Schauberger, Clemens; Middelboe, Mathias; Glud, Ronnie N (2024): Quantification of microbial cells and virus-like particles in sediments from Kermadec Trench [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.965926
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Published: 2024-03-04 • DOI registered: 2024-04-02
Abstract:
Sediment cores from sites K3, K4, K5, and K7 were recovered by subsampling a box corer (50 × 50 cm), while sediment cores from sites K4 and K6 were collected using an autonomous lander system. Microbes and virus-like particles were extracted from sediments in a 3°C room using a modified version of the washing protocol of Danovaro and Middelboe, 2010 (see Schauberger et al., 2021). After the washing procedure, the extracted microbial cells and virus-like particles were fixed with 25% glutaraldehyde (1% final concentration) and stored at −80°C prior to flow cytometry. These samples were measured in triplicates using a BD FACSCanto™ II flow cytometer, after staining with SYBR Green I. Sediment extracts were diluted 1 : 10 in 0.02 μm-filtered TE Buffer prior to all measurements. The flow rate was 5–7 μl/min, as determined by BD Trucount™ Beads. The laser settings and gating examples can be found in the Supporting Information of Schauberger et al. (2021).
Keyword(s):
Related to:
Schauberger, Clemens; Middelboe, Mathias; Larsen, Morten; Peoples, Logan M; Bartlett, Douglas H; Kirpekar, Finn; Rowden, Ashley A; Wenzhöfer, Frank; Thamdrup, Bo; Glud, Ronnie N (2021): Spatial variability of prokaryotic and viral abundances in the Kermadec and Atacama Trench regions. Limnology and Oceanography, 66(6), 2095-2109, https://doi.org/10.1002/lno.11711
Funding:
Danish National Research Foundation (DG), grant/award no. DNRF145: Danish Center for Hadal Research, HADAL
Coverage:
Median Latitude: -31.558486 * Median Longitude: -176.940020 * South-bound Latitude: -32.187000 * West-bound Longitude: -177.398500 * North-bound Latitude: -30.380700 * East-bound Longitude: -176.561000
Date/Time Start: 2017-11-30T00:00:00 * Date/Time End: 2017-12-10T11:01:02
Minimum DEPTH, sediment/rock: 0.005 m * Maximum DEPTH, sediment/rock: 0.375 m
Event(s):
TAN1711_K3 (Site K3) * Latitude: -30.380700 * Longitude: -176.641300 * Date/Time Start: 2017-12-03T09:33:01 * Date/Time End: 2017-12-03T15:33:02 * Elevation: -9540.0 m * Location: Kermadec Trench * Campaign: TAN1711 * Basis: Tangaroa * Method/Device: Box corer (BC)
Parameter(s):
| # | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
|---|---|---|---|---|---|---|
| 1 | Event label | Event | ||||
| 2 | Station label | Station | Schauberger, Clemens | |||
| 3 | Latitude of event | Latitude | ||||
| 4 | Longitude of event | Longitude | ||||
| 5 | Date/Time of event | Date/Time | ||||
| 6 | Elevation of event | Elevation | m | |||
| 7 | Depth, top/min | Depth top | m | Schauberger, Clemens | ||
| 8 | Depth, bottom/max | Depth bot | m | Schauberger, Clemens | ||
| 9 | DEPTH, sediment/rock | Depth sed | m | Schauberger, Clemens | Geocode | |
| 10 | Microbial abundance, cells | Microbial abund | #/ml | Schauberger, Clemens | Flow cytometry system, Becton Dickinson, FACSCanto II | |
| 11 | Microbial abundance, standard deviation | Microbial abund std dev | ± | Schauberger, Clemens | ||
| 12 | Viral abundance | Virus | #/ml | Schauberger, Clemens | Flow cytometry system, Becton Dickinson, FACSCanto II | |
| 13 | Viral abundance, standard deviation | Virus std dev | ± | Schauberger, Clemens | ||
| 14 | Carbon, organic, total | TOC | % | Schauberger, Clemens |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
914 data points