672 | -45.0005 | 2007-01-29T13:17 | -3021 | NA.1 | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | Schauer et al. (2011) | Oceanic soft sediment; control site; not seep-influenced | 675E6 | 698E6 | 8.89E3 | 12.9E3 | 1.3E0 | 1.8E0 | 4.07E6 | 4.37E6 | 600E-3 | 600E-3 | 2 |
| MSM04/3_259-ROV | 14.7522 | -44.9805 | 2007-02-01T13:20 | -3032 | NA.2 | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | Schauer et al. (2011) | Logatchev hydrothermal vent field; Anya`s Garten; mat covered (elemental sulfur) | 1.35E9 | 2.01E9 | 5.15E3 | 7.82E3 | 400E-3 | 400E-3 | 0.0E0 | 0.0E0 | 0.0E0 | 0.0E0 | 4 |
| MSM04/3_271-ROV | 14.7526 | -44.9776 | 2007-02-05T13:08 | -3042 | NA.3 | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | Schauer et al. (2011) | Logatchev hydrothermal vent field; Quest, near T-logger #19; mat-free | 443E6 | 579E6 | 7.45E3 | 11.6E3 | 1.7E0 | 2.0E0 | 7.09E6 | 12.9E6 | 1.6E0 | 2.2E0 | 4 |
| AT26-23-12 | 9.8833 | -104.2333 | -2800 | NP.1 | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | S. Dyksma, unpublished data | dive 4774; soft silt mud | 1.47E9 | 1.53E9 | 8.18E3 | 21.9E3 | 600E-3 | 1.4E0 | 69E6 | 93E6 | 4.7E0 | 6.1E0 | 2 | |
| AT26-23-05 | 9.9000 | -104.2667 | -2600 | NP.2a | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | S. Dyksma, unpublished data | dive 4774; soft silt mud | 2.04E9 | 2.55E9 | 110E3 | 156E3 | 5.4E0 | 6.1E0 | 82.4E6 | 126E6 | 4.0E0 | 4.9E0 | 8 | |
| AT26-23-05 | 9.9000 | -104.2667 | -2600 | NP.2b | 0.10 | 0.12 | 0.110 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | subsurface sediment | CARD-FISH | S. Dyksma, unpublished data | dive 4774; soft silt mud | 1.03E9 | 1.11E9 | 0.0E0 | 0.0E0 | 0.0E0 | 0.0E0 | 0.0E0 | 0.0E0 | 2 | |||
| GeoB12202-1 | 24.7000 | 63.1667 | 2007-10-09T02:15 | -1527 | IO.1 | 0.00 | 0.02 | 0.010 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | Sokoll et al. (2012) | OMZ; N-limited; high seasonal surface production; GeoB St. No. 12202-1 | 1.23E9 | 1.27E9 | 60.1E3 | 93.1E3 | 4.9E0 | 7.3E0 | 49.1E6 | 50.1E6 | 4.0E0 | 3.9E0 | 2 |
| GeoB12202-2 | 24.7000 | 63.1667 | 2007-10-09T03:50 | -1526 | IO.2 | 0.00 | 0.02 | 0.010 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | Sokoll et al. (2012) | OMZ; N-limited; high seasonal surface production;GeoB St. No. 12202-2 | 1.33E9 | 1.44E9 | 71.2E3 | 93.2E3 | 5.4E0 | 6.5E0 | 54.7E6 | 59.7E6 | 4.1E0 | 4.1E0 | 2 |
| PS73/127-7 | -47.9923 | -16.0040 | 2009-01-31T03:51 | -4077 | SA.1a | 0.00 | 0.02 | 0.010 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | fluffy layer ontop of sediment | CARD-FISH | Thiele et al. (2015) | iron fertilization experiment LOHAFEX; cold-core eddy | 885E6 | 895E6 | 132E3 | 172E3 | 14.9E0 | 19.2E0 | 40.6E6 | 41.6E6 | 4.6E0 | 4.6E0 | 2 |
| PS73/127-7 | -47.9923 | -16.0040 | 2009-01-31T03:51 | -4077 | SA.1b | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | Thiele et al. (2015) | iron fertilization experiment LOHAFEX; cold-core eddy | 878E6 | 881E6 | 56.9E3 | 67.9E3 | 6.5E0 | 7.7E0 | 29.1E6 | 49.3E6 | 3.3E0 | 5.6E0 | 2 |
| SO242/2_147-148 | -7.1006 | -88.4140 | 2015-09-02T00:00 | -4198 | SP.1 | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | this study | DEA.W.undisturbed | 663E6 | 826E6 | 6.46E3 | 8.74E3 | 1.0E0 | 1.1E0 | 13.1E6 | 21.8E6 | 2.0E0 | 2.6E0 | 4 |
| SO242/2_194-1 | -7.0761 | -88.5266 | 2015-09-15T02:36 | -4079 | SP.2 | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | this study | DEA.W.undisturbed | 711E6 | 743E6 | 2.21E3 | 3.36E3 | 300E-3 | 500E-3 | 10.1E6 | 13.1E6 | 1.4E0 | 1.8E0 | 4 |
| SO242/2_198_MUC | -7.1256 | -88.4509 | 2015-09-03T00:00 | SP.6a | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | polymetallic nodule | CARD-FISH | this study | Ref.noduleOnTopOfSediment | 453E6 | 555E6 | 4.04E3 | 5.11E3 | 900E-3 | 900E-3 | 0.0E0 | 0.0E0 | 0.0E0 | 0.0E0 | 2 | |
| SO242/2_198_MUC | -7.1256 | -88.4509 | 2015-09-03T00:00 | SP.8a | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | polymetallic nodule | CARD-FISH | this study | Ref.noduleOnTopOfSediment | 484E6 | 585E6 | 0.0E0 | 0.0E0 | 0.0E0 | 0.0E0 | 0.0E0 | 0.0E0 | 0.0E0 | 2 | ||
| PS79/086-28 | -51.9790 | -12.0352 | 2012-02-01T18:59 | AntO.1 | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | Ruff et al. (2014) | B86; short exposure to bloom-derived material | 394E6 | 492E6 | 23E3 | 32.2E3 | 5.8E0 | 6.5E0 | 19.7E6 | 32.8E6 | 5.0E0 | 6.7E0 | 8 | |
| PS79/141-9 | -51.2672 | -12.6177 | 2012-02-18T22:58 | AntO.2 | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | Ruff et al. (2014) | B141; long exposure to bloom-derived material | 332E6 | 504E6 | 8.31E3 | 15.4E3 | 2.5E0 | 3.1E0 | 16.2E6 | 25.7E6 | 4.9E0 | 5.1E0 | 8 | |
| PS81/606-1 | -51.4298 | 14.2223 | 2013-11-16T17:51 | -4469 | AntO.3d | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | this study | control outside the ridge valley | 297E6 | 332E6 | 18E3 | 23.7E3 | 6.1E0 | 7.1E0 | 7.64E6 | 9.28E6 | 2.6E0 | 2.8E0 | 6 |
| PS93/067-2 | 78.6280 | 10.5838 | 2015-08-06T17:23 | -67 | AO.9a | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | this study | FixO3 I | 2.43E9 | 2.68E9 | 107E3 | 127E3 | 4.4E0 | 4.7E0 | 32.9E6 | 36.9E6 | 1.4E0 | 1.4E0 | 2 |
| PS93/067-2 | 78.6280 | 10.5838 | 2015-08-06T17:23 | -67 | AO.9b | 0.02 | 0.03 | 0.025 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | subsurface sediment | CARD-FISH | this study | FixO3 I | 2.32E9 | 2.58E9 | 75.4E3 | 87E3 | 3.3E0 | 3.4E0 | 4.01E6 | 4.57E6 | 200E-3 | 200E-3 | 2 |
| PS79/177-3 | -53.8088 | -52.3552 | 2012-03-07T13:22 | -339 | AntO.7 | 0.00 | 0.01 | 0.005 | marine benthic biome(ENVO:01000024) | marine sediment(ENVO:00002113) | marine benthic feature(ENVO:01000105) | surface sediment | CARD-FISH | Ruff et al. (2014) | R177; reference station | 605E6 | 2.36E9 | 37.3E3 | 87.4E3 | 3.7E0 | 6.2E0 | 24.5E6 | 111E6 | 4.0E0 | 4.7E0 | 6 |