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PANGAEA tech-keyword 'deNBIFISH' (10 data sets)

Mostrando recursos 1 - 18 de 18

  1. Composition of bacterioplankton in the North Atlantic subtropical gyre

    Gomez-Pereira, Paola R; Hartmann, Manuela; Grob, C; Tarran, Glen A; Martin, Adrian Peter; Fuchs, Bernhard M; Scanlan, David J; Zubkov, Mikhail V
    Subtropical oceanic gyres are the most extensive biomes on Earth where SAR11 and Prochlorococcus bacterioplankton numerically dominate the surface waters depleted in inorganic macronutrients as well as in dissolved organic matter. In such nutrient poor conditions bacterioplankton could become photoheterotrophic. We assessed the photoheterotrophy of the key microbial taxa in the North Atlantic oligotrophic gyre and adjacent regions. The experimental work was performed on board the Royal Research Ship James Cook (cruise no. JC53, October-November 2010) as part of the Atlantic Meridional Transect programme, and on board the Royal Research Ship Discovery (cruise no. D369, August-September 2011). At each station,...

  2. Biomarker concentrations and isotopic signatures in sediment of Gullfaks and Tommeliten methane seeps in the Northern North Sea

    Wegener, Gunter; Shovitri, M; Knittel, Katrin; Niemann, H; Hovland, Martin; Boetius, Antje

  3. Microbial community, biomarker concentrations and their isotopic signature in sediment of Gullfaks and Tommeliten methane seeps in the Northern North Sea

    Wegener, Gunter; Shovitri, M; Knittel, Katrin; Niemann, H; Hovland, Martin; Boetius, Antje
    Gullfaks is one of the four major Norwegian oil and gas fields, located in the northeastern edge of the North Sea Plateau. Tommeliten lies in the greater Ekofisk area in the central North Sea. During the cruises HE 208 and AL 267 several seep locations of the North Sea were visited. At the Heincke seep at Gullfaks, sediments were sampled in May 2004 (HE 208) using a video-guided multiple corer system (MUC; Octopus, Kiel). The samples were recovered from an area densely covered with bacterial mats where gas ebullition was observed. The coarse sands limited MUC penetration depth to maximal...

  4. Chemical analysis and Microbial community composition of surface water samples from the Southern Lagoon of Venice

    Simonato, Francesca; Gomez-Pereira, Paola R; Fuchs, Bernhard M; Amann, Rudolf
    The Lagoon of Venice is a large water basin that exchanges water with the Northern Adriatic Sea through three large inlets. We examined two adjacent sites within the Southern Basin and at the Chioggia inlet in autumn 2007 and summer 2008. A pilot study in June 2007 on a surface water sample from Chioggia with a rather high salinity of 36.9 PSU had revealed a conspicuous bloom of CF319a-positive cells likely affiliated with the Cytophaga /Flavobacteria cluster of Bacteroidetes. These flavobacterial abundances were one to two orders of magnitude higher than in other marine surface waters. DAPI-stained cells were identified...

  5. Chemical analysis of surface water samples from the Southern Lagoon of Venice

    Simonato, Francesca; Gomez-Pereira, Paola R; Fuchs, Bernhard M; Amann, Rudolf

  6. Bacterioplankton groups of surface water samples from the Southern Lagoon of Venice

    Simonato, Francesca; Gomez-Pereira, Paola R; Fuchs, Bernhard M; Amann, Rudolf

  7. Microbial community composition in fresh water at different stations

    Glöckner, Frank Oliver; Fuchs, Bernhard M; Amann, Rudolf I
    Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes was used to investigate the phylogenetic composition of bacterioplankton communities in several freshwater and marine samples. An average of about 50% of the cells were detected by probes for the domains Bacteria and Archaea. Cells were concentrated from water samples (1 to 100 ml) on white polycarbonate filters (diameter, 47 mm; pore size, 0.2 mm; type GTTP 4700 [Millipore, Eschborn, Germany]) by applying a vacuum of <25 kPa. They were subsequently fixed by covering the filter with 3 ml of a freshly prepared, phosphate-buffered saline (pH 7.2)-4% paraformaldehyde (Sigma, Deisenhofen, Germany)...

  8. Anaerobic methanotrophic archaea-2 and Desulfosarcina/Desulfococcus group in sediments at different stations

    Schreiber, L; Holler, L; Knittel, Katrin; Meyerdierks, Anke; Amann, Rudolf
    The anaerobic oxidation of methane (AOM) with sulfate as terminal electron acceptor is mediated by consortia of methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). In sediment samples from Hydrate Ridge, the Isis Mud Volcano and the Gulf of Mexico, DSS cells accounted for 3-6% of all DAPI-stained single cells. Out of these, 8-17% were labelled with probe SEEP1a-1441. This translated into relative abundances of single SEEP-SRB1a cells of 0.3% to 0.7%. Contrastingly, in a sediment sample from the Gullfaks oil field, DSS cells accounted for 18% and SEEP-SRB1a for 9% of all single cells. This sediment sample also featured an...

  9. NOR5/OM60 clade of the Yangtze River estuary

    Yan, Shi; Fuchs, Bernhard M; Lenk, Sabine; Harder, Jens; Wulf, Jörg; Jiao, Nianzhi; Amann, Rudolf
    The phylogeny, abundance, and biogeography of the NOR5/OM60 clade was investigated. This clade includes "Congregibacter litoralis" strain KT71, the first cultured representative of marine aerobic anoxygenic phototrophic Gammaproteobacteria. Most of the NOR5/OM60 sequences were retrieved from marine coastal settings, whereas there were fewer from open-ocean surface waters, deep-sea sediment, freshwater, saline lakes and soil. The abundance of members of the NOR5/OM60 clade in various marine sites was determined by fluorescence in situ hybridization using a newly designed and optimized probe set. Relative abundances in coastal marine waters off the Yangtze estuary were up to 3% of the total 4',6-diamidino-2-phenylindole (DAPI)...

  10. Relative abundance of anaerobic methanotrophic archaea in bacterial mat Cascadia margin off Oregon

    Knittel, Katrin; Lösekann, Tina; Boetius, Antje; Kort, Renate; Amann, Rudolf
    The microbially mediated anaerobic oxidation of methane (AOM) is the major biological sink of the greenhouse gas methane in marine sediments (doi:10.1007/978-94-009-0213-8_44) and serves as an important control for emission of methane into the hydrosphere. The AOM metabolic process is assumed to be a reversal of methanogenesis coupled to the reduction of sulfate to sulfide involving methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) as syntrophic partners which were describes amongst others in Boetius et al. (2000; doi:10.1038/35036572). In this study, 16S rRNA-based methods were used to investigate the distribution and biomass of archaea in samples from sediments above outcropping methane...

  11. Microbial community composition and bacterioplankton at time series station Helgoland Roads, North Sea

    Fuchs, Bernhard M; Bennke, Christin M; Reintjes, Greta; Kassabgy, Mariette; Amann, Rudolf I
    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'...

  12. Microbial community in sediment of Gullfaks and Tommeliten methane seeps in the Northern North Sea

    Wegener, Gunter; Shovitri, M; Knittel, Katrin; Niemann, H; Hovland, Martin; Boetius, Antje

  13. Chloroflexus spp. and Sulfurihydrogenibium spp. in microbial mats of the Nakabusa hot spring, Japan

    Kubo, Kyoko; Knittel, Katrin; Amann, Rudolf; Fukui, F; Matsuura, Katsumi
    Microbial mats develop in a wide range of aquatic habitats, such as geothermal hot springs, hypersaline ponds, marine cold seeps or hydrothermal vents. The Nakabusa hot spring is located in the Nagano Prefecture, Japan (36.3875N, 137.75E), dense olive-green microbial mats develop in regions where the slightly alkaline, sulfidic effluent has cooled to 65°C. The microbial community of such mats was analyzed by focusing on the diversity, as well as the in situ distribution and function of bacteria involved in sulfur cycling. Microbial mat samples were kept in sterile plastic tubes (for molecular analysis) or glass bottles completely filled with hot...

  14. Microbial community composition in sediments of the Hydrate Ridge (Cascadian Margin) collected during RV SONNE cruises SO143 (1999) and SO148-1 (2000)

    Knittel, Katrin; Boetius, Antje; Lemke, Andreas; Eilers, Heike; Lochte, Karin; Pfannkuche, Olaf; Linke, Peter; Amann, Rudolf
    Cold seep environments such as sediments above outcropping hydrate at Hydrate Ridge (Cascadia margin off Oregon) are characterized by methane venting, high sulfide fluxes caused by the anaerobic oxidation of methane, and the presence of chemosynthetic communities. This investigation deals with the diversity and distribution of sulfate-reducing bacteria, some of which are directly involved in the anaerobic oxidation of methane as syntrophic partners of the methanotrophic archaea. The composition and activity of the microbial communities at methane vented and nonvented sediments are compared by quantitative methods including total cell counts, fluorescence in situ hybridization (FISH). Bacteria involved in the degradation...

  15. Hydrochemical and microbiological properties of groundwater from pristine aquifer sampled at the Lower Rhine Embayment

    Detmers, Jan; Strauss, H; Schulte, U; Bergmann, A; Knittel, Katrin; Kuever, Jan
    The hydrochemistry and the microbial diversity of a pristine aquifer system near Garzweiler, Germany next to the open-pit lignite mine Garzweiler 1, were characterized. Hydrogeochemical and isotopic data indicate a recent activity of sulfate-reducing bacteria in the Tertiary marine sands. The community structure in the aquifer was studied by fluorescence in situ hybridization (FISH). Up to 7.3 x 10**5 cells/ml were detected by DAPIstaining. Bacteria (identified by the probe EUB338) were dominant, representing 51.9% of the total cell number (DAPI). Another 25.7% of total cell were affiliated with the domain Archaea as identified by the probe ARCH915. Within the domain...

  16. Microbial community composition of sandy intertidal sediments of Sylt-Rømø Basin, Wadden Sea

    Musat, Niculina; Werner, Ursula; Knittel, Katrin; Kolb, Steffen; Dodenhof, Tanja; van Beusekom, Justus; de Beer, Dirk; Dubilier, Nicole; Amann, Rudolf
    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...

  17. Microbial community in the sediment of the arctic Smeerenburgfjorden

    Ravenschlag, Katrin; Sahm, Kerstin; Amann, Rudolf
    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, 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...

  18. Community structure of sulfate reducing bacteria in the sediment of the arctic Smeerenburgfjorden

    Ravenschlag, Katrin; Sahm, Kerstin; Knoblauch, Christian; Jørgensen, Bo Barker; Amann, Rudolf I
    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, Details of probes and formamide concentrations which were used are listed in futher details.. Means were calculated...

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