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  • PANGAEA  (16)
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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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    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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    DATA PANGAEA
  • 4
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    Hydrochemistry measurements and diazotroph abundances (2016)
    PANGAEA
    In:  Supplement to: Martínez-Pérez, Clara; Mohr, Wiebke; Löscher, Carolin R; Dekaezemacker, Julien; Littmann, Sten; Yilmaz, Pelin; Lehnen, Christina; Fuchs, Bernhard M; Lavik, Gaute; Schmitz, Ruth A; LaRoche, Julie; Kuypers, Marcel MM (2016): The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle. Nature Microbiology, 1, 16163, https://doi.org/10.1038/nmicrobiol.2016.163
    Details
    Publication Date: 2023-10-28
    Description: Microbial dinitrogen (N2) fixation, the nitrogenase enzyme-catalysed reduction of N2 gas into biologically available ammonia, is the main source of new nitrogen (N) in the ocean. For more than 50 years, oceanic N2 fixation has mainly been attributed to the activity of the colonial cyanobacterium Trichodesmium. Other smaller N2-fixing microorganisms (diazotrophs)--in particular the unicellular cyanobacteria group A (UCYN-A)--are, however, abundant enough to potentially contribute significantly to N2 fixation in the surface waters of the oceans. Despite their abundance, the contribution of UCYN-A to oceanic N2 fixation has so far not been directly quantified. Here, we show that in one of the main areas of oceanic N2 fixation, the tropical North Atlantic7, the symbiotic cyanobacterium UCYN-A contributed to N2 fixation similarly to Trichodesmium. Two types of UCYN-A, UCYN-A1 and -A2, were observed to live in symbioses with specific eukaryotic algae. Single-cell analyses showed that both algae-UCYN-A symbioses actively fixed N2, contributing ~20% to N2 fixation in the tropical North Atlantic, revealing their significance in this region. These symbioses had growth rates five to ten times higher than Trichodesmium, implying a rapid transfer of UCYN-A-fixed N into the food web that might significantly raise their actual contribution to N2 fixation. Our analysis of global 16S rRNA gene databases showed that UCYN-A occurs in surface waters from the Arctic to the Antarctic Circle and thus probably contributes to N2 fixation in a much larger oceanic area than previously thought. Based on their high rates of N2 fixation and cosmopolitan distribution, we hypothesize that UCYN-A plays a major, but currently overlooked role in the oceanic N cycle.
    Keywords: Center for Marine Environmental Sciences; Climate - Biogeochemistry Interactions in the Tropical Ocean; MARUM; SFB754
    Type: Dataset
    Format: application/zip, 2 datasets
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  • 5
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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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  • 6
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    (Table 3) Relative abundances in percentages of attached and free-living microbesa from water sample station GeoB15704-2 (2015)
    PANGAEA
    Details
    Publication Date: 2024-02-02
    Keywords: 604; Alteromonas; Bacteroidetes; Center for Marine Environmental Sciences; Comment; DEPTH, water; GeoB15704-2; In situ pump; ISP; Maria S. Merian; MARUM; MSM18/1; Planctomycetes, cells; Pseudoalteromonas; Roseobacter; Synechococcus
    Type: Dataset
    Format: text/tab-separated-values, 49 data points
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  • 7
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    (Table 2) Microbial numbers and relative abundances for aggregate-attached and free-living organisms from water sample station GeoB15704-2 (2015)
    PANGAEA
    Details
    Publication Date: 2024-02-02
    Keywords: 604; Alteromonas; Alteromonas, cells; Bacteria; Bacteria, cells; Bacteroidetes; Bacteroidetes, cells; Center for Marine Environmental Sciences; Comment; DEPTH, water; Enrichment factor; Gammaproteobacteria; Gammaproteobacteria, cells; GeoB15704-2; In situ pump; ISP; Maria S. Merian; MARUM; MSM18/1; Planctomycetes; Planctomycetes, cells; Pseudoalteromonas; Pseudoalteromonas, cells; Roseobacter; Roseobacter, cells; SAR11; SAR11, cells; Standard deviation; Synechococcus; Synechococcus, cells; Thaumarchaeota; Thaumarchaeota, cells
    Type: Dataset
    Format: text/tab-separated-values, 120 data points
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  • 8
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    Hydrochemistry measured on water bottle samples during the R/V Meteor cruise M96 (May, 2013) across the Tropical North Atlantic (2016)
    PANGAEA
    Details
    Publication Date: 2024-02-02
    Description: The table includes hydrography (salinity, temperature, density, oxygen concentrations) and nutrient (nitrate, nitrite, ammonium, phosphate) measurements from surface waters (upper 200 m) across a 14 °N transect of the Tropical North Atlantic.
    Keywords: Ammonium; BOTTLE; Bottle samples; Center for Marine Environmental Sciences; Chlorophyll a; Chlorophyll fluorescence, Dr. Haardt Instruments; Climate - Biogeochemistry Interactions in the Tropical Ocean; Conductivity; CTD; CTD/Rosette; CTD 10; CTD 12; CTD 13; CTD 16; CTD 17; CTD 22; CTD 24; CTD 27; CTD 28; CTD 3; CTD 33; CTD 34; CTD 36; CTD 38; CTD 4; CTD 43; CTD 44; CTD 47; CTD 48; CTD 49; CTD 50; CTD 52; CTD 53; CTD 55; CTD 56; CTD 61; CTD 62; CTD 9; CTD-RO; Date/Time of event; Density, mass density; DEPTH, water; Elevation of event; Event label; Julian day; Latitude of event; Longitude of event; M96; M96_1004-1; M96_1012-1; M96_1047-1; M96_1054-1; M96_622-1; M96_626-1; M96_649-1; M96_650-1; M96_660-1; M96_670-1; M96_692-1; M96_701-1; M96_755-1; M96_769-1; M96_793-1; M96_800-1; M96_839-1; M96_847-1; M96_863-1; M96_872-1; M96_913-1; M96_920-1; M96_945-1; M96_954-1; M96_962-1; M96_970-1; M96_985-1; M96_990-1; MARUM; Meteor (1986); Nitrate; Nitrite; Optional event label; Oxygen; Oxygen sensor, SBE 43; Phosphate; Salinity; SFB754; Temperature, water
    Type: Dataset
    Format: text/tab-separated-values, 8508 data points
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  • 9
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    (Supplementary Table 1) Diazotroph abundances, CO2 and N2 fixation rates (2016)
    PANGAEA
    Details
    Publication Date: 2024-02-02
    Keywords: Carbon fixation rate; Center for Marine Environmental Sciences; Climate - Biogeochemistry Interactions in the Tropical Ocean; CTD/Rosette; CTD 10; CTD 13; CTD 17; CTD 24; CTD 28; CTD 34; CTD 38; CTD 4; CTD 44; CTD 47; CTD 50; CTD 53; CTD 56; CTD 62; CTD-RO; Date/Time of event; DEPTH, water; Elevation of event; Event label; Gammaproteobacteria, cells; Heterocystous cyanobacteria, abundance expressed in number of nifH gene copies; Latitude of event; Longitude of event; M96; M96_1012-1; M96_1054-1; M96_626-1; M96_650-1; M96_670-1; M96_701-1; M96_769-1; M96_800-1; M96_847-1; M96_872-1; M96_920-1; M96_945-1; M96_970-1; M96_990-1; MARUM; Meteor (1986); Nitrogen fixation rate; SFB754; Station label; Trichodesmium, abundance expressed in number of nifH gene copies; Unicellular cyanobacteria-A, abundance expressed in number of nifH gene copies; Unicellular cyanobacteria-B, abundance expressed in number of nifH gene copies; Unicellular cyanobacteria-C, abundance expressed in number of nifH gene copies
    Type: Dataset
    Format: text/tab-separated-values, 924 data points
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  • 10
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    Nutrient concentrations along a North-South transect in the North Atlantic measured during Maria S. Merain cruise MSM03/1 (VISION) cruise (2013)
    PANGAEA
    In:  Supplement to: Gomez-Pereira, Paola R; Fuchs, Bernhard M; Alonso, Cecilia; Oliver, Matthew J; van Beusekom, Justus; Amann, Rudolf (2010): Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean. The ISME Journal, 4(4), 472-487, https://doi.org/10.1038/ismej.2009.142
    Details
    Publication Date: 2024-02-02
    Description: Samples were taken along a transect in the North Atlantic Ocean from 66°139.27'N; 29°136.65'W to 34°124.87'N; 28°128.90'W during the VISION cruise (diVersIty, Structure and functION) MSM03/01 on board the research vessel Maria S. Merian from September 21 to September 30, 2006. Along this transect, each station was sampled at 12 depths, from 10m down to 250m or 500m. Samples were collected with a rosette of 20-l Niskin bottles mounted on a conductivity-temperature-density profiler. Water samples for nutrients analysis were filtered directly after sampling through 0.45-µm in-line filters attached to a 60-ml pre-cleaned syringe into two 12-ml polystyrole tubes. Samples were stored at 4°C (dissolved silicate) or 80°C (ammonium, phosphate, nitrate and nitrite) The samples were spectrophotometrically measured with a continuous-flow analyzer using standard AA3 methods (Seal Analytical, Norderstedt, Germany) using a variant of the method of Grasshoff et al. (1983).
    Keywords: Ammonium; CFA; Continuous Flow Analysis; CTD/Rosette; CTD-RO; Date/Time of event; DEPTH, water; Event label; Latitude of event; Longitude of event; Maria S. Merian; MSM03/1; MSM03/1_902-1; MSM03/1_903-1; MSM03/1_904-1; MSM03/1_905-1; MSM03/1_906-1; MSM03/1_907-1; MSM03/1_908-1; MSM03/1_909-1; MSM03/1_910-1; MSM03/1_911-1; MSM03/1_912-1; MSM03/1_913-1; MSM03/1_914-1; MSM03/1_915-1; MSM03/1_916-1; MSM03/1_917-1; MSM03/1_918-1; MSM03/1_919-1; Nitrate; Nitrite; North Atlantic; Phosphate; Silicate; VISION
    Type: Dataset
    Format: text/tab-separated-values, 1072 data points
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    DATA PANGAEA
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