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PANGAEA tech-keyword 'deNBIMolEcol' (25 data sets)

Mostrando recursos 1 - 20 de 296

  1. Gene expression via Fluidigm chip system on Western Baltic spring-spawning herring (Clupea harengus)

    Roth, Olivia

  2. Experiment on effects of elevated pCO2 on bivalve dominated communities

    Schade, Hanna; Mevenkamp, Lisa; Guilini, Katja; Meyer, Stefanie; Gorb, Stanislav N; Abele, Doris; Vanreusel, Ann; Melzner, Frank
    Sandy communities were exposed to six different seawater pCO2 regimes for a total of three months (17.12.2011-06.03.2012) in a climate - controlled room. Six header tanks were continuously supplied with filtered seawater from Kiel Fjord, each one connected to six experimental units (EU) ensuring continuous seawater supply. Each EU consisted of a round plastic container with a volume of 12.5 L containing ca. 9.5 L of sediment and an overlying water column of ca. 3 L. The lower 10 cm of the sediment consisted of sieved sand taken from a local beach (Kiel, Falckenstein: 54°23,66 N; 10°11.56 E) while the...

  3. Individual codes, GenBank accession numbers and GenBank accession links for marine sponge-associated microbial metagenomes

    Horn, Hannes; Slaby, Beate M; Jahn, Martin T; Bayer, Kristina; Moitinho-Silva, Lucas; Förster, Frank; Abdelmohsen, Usama Ramadan; Hentschel, Ute
    Dataset contains metainformation to the samples used in the given pulication: links to Bioprojects, Biosamples, metagenome assemblies and raw data.

  4. Accession data for analysed Xestospongia testudinaria metatranscriptomes

    Jahn, Martin T; Markert, Sebastian M; Ryu, Taewoo; Ravasi, Timothy; Stigloher, Christian; Hentschel, Ute; Moitinho-Silva, Lucas
    Assigning functions to uncultivated environmental microorganisms continues to be a challenging endeavour. Here, we present a new microscopy protocol for fluorescence in situ hybridisation-correlative light and electron microscopy (FISH-CLEM) that enabled, to our knowledge for the first time, the identification of single cells within their complex microenvironment at electron microscopy resolution. Members of the candidate phylum Poribacteria, common and uncultivated symbionts of marine sponges, were used towards this goal. Cellular 3D reconstructions revealed bipolar, spherical granules of low electron density, which likely represent carbon reserves. Poribacterial activity profiles were retrieved from prokaryotic enriched sponge metatranscriptomes using simulation-based optimised mapping. We...

  5. Response of Arctic benthic bacterial deep-sea communities to different detritus composition during an ex-situ high pressure experiment

    Hoffmann, Katy; Hassenrück, Christiane; Salman-Carvalho, Verena; Holtappels, Moritz; Bienhold, Christina
    In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from 2,500 m water depth at the Long-Term Ecological Research Observatory HAUSGARTEN (stationPS93/050-5 and 6), were retrieved using a TV-guided multiple corer. Surface sediments (0 - 2 cm) of 16 cores were mixed with sterile filtered deep-sea water to a final sediment dilution of 3.5 fold. The slurries were split and supplemented with five different types of habitat-related detritus: chitin, as the most abundant biopolymer in the oceans, and four different naturally occurring Arctic algae species, i.e. Thalassiosira weissflogii, Emiliania huxleyi, Bacillaria sp. and Melosira arctica. Incubations were performed in...

  6. Quantitative analysis of oyster larval proteome provides new insights into the effects of multiple climate change stressors

    Dineshram, R; Chandramouli, K; Ko, W K Ginger; Zhang, Huoming; Qian, Pei Yuan; Ravasi, Timothy; Thiyagarajan, Vengatesen
    The metamorphosis of planktonic larvae of the Pacific oyster (Crassostrea gigas) underpins their complex life-history strategy by switching on the molecular machinery required for sessile life and building calcite shells. Metamorphosis becomes a survival bottleneck, which will be pressured by different anthropogenically induced climate change-related variables. Therefore, it is important to understand how metamorphosing larvae interact with emerging climate change stressors. To predict how larvae might be affected in a future ocean, we examined changes in the proteome of metamorphosing larvae under multiple stressors: decreased pH (pH 7.4), increased temperature (30 °C), and reduced salinity (15 psu). Quantitative protein expression...

  7. Sampling information, length measurements, DNA alignments, models and phylogenetics trees for Oithona similis s.l.

    Cornils, Astrid; Wend-Heckmann, Britta; Held, Christoph
    Traditionally, many small-sized copepod species are considered to be widespread, bipolar or cosmopolitan. However, these large-scale distribution patterns need to be re-examined in view of increasing evidence of cryptic and pseudo-cryptic speciation in pelagic copepods. Here, we present a phylogeographic study of Oithona similis s.l. populations from the Arctic Ocean, the Southern Ocean and its northern boundaries, the North Atlantic and the Mediterrranean Sea. O. similis s.l. is considered as one of the most abundant species in temperate to polar oceans and acts as an important link in the trophic network between the microbial loop and higher trophic levels such...

  8. Metadata und statistic analysis of archael and bacterial sequences originating from sediments of the Håkon Mosby mud volcano (Z1-Z3, all habitats)

    Ruff, S Emil; Ramette, Alban; Boetius, Antje
    DNA extraction was carried out as described on the MICROBIS project pages (http://icomm.mbl.edu/microbis ) using a commercially available extraction kit. We amplified the hypervariable regions V4-V6 of archaeal and bacterial 16S rRNA genes using PCR and several sets of forward and reverse primers (http://vamps.mbl.edu/resources/primers.php). Massively parallel tag sequencing of the PCR products was carried out on a 454 Life Sciences GS FLX sequencer at Marine Biological Laboratory, Woods Hole, MA, following the same experimental conditions for all samples. Sequence reads were submitted to a rigorous quality control procedure based on mothur v30 (doi:10.1128/AEM.01541-09) including denoising of the flow grams using...

  9. Interactive effects of salinity and elevated CO2 levels on juvenile eastern oysters, Crassostrea virginica

    Dickinson, Gary H; Ivanina, Anna; Matoo, Omera B; Pörtner, Hans-Otto; Lannig, Gisela; Bock, C; Beniash, Elia; Sokolova, Inna M
    Rising levels of atmospheric CO2 lead to acidification of the ocean and alter seawater carbonate chemistry, which can negatively impact calcifying organisms, including mollusks. In estuaries, exposure to elevated CO2 levels often co-occurs with other stressors, such as reduced salinity, which enhances the acidification trend, affects ion and acid-base regulation of estuarine calcifiers and modifies their response to ocean acidification. We studied the interactive effects of salinity and partial pressure of CO2 (PCO2) on biomineralization and energy homeostasis in juveniles of the eastern oyster, Crassostrea virginica, a common estuarine bivalve. Juveniles were exposed for 11 weeks to one of two...

  10. 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,...

  11. 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

  12. 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...

  13. 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...

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

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

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

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

  16. 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)...

  17. 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...

  18. 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)...

  19. 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...

  20. 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'...

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