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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: 2024-03-04DOI registered: 2024-04-02

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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):
Abundance; Bacteria; Deep sea; flow cytometry; Hadal trench; organic matter; prokaryote; sediment; virus-like particles
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)
TAN1711_K4-1 (Site K4)  * Latitude: -31.140200 * Longitude: -176.808000 * Date/Time Start: 2017-12-08T03:47:01 * Date/Time End: 2017-12-08T09:47:02 * Elevation: -9300.0 m * Location: Kermadec Trench * Campaign: TAN1711 * Basis: Tangaroa * Method/Device: Box corer (BC)
TAN1711_K5-1 (Site K5)  * Latitude: -31.935700 * Longitude: -177.291300 * Date/Time Start: 2017-12-10T05:01:01 * Date/Time End: 2017-12-10T11:01:02 * Elevation: -10010.0 m * Location: Kermadec Trench * Campaign: TAN1711 * Basis: Tangaroa * Method/Device: Box corer (BC)
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
Event labelEvent
Station labelStationSchauberger, Clemens
Latitude of eventLatitude
Longitude of eventLongitude
Date/Time of eventDate/Time
Elevation of eventElevationm
Depth, top/minDepth topmSchauberger, Clemens
Depth, bottom/maxDepth botmSchauberger, Clemens
DEPTH, sediment/rockDepth sedmSchauberger, ClemensGeocode
10 Microbial abundance, cellsMicrobial abund#/mlSchauberger, ClemensFlow cytometry system, Becton Dickinson, FACSCanto II
11 Microbial abundance, standard deviationMicrobial abund std dev±Schauberger, Clemens
12 Viral abundanceVirus#/mlSchauberger, ClemensFlow cytometry system, Becton Dickinson, FACSCanto II
13 Viral abundance, standard deviationVirus std dev±Schauberger, Clemens
14 Carbon, organic, totalTOC%Schauberger, Clemens
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
914 data points

Data

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


Event

Station

Latitude

Longitude

Date/Time

Elevation [m]

Depth top [m]

Depth bot [m]

Depth sed [m]
10 
Microbial abund [#/ml]
11 
Microbial abund std dev [±]
12 
Virus [#/ml]
13 
Virus std dev [±]
14 
TOC [%]
TAN1711_K3 Site K3-30.3807-176.64132017-12-03T09:33:01-95400.0000.0100.0059.07E0071.69E0072.10E0082.23E0070.323
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.0100.0200.0155.75E0075.10E0061.75E0085.23E0060.229
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.0200.0400.0304.66E0071.11E0061.76E0086.70E0060.261
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.0400.0600.0503.44E0073.38E0062.01E0082.32E0070.308
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.0600.0800.0702.46E0079.76E0061.96E0082.15E0070.198
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.0800.1000.0902.27E0075.27E0061.10E0082.83E0070.233
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.1000.1500.1254.14E0072.77E0052.03E0087.80E0070.275
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.1500.2000.1754.05E0073.27E0061.60E0084.34E0070.269
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.2000.2500.2255.70E0076.10E0051.06E0081.08E0070.269
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.2500.3000.2756.48E0071.11E0071.34E0088.83E0070.318
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.3000.3500.3251.53E0088.37E0063.17E0085.88E007
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.3500.4000.3751.41E0081.37E0071.92E0086.04E007
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.0000.0100.0053.65E0076.53E0052.05E0081.05E0070.281
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.0100.0200.0152.15E0071.48E0061.44E0081.17E0070.212
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.0200.0400.0303.25E0071.04E0061.97E0081.35E0070.246
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.0400.0600.0501.74E0073.53E0062.62E0086.49E0060.269
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.0600.0800.0701.49E0071.84E0061.99E0081.81E0070.193
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.0800.1000.0901.07E0072.67E0051.05E0085.50E0070.213
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.1000.1500.1251.49E0071.04E0061.07E0083.29E0070.261
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.1500.2000.1751.65E0078.90E0041.56E0089.34E0070.263
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.2000.2500.2252.69E0071.31E0061.04E0088.22E0070.259
TAN1711_K3Site K3-30.3807-176.64132017-12-03T09:33:01-95400.2500.3000.2753.66E0078.01E0055.41E0073.41E0070.335
TAN1711_K4-1 Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0000.0100.0052.68E0071.36E0051.24E0071.75E0070.462
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0100.0200.0151.15E0079.98E0051.26E0077.98E0060.267
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0200.0400.0301.23E0072.27E0051.99E0075.07E0060.184
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0400.0600.0501.38E0072.81E0062.51E0077.15E0060.201
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0600.0800.0703.44E0072.00E0061.04E0084.99E0050.194
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0800.1000.0903.22E0074.08E0061.06E0084.57E0050.153
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.1000.1500.1252.37E0074.04E0064.56E0075.20E0060.394
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.1500.2000.1751.03E0072.72E0054.43E0074.11E0060.344
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.2000.2500.2252.98E0067.26E0058.96E0064.57E005
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.2500.3000.2753.97E0063.95E0062.27E0071.79E007
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0000.0100.0051.96E0073.87E0062.70E0076.06E0060.432
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0100.0200.0151.18E0075.58E0053.09E0073.39E0060.227
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0200.0400.0301.34E0072.31E0063.45E0079.34E0060.174
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0400.0600.0501.87E0073.90E0064.52E0071.13E0060.158
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0600.0800.0704.03E0073.61E0062.69E0081.00E0070.206
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0800.1000.0902.91E0074.83E0051.40E0081.93E0070.138
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.1000.1500.1252.20E0071.45E0068.05E0072.77E0070.376
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.1500.2000.1751.97E0074.91E0069.16E0075.44E0060.344
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.2000.2500.2251.25E0066.32E0051.32E0072.16E006
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.2500.3000.2752.43E0069.67E0051.59E0074.47E006
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0000.0100.0057.69E0071.20E0071.14E0086.85E0070.447
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0100.0200.0158.56E0075.72E0051.10E0081.62E0070.247
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0200.0400.0302.07E0071.26E0062.06E0076.71E0050.179
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0400.0600.0501.10E0071.60E0061.03E0078.09E0060.179
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0600.0800.0701.36E0071.87E0062.29E0071.28E0070.200
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.0800.1000.0901.37E0071.83E0065.60E0072.71E0070.145
TAN1711_K4-1Site K4-31.1402-176.80802017-12-08T03:47:01-93000.1000.1500.1252.27E0072.67E0051.19E0083.48E0070.385
TAN1711_K5-1 Site K5-31.9357-177.29132017-12-10T05:01:01-100100.0000.0100.0052.98E0071.34E0063.00E0072.42E0070.216
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.0100.0200.0152.48E0073.73E0054.49E0077.66E0060.253
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.0200.0400.0303.22E0071.08E0063.72E0071.97E0070.261
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.0400.0600.0502.78E0072.35E0061.60E0077.72E0060.174
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.0600.0800.0701.86E0073.58E0062.22E0074.76E0050.168
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.0800.1000.0903.48E0073.99E0062.55E0074.90E0060.175
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.1000.1500.1256.26E0073.36E0051.19E0081.55E0070.291
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.1500.2000.1754.01E0071.80E0071.30E0083.83E0070.246
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.2000.2500.2255.32E0079.89E0068.20E0075.72E0070.244
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.2500.3000.2753.05E0078.58E0053.70E0072.53E0070.218
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.3000.3500.3253.87E0073.32E0068.28E0078.56E0070.187
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.0000.0100.0052.43E0071.82E0061.25E0086.11E0050.025
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.0100.0200.0152.38E0071.06E0061.61E0087.34E0050.096
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.0200.0400.0302.42E0072.73E0052.02E0081.10E0070.271
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.0400.0600.0502.12E0071.03E0078.75E0074.77E0060.174
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.0600.0800.0702.79E0078.59E0068.90E0076.36E0060.165
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.0800.1000.0901.13E0078.20E0054.54E0071.24E0070.148
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.1000.1500.1253.06E0071.34E0068.66E0071.47E0060.293
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.1500.2000.1754.49E0078.86E0061.14E0081.07E0070.251
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.2000.2500.2253.16E0075.77E0062.32E0084.73E0060.277
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.2500.3000.2752.44E0071.21E0071.91E0081.02E0070.262
TAN1711_K5-1Site K5-31.9357-177.29132017-12-10T05:01:01-100100.3000.3500.3251.87E0074.28E0061.40E0081.76E0070.297
TAN1711_K6 Site K6-32.1488-177.39852017-11-30T00:00:00-95550.0000.0100.0055.68E0071.69E0074.64E0081.03E0080.452
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.0100.0200.0154.47E0073.75E0076.62E0086.23E0070.426
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.0200.0400.0305.10E0074.09E0066.11E0081.70E0080.435
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.0400.0600.0503.11E0079.93E0062.92E0082.99E0060.392
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.0600.0800.0702.87E0077.80E0061.55E0089.45E0070.361
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.0800.1000.0901.97E0071.23E0061.04E0083.92E0060.362
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.1000.1500.1252.30E0072.66E0063.19E0085.34E0070.334
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.1500.2000.1753.58E0074.79E0067.52E0082.32E0080.321
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.2000.2500.2251.69E0071.49E0063.45E0081.16E0080.373
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.2500.3000.2758.67E0064.32E0062.35E0087.48E0070.323
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.3000.3500.3253.05E0079.49E0064.74E0082.18E0080.327
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.3500.4000.3753.81E0075.52E0064.97E0082.17E0080.305
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.0000.0100.0057.25E0072.32E0075.68E0088.14E0070.404
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.0100.0200.0154.54E0072.13E0066.97E0081.84E0060.381
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.0200.0400.0304.45E0071.41E0077.93E0083.37E0070.402
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.0400.0600.0502.67E0073.10E0063.74E0084.81E0070.372
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.0600.0800.0702.67E0072.92E0041.67E0081.54E0080.354
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.0800.1000.0902.10E0071.05E0061.78E0089.88E0070.342
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.1000.1500.1252.20E0071.55E0064.11E0084.55E0070.324
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.1500.2000.1755.13E0073.50E0067.67E0081.85E0080.331
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.2000.2500.2252.93E0074.82E0063.00E0082.24E0080.346
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.2500.3000.2754.57E0071.36E0072.67E0081.89E0080.323
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.3000.3500.3253.24E0071.08E0063.78E0081.35E0080.316
TAN1711_K6Site K6-32.1488-177.39852017-11-30T00:00:00-95550.3500.4000.3752.55E0071.55E0066.01E0082.82E0080.340
TAN1711_K7 Site K7-32.1870-176.56102017-12-10T00:00:00-60800.0000.0100.0057.21E0071.23E0071.24E0081.04E0060.386
TAN1711_K7Site K7-32.1870-176.56102017-12-10T00:00:00-60800.0100.0200.0155.68E0071.77E0058.07E0077.46E0060.354
TAN1711_K7Site K7-32.1870-176.56102017-12-10T00:00:00-60800.0200.0400.0303.91E0071.33E0072.65E0075.10E0060.303
TAN1711_K7Site K7-32.1870-176.56102017-12-10T00:00:00-60800.0400.0600.0503.46E0075.67E0054.72E0073.69E0060.298
TAN1711_K7Site K7-32.1870-176.56102017-12-10T00:00:00-60800.0600.0800.0702.77E0075.35E0062.02E0077.46E0050.296
TAN1711_K7Site K7-32.1870-176.56102017-12-10T00:00:00-60800.0800.1000.0902.03E0074.57E0062.73E0062.61E0060.319
TAN1711_K7Site K7-32.1870-176.56102017-12-10T00:00:00-60800.1000.1500.1251.01E0079.92E0059.11E0062.28E0060.299
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TAN1711_K7Site K7-32.1870-176.56102017-12-10T00:00:00-60800.0800.1000.0901.38E0079.41E0058.91E0064.59E0060.274
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