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  • 1
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    Relative abundances and microbial numbers of organisms from water sample station GeoB15704-2 (2015)
    PANGAEA
    In:  Supplement to: 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
    Details
    Publication Date: 2023-03-03
    Description: Due to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washed in situ to prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be "inherited" from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather than de novo colonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.
    Keywords: Center for Marine Environmental Sciences; MARUM
    Type: Dataset
    Format: application/zip, 2 datasets
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  • 2
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    Short term changes in polysaccharide utilisation during a spring phytoplankton bloom on Helgoland (2019)
    PANGAEA
    Details
    Publication Date: 2023-07-06
    Description: Spring phytoplankton blooms contribute significantly to global marine primary production. A large fraction of the bloom derived organic matter is available to heterotrophic bacteria in the form of polysaccharides. We analyzed changes in the modes of polysaccharide utilization (selfish uptake and extracellular hydrolysis) during a spring phytoplankton bloom using fluorescently labelled polysaccharide incubations coupled with 16s rRNA sequencing and fluorescence in situ hybridization. We found that in the early bloom phases there was high selfish activity of simple polysaccharides (laminarin) and low extracellular hydrolysis rates of a limited range of polysaccharides. During the course of the bloom both the selfish uptake and extracellular hydrolysis rates increased but only for a limited range of substrates. At the late bloom phase a wide range of substrate was extracellularly hydrolyzed and the level of selfish uptake decreased. We found that during a spring phytoplankton bloom the mode of substrate utilization depended on both the substrates structural complexity and the composition of the heterotrophic community related to the bloom phase.
    Keywords: Alteromonadales, substrate stained; Alteromonadales, targeted with ALT1413 oligonucleiotide FISH-Probe; Bacterioplankton; Bacteroidetes, substrate stained; Bacteroidetes, targeted with CF319a oligonucliotide FISH-Probe; DATE/TIME; DEPTH, water; Device type; Experiment day; Fluorescence in situ hybridization (FISH); German Bight, North Sea; HelgolandRoads_site; Kabeltonne; Microbial abundance, cells; Sample code/label; Sample ID; Size; Substrate type; Volume
    Type: Dataset
    Format: text/tab-separated-values, 1448 data points
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  • 3
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    Microbial community composition of sandy intertidal sediments of Sylt-Rømø Basin, Wadden Sea (2016)
    PANGAEA
    In:  Supplement to: Musat, Niculina; Werner, Ursula; Knittel, Katrin; Kolb, Steffen; Dodenhof, Tanja; van Beusekom, Justus; de Beer, Dirk; Dubilier, Nicole; Amann, Rudolf (2006): Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea. Systematic and Applied Microbiology, 29(4), 333-348, https://doi.org/10.1016/j.syapm.2005.12.006
    Details
    Publication Date: 2023-07-10
    Description: Molecular biological methods were used to investigate the microbial diversity and community structure in intertidal sandy sediments near the island of Sylt (Wadden Sea) at a site which was characterized for transport and mineralization rates in de Beer et al., (2005, hdl:10013/epic.21375). The sampling was performed during low tide in the middle of the flat, approximately 40 m in the offshore direction from the high water line on October 6, 1999, March 7, 2000, and July 5, 2000. Two parallel cores were collected from each season for molecular analyses. Within 2 h after sampling the sediment cores were sub-sampled and fixed in formaldehyde for FISH analysis. The cells were hybridized, stained with 4',6'-diamidino-2-phenylindole (DAPI) and microscopically counted as described previously [55]. Details of probes and formamide concentrations which were used are shown in further details. Counts are reported as means calculated from 10-15 randomly chosen microscopic fields corresponding to 700-1000 DAPI-stained cells. Values were corrected for the signals counted with the probe NON338. Fluorescence in situ hybridization (FISH)with group-specific rRNA-targeted oligonucleotide probes were used to characterize the microbial community structure over depth (0-12 cm) and seasons (March, July, October). We found high abundances of bacteria with total cell numbers up to 3×109 cells ml-1 and a clear seasonal variation, with higher values in July and October versus March. The microbial community was dominated by members of the Planctomycetes, the Cytophaga/Flavobacterium group, Gammaproteobacteria, and bacteria of the Desulfosarcina/Desulfococcus group. The high abundance (1.5×10**7 - 1.8×10**8 cells/ml accounting for 3-19% of all cells) of presumably aerobic heterotrophic polymer-degrading planctomycetes is in line with the high permeability, deep oxygen penetration, and the high rates of aerobic mineralization of algal biomass measured in the sandy sediments by de Beer et al., (2005, hdl:10013/epic.21375). The high and stable abundance of members of the Desulfosarcina/Desulfococcus group, both over depth and season, suggests that these bacteria may play a more important role than previously assumed based on low sulfate reduction rates in parallel cores de Beer et al., (2005).
    Keywords: Bacteria, targeted with EUB338 l oligonucleotides FISH-probe; Core; CORE; Cytophaga-Flavobacterium cluster, targeted with CF319a oligonucleotide FISH-probe; Date/Time of event; DEPTH, sediment/rock; Desulfusarcina/Desulfococcus, targeted with DSS658 oligonucleotide FISH-probe; Epifluorescence microscopy after DAPI staining; Event label; Fluorescence in situ hybridization (FISH); Gammaproteobacteria, targeted with Gam42a oligonucleotide FISH-probe; Latitude of event; Longitude of event; Planctomycetales, targeted with PLA886 oligonucleotide FISH-probe; Prokaryotes, number of cell; WaddenSea_Sylt-03-2000; WaddenSea_Sylt-06-1999; WaddenSea_Sylt-07-2000; WaddenSea_Sylt-10-1999; Wadden Sea, North Sea, Germany
    Type: Dataset
    Format: text/tab-separated-values, 362 data points
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  • 4
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    Microbial community in the sediment of the arctic Smeerenburgfjorden (2016)
    PANGAEA
    In:  Supplement to: Ravenschlag, Katrin; Sahm, Kerstin; Amann, Rudolf (2001): Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Applied and Environmental Microbiology, 67(1), 387-395, https://doi.org/10.1128/AEM.67.1.387-395.2001
    Details
    Publication Date: 2023-07-10
    Description: Fluorescence in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes were used to investigate the phylogenetic composition of a marine Arctic sediment (Svalbard). Hybridization and microscopy counts of hybridized and 4',6'-diamidino-2-phenylindole (DAPI)-stained cells were performed as described previously from Snaidr et al. (1997, http://aem.asm.org/content/63/7/2884.full.pdf). Means were calculated from 10 to 20 randomly chosen fields on each filter section, corresponding to 800 to 1,000 DAPI-stained cells. Counting results were always corrected by subtracting signals observed with the probe NON338. Formamide concentrations are given in further details. FISH resulted in the detection of a large fraction of microbes living in the top 5 cm of the sediment. Up to 65.4% ± 7.5% of total DAPI cell counts hybridized to the bacterial probe EUB338, and up to 4.9% ± 1.5% hybridized to the archaeal probe ARCH915. Besides delta-proteobacterial sulfate-reducing bacteria (up to 16% 52) members of the Cytophaga-Flavobacterium cluster were the most abundant group detected in this sediment, accounting for up to 12.8% of total DAPI cell counts. Furthermore, members of the order Planctomycetales accounted for up to 3.9% of total cell counts. In accordance with previous studies, these findings support the hypothesis that these bacterial groups are not simply settling with organic matter from the pelagic zone but are indigenous to the anoxic zones of marine sediments. Members of the gamma-proteobacteria also constituted a significant fraction in this sediment (6.1% ± 2.5% of total cell counts). A new probe (GAM660) specific for sequences affiliated with free-living or endosymbiotic sulfur-oxidizing bacteria was developed. A significant number of cells was detected by this probe (2.1% ± 0.7% of total DAPI cell counts), showing no clear zonation along the vertical profile. Gram-positive bacteria and the beta-proteobacteria were near the detection limit in all sediments.
    Keywords: Archaea, targed with ARCH915 oligonucleotide FISH-probe; Bacteria, targeted with EUB338 l oligonucleotides FISH-probe; Core; CORE; Cytophaga-Flavobacterium cluster, targeted with CF319a oligonucleotide FISH-probe; DEPTH, sediment/rock; Epifluorescence microscopy after DAPI staining; Event label; Fluorescence in situ hybridization (FISH); Gammaproteobacteria, targeted with Gam42a oligonucleotide FISH-probe; Gammaproteobacteria, targeted with GAM660 oligonucleotide FISH-probe; Latitude of event; Longitude of event; Planctomycetales, targeted with PLA886 oligonucleotide FISH-probe; Prokaryotes, abundance as single cells; SBF_19980728; Smeerenburgfjorden, Svalbard
    Type: Dataset
    Format: text/tab-separated-values, 220 data points
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  • 5
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    A biogeographical study of microbial substrate utilisation in the Atlantic Ocean (2018)
    PANGAEA
    In:  Supplement to: Reintjes, Greta; Arnosti, Carol; Fuchs, Bernhard M; Amann, Rudolf (2019): Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation. The ISME Journal, 13(5), 1119-1132, https://doi.org/10.1038/s41396-018-0326-3
    Details
    Publication Date: 2023-07-10
    Description: A large fraction of the organic matter fixed in the oceans is transformed and remineralised by marine heterotrophic microorganisms. They, therefore, play a critical role in the marine carbon cycle. In this study, we set out to identify the roles played by individual heterotrophic bacteria in the degradation of high molecular weight polysaccharides. At five sites in the Atlantic Ocean, we investigated the processing of organic matter in microbial communities by tracking the changes in community composition (fluorescence in situ hybridisation (FISH), 16S rRNA tag sequencing) in substrate incubation using a defined concentration of a known fluorescently labelled polysaccharide (FLA-laminarin, FLA-xylan, and FLA-chondroitin sulfate). Additionally, we tracked the dynamics of substrate processing (selfish uptake and extracellular hydrolysis) within the microbial communities between sites. We found that the same substrate was processed in different ways by different members of a pelagic microbial community which points to significant follow-on effects for carbon cycling.
    Keywords: Abundance; Alteromonadales, substrate stained; Alteromonadales, targeted with ALT1413 oligonucleiotide FISH-Probe; AMT22-46; ATM22; ATM22_JC079_CTD-24; ATM22_JC079_CTD-38; ATM22_JC079_CTD-57; ATM22_JC079_CTD-8; Bacteroidetes, substrate stained; Bacteroidetes, targeted with CF319a oligonucliotide FISH-Probe; Catenovulum, substrate stained; Catenovulum, targets with CAT653 oligonucleotide FISH-Probe; CTD/Rosette; CTD-RO; Date/Time of event; DEPTH, water; Event label; Experiment day; Fluorescence in situ hybridization (FISH); James Cook; JC079; JC079-04; JC079-12; JC079-19; JC079-28; JC079-46; Latitude of event; Longitude of event; Microbial abundance, cells; Optional event label; Planctomycetes, substrate stained; Planctomycetes, targeted with PLA46 oligonucliotide FISH-Probe; Sample ID; Substrate type
    Type: Dataset
    Format: text/tab-separated-values, 3490 data points
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  • 6
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    Relative abundance of prokaryotic picoplankton populations in the Atlantic Ocean (2013)
    PANGAEA
    In:  Supplement to: Schattenhofer, Martha; Fuchs, Bernhard M; Amann, Rudolf; Zubkov, Mikhail V; Tarran, Glen A; Pernthaler, Jakob (2009): Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean. Environmental Microbiology, 11(8), 2078-2093, https://doi.org/10.1111/j.1462-2920.2009.01929.x
    Details
    Publication Date: 2023-09-23
    Description: Members of the prokaryotic picoplankton are the main drivers of the biogeochemical cycles over large areas of the world's oceans. In order to ascertain changes in picoplankton composition in the euphotic and twilight zones at an ocean basin scale we determined the distribution of 11 marine bacterial and archaeal phyla in three different water layers along a transect across the Atlantic Ocean from South Africa (32.9°S) to the UK (46.4°N) during boreal spring. Depth profiles down to 500 m at 65 stations were analysed by catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) and automated epifluorescence microscopy. There was no obvious overall difference in microbial community composition between the surface water layer and the deep chlorophyll maximum (DCM) layer. There were, however, significant differences between the two photic water layers and the mesopelagic zone. SAR11 (35 ± 9%) and Prochlorococcus (12 ± 8%) together dominated the surface waters, whereas SAR11 and Crenarchaeota of the marine group I formed equal proportions of the picoplankton community below the DCM (both ~15%). However, due to their small cell sizes Crenarchaeota contributed distinctly less to total microbial biomass than SAR11 in this mesopelagic water layer. Bacteria from the uncultured Chloroflexi-related clade SAR202 occurred preferentially below the DCM (4-6%). Distinct latitudinal distribution patterns were found both in the photic zone and in the mesopelagic waters: in the photic zone, SAR11 was more abundant in the Northern Atlantic Ocean (up to 45%) than in the Southern Atlantic gyre (~25%), the biomass of Prochlorococcus peaked in the tropical Atlantic Ocean, and Bacteroidetes and Gammaproteobacteria bloomed in the nutrient-rich northern temperate waters and in the Benguela upwelling. In mesopelagic waters, higher proportions of SAR202 were present in both central gyre regions, whereas Crenarchaeota were clearly more abundant in the upwelling regions and in higher latitudes. Other phylogenetic groups such as the Planctomycetes, marine group II Euryarchaeota and the uncultured clades SAR406, SAR324 and SAR86 rarely exceeded more than 5% of relative abundance.
    Keywords: Alteromonas/Colwellia, targeted with Alt1413 oligonucleotide FISH-probe; AMT16; AMT16/1; AMT16/11; AMT16/12; AMT16/13; AMT16/14; AMT16/15; AMT16/16; AMT16/17; AMT16/18; AMT16/19; AMT16/2; AMT16/20; AMT16/21; AMT16/22; AMT16/23; AMT16/24; AMT16/25; AMT16/26; AMT16/27; AMT16/28; AMT16/29; AMT16/3; AMT16/30; AMT16/31; AMT16/32; AMT16/33; AMT16/34; AMT16/35; AMT16/37; AMT16/38; AMT16/39; AMT16/4; AMT16/40; AMT16/41; AMT16/42; AMT16/43; AMT16/45; AMT16/46; AMT16/47; AMT16/48; AMT16/49; AMT16/5; AMT16/50; AMT16/51; AMT16/52; AMT16/53; AMT16/54; AMT16/55; AMT16/56; AMT16/57; AMT16/58; AMT16/59; AMT16/6; AMT16/60; AMT16/61; AMT16/62; AMT16/63; AMT16/64; AMT16/65; AMT16/7; AMT16/8; AMT16/9; Bacteria, targed with EUB338(I-III) oligonucleotide FISH-probe; Bacteroidetes, targeted with CF319a oligonucleotide FISH-probe; Benguela Current Coastal Province; Bottle, Niskin; Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH); Crenarchaeota marine group I, targeted with Cren554 oligonucleotide FISH-probe; D294; D294/1; D294/11; D294/12; D294/13; D294/14; D294/15; D294/16; D294/17; D294/18; D294/19; D294/2; D294/20; D294/21; D294/22; D294/23; D294/24; D294/25; D294/26; D294/27; D294/28; D294/29; D294/3; D294/30; D294/31; D294/32; D294/33; D294/34; D294/35; D294/37; D294/38; D294/39; D294/4; D294/40; D294/41; D294/42; D294/43; D294/45; D294/46; D294/47; D294/48; D294/49; D294/5; D294/50; D294/51; D294/52; D294/53; D294/54; D294/55; D294/56; D294/57; D294/58; D294/59; D294/6; D294/60; D294/61; D294/62; D294/63; D294/64; D294/65; D294/7; D294/8; D294/9; DEPTH, water; Discovery (1962); Epifluorescence microscopy after DAPI staining; Euryarchaeota marine group II, targeted with Eury806 oligonucleotide FISH-probe; Event label; Gammaproteobacteria, targeted with Gam42a oligonucleotide FISH-probe; Latitude of event; Longitude of event; NIS; North Atlantic Gyral Province; Northern Atlantic Drift; Oceanospirillum, targeted with Oce232 oligonucleotide FISH-probe; Planctomycetes, targeted with Pla46 oligonucleotide FISH-probe; Prochlorococcus, targeted with PRO405 oligonucleotide FISH-probe; Prokaryotes; Pseudoalteromonas, targeted with PSA184 oligonucleotide FISH-probe; SAR11 clade, targeted with SAR11-441 oligonucleotide FISH-probe; SAR202 clade, targeted with SAR202-312R oligonucleotide FISH-probe; SAR324 clade, targeted with SAR324-1412 oligonucleotide FISH-probe; SAR406 clade, targeted with SAR406-97 oligonucleotide FISH-probe; SAR86 clade, targeted with SAR86-1245 oligonucleotide FISH-probe; South Atlantic Gyral Province; Vibrio, targeted with GV841 oligonucleotide FISH-probe; western tropical Atlantic
    Type: Dataset
    Format: text/tab-separated-values, 3986 data points
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  • 7
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    Microbial community composition and bacterioplankton at time series station Helgoland Roads, North Sea (2016)
    PANGAEA
    Details
    Publication Date: 2024-02-23
    Description: A process of global importance in carbon cycling is the remineralization of algae biomass by heterotrophic bacteria, most notably during massive marine algae blooms. Such blooms can trigger secondary blooms of planktonic bacteria that consist of swift successions of distinct bacterial clades, most prominently members of the Flavobacteriia, Gammaproteobacteria and the alphaproteobacterial Roseobacter clade. This study explores such successions during spring phytoplankton blooms in the southern North Sea (German Bight) for four consecutive years. The surface water samples were taken at Helgoland Island about 40 km offshore in the southeastern North Sea in the German Bight at the station 'Kabeltonne' (54° 11.3' N, 7° 54.0' E) between the main island and the minor island, Düne (German for 'dune') using small research vessels (http://www.awi.de/en/expedition/ships/more-ships.html). Water depths at this site fluctuate from 6 to 10 m over the tidal cycle. Samples were processed as described previously (Teeling et al., 2012; doi:10.7554/eLife.11888.001) in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Assessment of absolute cell numbers and bacterioplankton community composition was carried out as described previously (Thiele et al., 2011; doi:10.1016/B978-0-444-53199-5.00056-7). To obtain total cell numbers, DNA of formaldehyde fixed cells filtered on 0.2 mm pore sized filters was stained with 4',6-diamidino-2-phenylindole (DAPI). Fluorescently labeled cells were subsequently counted on filter sections using an epifluores-cence microscope. Likewise, bacterioplankton community composition was assessed by catalyzedreporter deposition fluorescence in situ hybridization (CARD-FISH) of formaldehyde fixed cells on 0.2 mm pore sized filters.
    Keywords: Actinobacteria, targeted with HGC69a oligonucleotides FISH-probe; Alphaproteobacteria, targeted with ALF968 oligonucleotides FISH-probe; Alteromonas/Colwellia, targeted with Alt1413 oligonucleotide FISH-probe; Archaea, targed with ARCH915 oligonucleotide FISH-probe; Bacteria, targed with EUB338(I-III) oligonucleotide FISH-probe; Bacterioplankton; Balneatrix, targeted with Bal731 oligonucleotides FISH-probe; Betaproteobacteria, targeted with BET42a oligonucleotides FISH-probe; Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH); Crenarchaeota marine group I, targeted with Cren554 oligonucleotide FISH-probe; Cytophaga-Flavobacterium cluster, targeted with CF319a oligonucleotide FISH-probe; DATE/TIME; DEPTH, water; Epifluorescence microscopy after DAPI staining; Euryarchaeota marine group II, targeted with Eury806 oligonucleotide FISH-probe; Formosa, targeted with FORM181A oligonucleotides FISH-probe; Formosa, targeted with FORM181B oligonucleotides FISH-probe; Gammaproteobacteria, targeted with Gam42a oligonucleotide FISH-probe; German Bight, North Sea; Glaciecola, targeted with Glac227 oligonucleotides FISH-probe; HelgolandRoads_bacterioplankton_2009-2012; Julian day; Kabeltonne; Marinoscillum, targeted with CYT-734 oligonucleotides FISH-probe; NAC11-7 clade, targeted with NAC11-7-1030 oligonucleotides FISH-probe; Non-bacteria control, targeted with NON338 oligonucleotides FISH-probe; NOR5 clade, targeted with NOR5-730 oligonucleotides FISH-probe; NS3a clade, targeted with NS3a-840 oligonucleotides FISH-probe; NS5 clade, targeted with NS5/DE2-471 oligonucleotides FISH-probe; NS5 clade, targeted with NS5/VIS1-575 oligonucleotides FISH-probe; NS9 clade, targeted with NS9-664 oligonucleotides FISH-probe; OM182 clade, targeted with OM182-707 oligonucleotides FISH-probe; Pirellula group D, targeted with PirD1039 oligonucleotides FISH-probe; Planctomyce group A, targeted with PlaA1228 oligonucleotides FISH-probe; Planctomycete group B, targeted with uPlaB440 oligonucleotides FISH-probe; Planctomycetes, targeted with Pla46 oligonucleotide FISH-probe; Polaribacter, targeted with POL740 oligonucleotides FISH-probe; Pseudoalteromonas, targeted with PSA184 oligonucleotide FISH-probe; Reinekea, targeted with REI731 oligonucleotides FISH-probe; Roseobacter clade, targeted with RCA1000 oligonucleotides FISH-probe; Roseobacter clade, targeted with ROS537 oligonucleotides FISH-probe; SAR11 clade, targeted with SAR11-441 oligonucleotide FISH-probe; SAR11 clade, targeted with SAR11-486 oligonucleotides FISH-probe; SAR324 clade, targeted with SAR324-1412 oligonucleotide FISH-probe; SAR86 clade, targeted with SAR86-1245 oligonucleotide FISH-probe; SAR92 clade, targeted with SAR92-627 oligonucleotides FISH-probe; Ulvibacter, targeted with ULV995 oligonucleotides FISH-probe; Vibrio, targeted with GV841 oligonucleotide FISH-probe; VIS6 clade, targeted with VIS6-814 oligonucleotides FISH-probe
    Type: Dataset
    Format: text/tab-separated-values, 5239 data points
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  • 8
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    Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden (2016)
    PANGAEA
    In:  Supplement to: Ravenschlag, Katrin; Sahm, Kerstin; Knoblauch, Christian; Jørgensen, Bo Barker; Amann, Rudolf I (2000): Community Structure, Cellular rRNA Content, and Activity of Sulfate-Reducing Bacteria in Marine Arctic Sediments. Applied and Environmental Microbiology, 66(8), 3592-3602, https://doi.org/10.1128/AEM.66.8.3592-3602.2000
    Details
    Publication Date: 2024-01-20
    Description: The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburgfjorden, Svalbard) was characterized by both fluorescence in situ hybridization (FISH) by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes. Samples stored in PBS-ethanol were diluted and treated by mild sonication. A 10-ml aliquot of a 1:40 dilution was filtered onto a 0.2-mm-pore-size type GTTP polycarbonate filter (Millipore, Eschborn, Germany). Hybridization and microscopic counting of hybridized and 49,69-diamidino-2-phenylindole (DAPI)-stained cells were performed as described previously from Snaidr et al. (1997, http://aem.asm.org/content/63/7/2884.full.pdf). Details of probes and formamide concentrations which were used are listed in futher details.. Means were calculated by using 10 to 20 randomly chosen fields for each filter section, which corresponded to 800 to 1,000 DAPI-stained cells. Counting results were always corrected by subtracting signals observed with probe NON338. The SRB community was dominated by members of the Desulfosarcina-Desulfococcus group. This group accounted for up to 73% of the SRB detected. The predominance was shown to be a common feature for different stations along the coast of Svalbard. In a top-to-bottom approach we aimed to further resolve the composition of this large group of SRB by using probes for cultivated genera. While this approach failed, directed cloning of probe-targeted genes encoding 16S rRNA was successful and resulted in sequences which were all affiliated with the Desulfosarcina-Desulfococcus group. A group of clone sequences (group SVAL1) most closely related to Desulfosarcina variabilis (91.2% sequence similarity) was dominant and was shown to be most abundant in situ, accounting for up to 54.8% of the total SRB detected.
    Keywords: Bacteria, sulfate reducing; Bacteria, targed with EUB338(I-III) oligonucleotide FISH-probe; Core; CORE; Date/Time of event; DEPTH, sediment/rock; Desulfobacterium spp., targeted with 221 oligonucleotides FISH-probe; Desulfobacter spp., targeted with DSB985 oligonucleotides FISH-probe; Desulfobulbus spp., targeted with 660 oligonucleotides FISH-probe; Desulforhopalus spp., targeted with DSR651 oligonucleotides FISH-probe; Desulfotalea spp., targeted with Sval428 oligonucleotides FISH-probe; Desulfovibrio spp., targeted with DSV698 oligonucleotides FISH-probe; Desulfuromonas spp., targeted with DRM432 oligonucleotides FISH-probe; Desulfusarcina/Desulfococcus, targeted with DSS658 oligonucleotide FISH-probe; Epifluorescence microscopy after DAPI staining; Event label; Fluorescence in situ hybridization (FISH); Latitude of event; Longitude of event; Prokaryotes, abundance as single cells; SBF_19980728; Smeerenburgfjorden, Svalbard; Svalbard clone group SVAL1, targeted with DSS225 oligonucleotide FISH-probe; Svalbard clones Sva0081/Sva0863, targeted with cl81-644 oligonucleotide FISH-probe
    Type: Dataset
    Format: text/tab-separated-values, 337 data points
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  • 9
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    Microbial community composition and polysaccharide processing potential in the South Pacific Gyre (2020)
    PANGAEA
    Details
    Publication Date: 2024-02-02
    Description: The South Pacific Gyre (SPG) covers 10% of the ocean's surface and is considered a marine biological desert. However, recent investigations have shown that primary production occurs throughout its deep euphotic zone and that this fuels the regeneration of nutrients and the recycling of organic matter. We set out to investigate the SPG's microbial communities' heterotrophic capability to utilize polysaccharides, an important marine organic matter component. Using fluorescently labeled polysaccharide (FLA-PS) incubations (Reintjes, et al., 2017), we analyzed the initial step of organic matter degradation by measuring both the rate of external hydrolysis and the rate of direct uptake of polysaccharides by marine microorganisms. Furthermore, we investigated the change in bacterial abundance and diversity during the FLA-PS incubations using direct cell counts and 16S rRNA sequencing. The presented dataset contains the microbial diversity, total cellular abundance, and direct FLA-PS uptake results generated during the FLA-PS incubations performed with six polysaccharides (laminarin, xylan, chondroitin sulfate, arabinogalactan, fucoidan, and pullulan) over 18 days. The incubations were performed with seawater from the epipelagic and bathypelagic (75 m, 160 m, 1250 m, and 2800 m) in the central gyre, and seawater from the epipelagic (75 m) at two stations adjacent to the gyre. Our study found that the SPG's microbial community showed remarkably high extracellular enzyme activities, and a considerable fraction of the microorganisms were capable of the direct uptake (selfish-uptake) of FLA-PS. Interestingly, a wide variety of bacteria were capable of cycling HMW organic matter using distinct polysaccharide processing mechanisms in the SPG. This research shows that the SPG features not only organisms capable of existing on the fine edge of minimal substrate concentrations but also those capable of taking advantage of abrupt changes in physical conditions and substrate availability
    Keywords: activity; Basis of event; Campaign of event; CTD/Rosette; CTD-RO; Date/Time of event; Day of experiment; DEPTH, water; Event label; Extracellular Enzyme Activity; FLA-PS; Fluorescence in situ hybridization (FISH); Fluorescently labeled polysaccharides (FLA-PS); Gyre; heterotrophy; Latitude of event; Location of event; Longitude of event; metabolism; microbial; Microbial abundance, cells; Pacific; polysaccharide; Sample ID; Sample method; SO245; SO245_2-2; SO245_6-1; SO245_8-1; Sonne_2; South Pacific Ocean; Substrate type; UltraPac, GEOTRACES; Volume
    Type: Dataset
    Format: text/tab-separated-values, 1618 data points
    Location Call Number Expected Availability
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  • 10
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    Unknown
    Hydrogen consumption by gills of Bathymodiolus spp. collected at the Comfortless cove and Lilliput hydrothermal vent fields in May 2006 (2013)
    PANGAEA
    Details
    Publication Date: 2024-02-02
    Description: The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.
    Keywords: Comment; DERIDGE; Event label; From Mantle to Ocean: Energy-, Material- and Life-cycles at Spreading Axes; Hydrogen; Hydrogen concentration; Hydrogen consumption rate; Hydrogen consumption rate per weight; M68/1; M68/1-20-ROV; M68/1-24-ROV; M68/1-39-ROV; M68/1-70-ROV; MARSUED3; Meteor (1986); Remote operated vehicle; ROV; Sample ID; Time in minutes; Tissue piece, number of; Wet mass
    Type: Dataset
    Format: text/tab-separated-values, 1582 data points
    Location Call Number Expected Availability
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    DATA PANGAEA
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