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  • 2020-2024  (12)
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  • 1
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    Benthic bacterial communities in sandy surface sediments (Helgoland Roads, North Sea) (2021)
    PANGAEA
    Details
    Publication Date: 2024-04-20
    Description: Coastal sands are biocatalytic filters for dissolved and particulate organic matter of marine and terrestrial origin. In this study, we accessed the variability of benthic bacterial communities over two annual cycles at Helgoland Roads (North Sea, German Bight) sediments, where primary production does not occur during winter. Sediment cores were obtained by scientific divers. Benthic community structure in surface sediments (0-2 cm depth) was studied by 16S rRNA-based taxonomy (16S rRNA gene sequencing using primers S-D-Bact-0341-b-S-17 and S-D-Bact-0785-a-A-21, Illumina sequencing platform HiSeq2500, 2x250 bases, paired-end). Total organic carbon content was determined using 25-50 mg of freeze-dried sediments. To determine organic carbon, inorganic carbon was removed with 1 M HCl before analysis. Samples were analyzed in an Euro EA-CNS elemental analyser (HEKAtech, column temperature 75°C; carrier gas helium at 80 ml min-1, reactor temperature 1000°C with oxygen flow 10 ml min-1, oxidation time 7.9 sec) with thermal conductivity detection. Calibration was done with sulfanilamide (0.2 to 2 mg) standards.
    Keywords: 16S rRNA gene tags; bacterial community composition; German Bight; marine sediment; North Sea; TOC
    Type: Dataset
    Format: application/zip, 2 datasets
    Location Call Number Expected Availability
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  • 2
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    Benthic bacterial communities in coastal sandy sediments (Isfjorden, Svalbard) (2021)
    PANGAEA
    Details
    Publication Date: 2024-04-20
    Description: Coastal sands are biocatalytic filters for dissolved and particulate organic matter of marine and terrestrial origin. In this study, we accessed the variability of benthic bacterial communities over two annual cycles in Isfjorden (Svalbard, 78°N) sediments, where primary production does not occur during winter. Sandy sediment samples were obtained with a Van Veen grab. Benthic community structure in surface sediments (0-2 cm depth) was studied on the level of cell counts (DAPI staining, CARD-FISH) and 16S rRNA-based taxonomy (16S rRNA gene sequencing using primers S-D-Bact-0341-b-S-17 and S-D-Bact-0785-a-A-21, Illumina sequencing platform HiSeq2500, 2x250 bases, paired-end). Prior to DAPI staining and CARD-FISH, formaldehyde-fixed Svalbard sediment samples were sonicated on ice with a type MS2.5 probe (Sonoplus mini20; Bandelin, Berlin, Germany). Six sonication steps were done at a setting of 30 s, an amplitude of 86% and pulse of 0.2 s. Combined supernatants were filtered onto 0.2 µm pore size polycarbonate filters (GTTP, Millipore, Eschborn, Germany). Total organic carbon, total carbon, total organic nitrogen and total nitrogen contents were determined using 25-50 mg of freeze-dried sediments. To determine organic carbon, inorganic carbon was removed with 1 M HCl before analysis. Samples were analyzed in an Euro EA-CNS elemental analyser (HEKAtech, column temperature 75°C; carrier gas helium at 80 ml min-1, reactor temperature 1000°C with oxygen flow 10 ml min-1, oxidation time 7.9 sec) with thermal conductivity detection. Calibration was done with sulfanilamide (0.2 to 2 mg) standards.
    Keywords: Arctic; bacterial community composition; CARD-FISH; marine sediment; Svalbard; TOC
    Type: Dataset
    Format: application/zip, 2 datasets
    Location Call Number Expected Availability
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  • 3
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    Read frequencies of 16S rRNA genes of surface sediment samples from Isfjorden, Svalbard (2021)
    PANGAEA
    Details
    Publication Date: 2024-04-20
    Keywords: Arctic; bacterial community composition; Binary Object; Binary Object (File Size); Binary Object (Media Type); CARD-FISH; File content; ISF_05; ISF_06; ISF_07; ISF_23; Isfjord, Svalbard; marine sediment; Svalbard; Svalbard, Isfjorden; TOC; van Veen Grab; VGRAB
    Type: Dataset
    Format: text/tab-separated-values, 2 data points
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  • 4
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    Seasonal grain-size measurements of surface sediments off Helgoland (2021)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    Description: All sediment samples were obtained from Helgoland Roads (54.18°N, 7.90°E), which is located between the main island and the dune from Helgoland in the North Sea, German Bight, by scientific divers of the Alfred Wegner Institute (Bremerhaven, Germany) using push cores. Repeated sediment sampling was performed on a total of nineteen sampling dates in 2018 and 2019. Particle-size measurements were performed in the Particle-Size Laboratory at MARUM, University of Bremen with a Beckman Coulter Laser Diffraction Particle Size Analyzer LS 13320. Prior to the measurements, the samples were boiled with approximately 0.3 g tetra-sodium diphosphate decahydrate (Na~4~P~2~O~7~ * 10H~2~O, 3 min) to destroy aggregates. Sample preparation and measurements were carried out with deionized, degassed and filtered water (filter mesh size: 0.2 µm) to reduce the potential influence of gas bubbles or particles within the water. The obtained results provide the particle-size distribution of a sample from 0.04 to 2000 μm divided in 116 size classes. The calculation of the particle sizes relies on the Fraunhofer diffraction theory and the Polarization Intensity Differential Scattering (PIDS) for particles from 0.4 to 2000 µm and from 0.04 to 0.4 µm, respectively. The reproducibility is checked regularly by replicate analyses of three internal glass-bead standards and is found to be better than ±0.7 µm for the mean and ±0.6 µm for the median particle size (1sigma). The average standard deviation integrated over all size classes is better than ±4 vol% (note that the standard deviation of the individual size classes is not distributed uniformly). All provided statistic values are based on a geometric statistic.
    Keywords: German Bight; Helgoland; Seasonal grain-size distribution
    Type: Dataset
    Format: application/zip, 2 datasets
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  • 5
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    Seasonal grain-size measurements of surface sediments off Svalbard (2021)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    Description: All sediment samples were obtained from four stations close to the coast and within 1 km distance to each other (station 5: 78.11°N 14.35°E; station 6: 78.10°N 14.38°E; station 7: 78.10°N 14.38°E; station 23: 78.10°N 14.39°E) in Isfjorden, Svalbard, Arctic Ocean. The sampling was performed with a Van Veen grab deployed from R/V Farm. Six repeated sediment sampling campaigns took place between December 2017 and September 2019 (for further details see Miksch et al. 2020) Particle-size measurements were performed in the Particle-Size Laboratory at MARUM, University of Bremen with a Beckman Coulter Laser Diffraction Particle Size Analyzer LS 13320. Prior to the measurements, the samples were boiled with approximately 0.3 g tetra-sodium diphosphate decahydrate (Na~4~P~2~O~7~ * 10H~2~O, 3 min) to destroy aggregates. Sample preparation and measurements were carried out with deionized, degassed and filtered water (filter mesh size: 0.2 µm) to reduce the potential influence of gas bubbles or particles within the water. The obtained results provide the particle-size distribution of a sample from 0.04 to 2000 μm divided in 116 size classes. The calculation of the particle sizes relies on the Fraunhofer diffraction theory and the Polarization Intensity Differential Scattering (PIDS) for particles from 0.4 to 2000 µm and from 0.04 to 0.4 µm, respectively. The reproducibility is checked regularly by replicate analyses of three internal glass-bead standards and is found to be better than ±0.7 µm for the mean and ±0.6 µm for the median particle size (1 sigma). The average standard deviation integrated over all size classes is better than ±4 vol% (note that the standard deviation of the individual size classes is not distributed uniformly). All provided statistic values are based on a geometric statistic.
    Keywords: Isfjorden; Seasonal grain-size distribution; Svalbard
    Type: Dataset
    Format: application/zip, 2 datasets
    Location Call Number Expected Availability
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  • 6
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    Grain-size distribution of surface sediment samples from Helgoland Roads (2021)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    Keywords: Beckman Coulter Laser diffraction particle size analyzer LS 13 320; DATE/TIME; DEPTH, sediment/rock; German Bight; German Bight, North Sea; Helgoland; HelgolandRoads_site; Kabeltonne; Sample code/label; Seasonal grain-size distribution; Size fraction 0.044-0.04 µm; Size fraction 0.048-0.044 µm; Size fraction 0.053-0.048 µm; Size fraction 0.058-0.053 µm; Size fraction 0.064-0.058 µm; Size fraction 0.07-0.064 µm; Size fraction 0.077-0.07 µm; Size fraction 0.084-0.077 µm; Size fraction 0.093-0.084 µm; Size fraction 0.102-0.093 µm; Size fraction 0.112-0.102 µm; Size fraction 0.123-0.112 µm; Size fraction 0.134-0.123 µm; Size fraction 0.148-0.134 µm; Size fraction 0.162-0.148 µm; Size fraction 0.178-0.162 µm; Size fraction 0.195-0.178 µm; Size fraction 0.214-0.195 µm; Size fraction 0.235-0.214 µm; Size fraction 0.258-0.235 µm; Size fraction 0.284-0.258 µm; Size fraction 0.311-0.284 µm; Size fraction 0.342-0.311 µm; Size fraction 0.375-0.342 µm; Size fraction 0.412-0.375 µm; Size fraction 0.452-0.412 µm; Size fraction 0.496-0.452 µm; Size fraction 0.545-0.496 µm; Size fraction 0.598-0.545 µm; Size fraction 0.657-0.598 µm; Size fraction 0.721-0.657 µm; Size fraction 0.791-0.721 µm; Size fraction 0.869-0.791 µm; Size fraction 0.953-0.869 µm; Size fraction 1.047-0.954 µm; Size fraction 1.149-1.047 µm; Size fraction 1.261-1.149 µm; Size fraction 1.385-1.261 µm; Size fraction 1.520-1.385 µm; Size fraction 1.669-1.520 µm; Size fraction 1.832-1.669 µm; Size fraction 10.78-9.819 µm; Size fraction 101.1-92.1 µm; Size fraction 1041-948.3 µm; Size fraction 11.83-10.78 µm; Size fraction 111-101.1 µm; Size fraction 1143-1041 µm; Size fraction 12.99-11.83 µm; Size fraction 121.8-111 µm; Size fraction 1255-1143 µm; Size fraction 133.7-121.8 µm; Size fraction 1377-1255 µm; Size fraction 14.26-12.99 µm; Size fraction 146.8-133.7 µm; Size fraction 15.65-14.26 µm; Size fraction 1512-1377 µm; Size fraction 161.2-146.8 µm; Size fraction 1660-1512 µm; Size fraction 17.18-15.65 µm; Size fraction 176.9-161.2 µm; Size fraction 18.86-17.18 µm; Size fraction 1822-1660 µm; Size fraction 194.2-176.9 µm; Size fraction 2.000-1.822 mm; Size fraction 2.010-1.832 µm; Size fraction 2.208-2.011 µm; Size fraction 2.423-2.208 µm; Size fraction 2.66-2.423 µm; Size fraction 2.92-2.66 µm; Size fraction 20.70-18.86 µm; Size fraction 213.2-194.2 µm; Size fraction 22.73-20.70 µm; Size fraction 234.1-213.2 µm; Size fraction 24.95-22.73 µm; Size fraction 256.9-234.1 µm; Size fraction 27.38-24.95 µm; Size fraction 282.1-256.9 µm; Size fraction 3.206-2.920 µm; Size fraction 3.519-3.206 µm; Size fraction 3.862-3.519 µm; Size fraction 30.07-27.38 µm; Size fraction 309.6-282.1 µm; Size fraction 33.01-30.07 µm; Size fraction 339.9-309.6 µm; Size fraction 36.24-33.01 µm; Size fraction 373.1-339.9 µm; Size fraction 39.77-36.24 µm; Size fraction 4.241-3.862 µm; Size fraction 4.656-4.241 µm; Size fraction 409.6-373.1 µm; Size fraction 43.67-39.78 µm; Size fraction 449.7-409.6 µm; Size fraction 47.94-43.67 µm; Size fraction 493.6-449.7 µm; Size fraction 5.111-4.656 µm; Size fraction 5.611-5.111 µm; Size fraction 52.63-47.94 µm; Size fraction 541.9-493.6 µm; Size fraction 57.77-52.63 µm; Size fraction 594.9-541.9 µm; Size fraction 6.159-5.611 µm; Size fraction 6.761-6.159 µm; Size fraction 63.42-57.77 µm; Size fraction 653.0-594.9 µm; Size fraction 69.62-63.42 µm; Size fraction 7.421-6.761 µm; Size fraction 716.9-653.0 µm; Size fraction 76.43-69.62 µm; Size fraction 786.9-716.9 µm; Size fraction 8.148-7.422 µm; Size fraction 8.944-8.147 µm; Size fraction 83.90-76.43 µm; Size fraction 863.9-786.9 µm; Size fraction 9.819-8.944 µm; Size fraction 92.1-83.9 µm; Size fraction 948.2-863.9 µm
    Type: Dataset
    Format: text/tab-separated-values, 2223 data points
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  • 7
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    Grain-size statistics of surface sediments off Helgoland (2021)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    Keywords: Beckman Coulter Laser diffraction particle size analyzer LS 13 320; Covariance; DATE/TIME; DEPTH, sediment/rock; Geometric statistic; German Bight; German Bight, North Sea; Helgoland; HelgolandRoads_site; Kabeltonne; Kurtosis; Mean, statistical; Median, statistical; Mode, grain size; Mode, standard deviation; Percentile 10; Percentile 50; Percentile 90; Ratio; Sample code/label; Seasonal grain-size distribution; Size fraction; Skewness; Surface area; Variance; Volume
    Type: Dataset
    Format: text/tab-separated-values, 494 data points
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  • 8
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    Total organic carbon, organic carbon, and ENA accession numbers of surface sediment samples from Helgoland Roads, North Sea (2021)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    Keywords: 16S rRNA gene tags; Accession number, genetics; bacterial community composition; Carbon, organic, total; Carbon, total; DATE/TIME; Depth, bottom/max; DEPTH, sediment/rock; Depth, top/min; Element analyser CNS; German Bight; German Bight, North Sea; HelgolandRoads_site; Kabeltonne; marine sediment; North Sea; Sample code/label; Sequence read archive; bacteria; TOC
    Type: Dataset
    Format: text/tab-separated-values, 114 data points
    Location Call Number Expected Availability
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  • 9
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    Benthic community structure in surface sediments from Isfjorden, Svalbard (2021)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    Keywords: Accession number, genetics; Actinomarinales, cell abundance, targeted by oligonucleotide FISH probe ACM1218; Arctic; Bacteria, cell abundance, targeted by oligonucleotide FISH probe EUB338-I-III; bacterial community composition; Bacteroidota, cell abundance, targeted by oligonucleotide FISH probe CF319a; Calculated from DADA2 analysis; Carbon, organic, total; Carbon, total; CARD-FISH; Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH); Chlorophyll a; Cyclops-7, submersible sensor, Turner Designs, San Jose, USA; DATE/TIME; Depth, bottom/max; DEPTH, sediment/rock; Depth, top/min; DEPTH, water; Desulfobacterota, cell abundance, targeted by oligonucleotide FISH probe DELTA495a-c; Desulfobacterota of the Desulfosarcina/Desulfococcus branch cell abundance, targeted by oligonucleotide FISH probe DSS658; ELEVATION; Epifluorescence microscopy after DAPI staining; Event label; Gammaproteobacteria, cell abundance, targeted by oligonucleotide FISH probe GAM42a; Inverse Simpson index of diversity; ISF_05; ISF_06; ISF_07; ISF_23; Isfjord, Svalbard; Latitude of event; Longitude of event; marine sediment; Microtrichales, cell abundance, targeted by oligonucleotide FISH probe MIT1218; Nitrogen, organic, total; Nitrogen, total; Planctomycetota, cell abundance, targeted by oligonucleotide FISH probe PLA46; Prokaryotes, cell abundance; Salinity, absolute; Sample code/label; Sequence read archive; bacteria; Shannon Diversity Index; Svalbard; Svalbard, Isfjorden; Temperature, in rock/sediment; TOC; van Veen Grab; Verrucomicrobiota, cell abundance, targeted by oligonucleotide FISH probe EUB338-III; VGRAB
    Type: Dataset
    Format: text/tab-separated-values, 547 data points
    Location Call Number Expected Availability
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  • 10
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    Grain-size statistics of surface sediment samples off Svalbard (2021)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    Keywords: Beckman Coulter Laser diffraction particle size analyzer LS 13 320; Covariance; DATE/TIME; DEPTH, sediment/rock; Event label; Geometric statistic; ISF_05; ISF_06; ISF_07; ISF_23; Isfjord, Svalbard; Isfjorden; Kurtosis; Latitude of event; Longitude of event; Mean, statistical; Median, statistical; Mode, grain size; Mode, standard deviation; Percentile 10; Percentile 50; Percentile 90; Ratio; Sample code/label; Seasonal grain-size distribution; Size fraction; Skewness; Surface area; Svalbard; Svalbard, Isfjorden; van Veen Grab; Variance; VGRAB; Volume
    Type: Dataset
    Format: text/tab-separated-values, 572 data points
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