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  • 1
    Online Resource
    Online Resource
    Karlsruhe : Karlsruher Institut für Technologie, [Institut für Nukleare Entsorgung]
    Keywords: Forschungsbericht ; Radionuklid ; Verwitterung ; Zement
    Type of Medium: Online Resource
    Pages: 1 Online-Ressource (38 Seiten, 4,70 MB) , Illustrationen, Diagramme
    Language: German
    Note: Förderkennzeichen BMWK 02E11415C , Verbundnummer 01163584 , Literaturverzeichnis: Seite 33-36
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  • 2
    Publication Date: 2021-02-08
    Description: Hydrogen is one of the most common elements on Earth. The enzymes converting molecular hydrogen into protons and electrons are the hydrogenases. Hydrogenases are ubiquitously distributed in all three domains of life where they play a central role in cell metabolism. So far, the recovery of hydrogenases has been restricted to culture-dependent and sequence-based approaches. We have recently developed the only activity-based screen for seeking H-2-uptake enzymes from metagenomes without having to rely on enrichment and isolation of hydrogen-oxidizing microorganisms or prior metagenomic sequencing. When screening 14,400 fosmid clones from three hydrothermal vent metagenomes using this solely activity-based approach, four clones with H-2-uptake activity were identified with specific activities of up to 258 +/- 19 nmol H-2/min/mg protein of partially purified membrane fractions. The respective metagenomic fragments exhibited mostly very low or no similarities to sequences in the public databases. A search with hidden Markov models for different hydrogenase groups showed no hits for three of the four metagenomic inserts, indicating that they do not encode for classical hydrogenases. Our activity-based screen serves as a powerful tool for the discovery of (novel) hydrogenases which would not have been identified by the currently available techniques. This screen can be ideally combined with culture- and sequence-based approaches to investigate the tremendous hydrogen-converting potential in the environment.
    Type: Article , PeerReviewed
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  • 3
    Publication Date: 2021-03-19
    Description: To assess the risk that mining of seafloor massive sulfides (SMS) from extinct hydrothermal vent environments has for changing the ecosystem irreversibly, we sampled SMS analogous habitats from the Kairei and the Pelagia vent fields along the Indian Ridge. In total 19.8 million 16S rRNA tags from 14 different sites were analyzed and the microbial communities were compared with each other and with publicly available data sets from other marine environments. The chimneys appear to provide habitats for microorganisms that are not found or only detectable in very low numbers in other marine habitats. The chimneys also host rare organisms and may function as a vital part of the ocean's seed bank. Many of the reads from active and inactive chimney samples were clustered into OTUs, with low or no resemblance to known species. Since we are unaware of the chemical reactions catalyzed by these unknown organisms, the impact of this diversity loss and bio-geo-coupling is hard to predict. Given that chimney structures can be considered SMS analogues, removal of sulfide deposits from the seafloor in the Kairei and Pelagia fields will most likely alter microbial compositions and affect element cycling in the benthic regions and probably beyond.
    Type: Article , PeerReviewed
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  • 4
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    Frontiers
    In:  Frontiers in Microbiology, 9 (2873).
    Publication Date: 2021-03-19
    Description: Deep-sea hydrothermal vents may provide one of the largest reservoirs on Earth for hydrogen-oxidizing microorganisms. Depending on the type of geological setting, hydrothermal environments can be considerably enriched in hydrogen (up to millimolar concentrations). As hot, reduced hydrothermal fluids ascend to the seafloor they mix with entrained cold, oxygenated seawater, forming thermal and chemical gradients along their fluid pathways. Consequently, in these thermally and chemically dynamic habitats biochemically distinct hydrogenases (adapted to various temperature regimes, oxygen and hydrogen concentrations) from physiologically and phylogenetically diverse Bacteria and Archaea can be expected. Hydrogen oxidation is one of the important inorganic energy sources in these habitats, capable of providing relatively large amounts of energy (237 kJ/mol H-2) for driving ATP synthesis and autotrophic CO2 fixation. Therefore, hydrogen-oxidizing organisms play a key role in deep-sea hydrothermal vent ecosystems as they can be considerably involved in light-independent primary biomass production. So far, the specific role of hydrogen-utilizing microorganisms in deep-sea hydrothermal ecosystems has been investigated by isolating hydrogen-oxidizers, measuring hydrogen consumption (ex situ), studying hydrogenase gene distribution and more recently by analyzing metatranscriptomic and metaproteomic data. Here we summarize this available knowledge and discuss the advent of new techniques for the identification of novel hydrogen-uptake and - evolving enzymes from hydrothermal vent microorganisms.
    Type: Article , PeerReviewed
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  • 5
    Publication Date: 2020-04-22
    Description: Summary The major goal of the RV METEOR cruise M156 to Cape Verdian waters and the Mauritanian upwelling area off West Africa was to contribute to a better quantitative understanding of the effects of mesoscale eddies on CO2 source/sink mechanisms and the biological carbon pump in eastern boundary upwelling areas as well as their effects to the oligotrophic periphery including the deep-sea floor. The cruise M156 (MOSES Eddy Study I) was conducted within the framework of the BMBF funded REEBUS project (Role of Eddies in the Carbon Pump of Eastern Boundary Upwelling Systems) by a consortium of physical, biological (benthic microbiology, bacterial plankton, protists) and biogeochemical oceanographers. Specific aims were i. the quantification of solute and particle fluxes within and at the periphery of eddies; ii. to determine the turnover of carbon species, air-sea gas exchange of CO2, iii. the determination of the protistan and bacterial plankton community structures in the surface layers of an eddy, and iv. to quantify the magnitude and variability of material fluxes to the seabed and turnover in the sediment underneath the eddy passage. To achieve these aims, the cruise had two major observing strategies: i. an intense benthic/pelagic program along the zonal eddy passage at 18°N. Along this corridor ranging from 24°20’ to 16°30’W, five benthic/pelagic stations (E1 to E5) in different water depths and distances from the Mauritanian coast were performed. The motivation for this survey has been to resolve zonal gradients in pelagic element cycling as well as of organic matter degradation and burial in the seabed, which in turn could potentially be linked with changes in eddy induced primary- and export production. ii. the detailed investigation of an individual eddy to investigate physical, biogeochemical and biological processes on meso- to submeso-scales (100km to 10m). Satellite data analysis was performed before and during the cruise to identify a suitable eddy from a combination of sea-level anomaly, ocean color as Chl-a proxy, and sea-surface temperature supplemented with shipboard current velocity measurements. A total of 171 stations were sampled. The water column program consists of 59 CTD casts, 29 MSS and 20 Marine Snow Catcher deployments. For biogeochemical measurements at the sea surface two deployments of a Lagrangian Surface Drifter and one Waveglider deployment were conducted. At the seafloor, we conducted 10 BIGO deployments. Ten seafloor imaging surveys were performed using the towed camera system OFOS, supplemented with 7 Multibeam and 1 Sidescan surveys. In deviation from the cruise proposal, the planned long-term deployment of a Lander, which was planned to record a time series of oxygen fluxes during the passage of an eddy, was not deployed due to a major delay in its design and manufacturing. The planned AUV (Girona 500) deployments at the shallow E5 station close to the Mauritanian coast station did also not take place. Despite moderate weather conditions, all deployments were successful, hence all the data and sample material aimed for has been achieved. It is to expect that as planned all scientific questions can be addressed. Especially in the synthesis of all REEBUS cruises and the consideration of data from earlier cruises (MSM17/4, M107) into this region a high scientific potential can be expected.
    Type: Report , NonPeerReviewed
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  • 6
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    Springer
    In:  In: Metagenomics: Methods and Protocols. , ed. by Streit, W. R. and Daniel, R. Springer, New York, NY, pp. 261-270. ISBN 978-1-4939-6689-9
    Publication Date: 2018-12-14
    Description: Here we outline how to identify hydrogenase enzymes from metagenomic libraries through an activity-based screening approach. A metagenomic fosmid library is constructed in E. coli and the fosmids are transferred into a hydrogenase deletion mutant of Shewanella oneidensis (ΔhyaB) via triparental mating. If a fosmid exhibits hydrogen uptake activity, S. oneidensis' phenotype is restored and hydrogenase activity is indicated by a color change of the medium from yellow to colorless. This new method enables screening of 48 metagenomic fosmid clones in parallel.
    Type: Book chapter , NonPeerReviewed
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  • 7
    Publication Date: 2023-02-08
    Description: Molecular hydrogen (H2) can serve as an electron source for a multitude of bacterial and archaeal hydrogen-oxidizing species, supporting heterotrophic and autotrophic growth. Although hydrogen is one of the most common elements on earth, its molecular form is mostly found in very low concentrations in the environment. Deep-sea hydrothermal vent systems however, are typically enriched in molecular hydrogen, reaching up to millimolar levels. Thus, they are considered as promising habitats for the identification of hydrogenotrophic microorganisms. The H2-uptake ability is conveyed by hydrogenases, enzymes catalyzing the interconversion of molecular hydrogen to protons and electrons. Up to now, hydrogenases have been detected by the laborious isolation of hydrogenotrophic Bacteria and Archaea (through culture-dependent methods) or by means of sequence-based culture-independent approaches. When using the latter approach however, only hydrogenases resembling known hydrogenase genes can be detected. Within the here presented study, a culture-independent, activity-based approach for the identification of novel H2-uptake active enzymes has been evaluated and optimized to deliver reproducible screening results. The screen is based on the complementation of a hydrogenase deletion mutant of Shewanella oneidensis MR-1 with foreign hydrogenase genes. The heterologous expression of alpha- and gammaproteobacterial as well as campylobacterotal hydrogenase genes has successfully been tested, building a prerequisite for the application of the screen. Three fosmid libraries were constructed with metagenomic DNA of three distinct hydrothermal vent fields from the Mid-Atlantic Ridge and the newly established activity-based hydrogenase screen was applied. This resulted in the identification of four hydrogen-uptake active enzymes (among 14,400 screened) clones, of which only one showed homologies to known hydrogenases. The overall microbial hydrogen oxidation potential in deep-sea hydrothermal vent systems is discussed focusing on the vent fields, which were sampled for the activitybased hydrogenase screen. Furthermore, the H2-uptake ability of the gammaproteobacterial Hydrogenovibrio sp. SP-41, isolated from hydrothermal fluids was studied. After sequencing of SP-41’s genome, a second H2-uptake hydrogenase was identified. By means of qRT-PCR it could be shown that this hydrogenase is expressed with similar expression patterns as the first uptake hydrogenase. Finally, an outlook on potential application scenarios for (vent-derived) hydrogenases is given.
    Type: Thesis , NonPeerReviewed
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  • 8
    Publication Date: 2023-02-08
    Description: Hydrogen can in the future serve as an advantageous carrier of renewable energy if its production via water electrolysis and utilization in fuel cells are realized with high energy efficiency and non-precious electrocatalysts. In an unprecedented novel combination of structured electrodes with hydrogen converting enzymes from the uncultured and thus largely inaccessible microbial majority (〉99 %) we address this challenge. The geometrically defined electrodes with large specific surface area allow for low overpotentials and high energy efficiencies to be achieved. Enzymatic hydrogen evolution electrocatalysts are used as alternatives to noble metals. The enzymes are harnessed from the environmental microbial DNA (metagenomes) of hydrothermal vents exhibiting dynamic hydrogen and oxygen concentrations and are recovered via a recently developed novel activity-based screening tool. The screen enables us to target currently unrecognized hydrogenase enzymes from metagenomes via direct expression in a surrogate host microorganism. This circumvents the need for cultivation of the source organisms, the primary bottleneck when harnessing enzymes from microbes. One hydrogen converting metagenome-derived enzyme exhibited high activity and unusually high stability when dispersed on a TiO2-coated polyacrylonitrile fiber electrode. Our results highlight the tremendous potential of enzymes derived from uncultured microorganisms for applications in energy conversion and storage technologies.
    Type: Article , PeerReviewed
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  • 9
    Publication Date: 2023-02-08
    Description: Microbial metabolisms in sediments play a pivotal role in marine element cycling. In hydrothermal sediments chemosynthetic microorganisms likely prevail, while in non-hydrothermally impacted sediment regimes microorganisms associated with organic matter decomposition are primarily recognized. To test how these microorganisms are distributed along the hitherto neglected transition zone influenced to different degrees by hydrothermal input we sampled four sediment sites: these were (i) near an active vent, (ii) the outer rim, and (iii) the inactive area of the Kairei hydrothermal field as well as (iv) sediments roughly 200 km south-east of the Kairei field. Chemistry and microbial community compositions were different at all sampling sites. Against expectations, the sediments near the active vent did not host typical chemosynthetic microorganisms and chemistry did not indicate current, extensive hydrothermal venting. Data from the outer rim area of the active Kairei field suggested microbially mediated saponite production and diffuse hydrothermal flow from below accompanied by increased metal concentrations. A steep redox gradient in the inactive Kairei field points towards significant redox driven processes resulting in dissolution of hydrothermal precipitates and intense metal mobilization. Local microorganisms were primarily Chloroflexi, Bacillales, Thermoplasmata, and Thaumarchaeota.
    Type: Article , PeerReviewed
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  • 10
    Publication Date: 2022-01-31
    Description: Background Obligate sulfur oxidizing chemolithoauthotrophic strains of Hydrogenovibrio crunogenus have been isolated from multiple hydrothermal vent associated habitats. However, a hydrogenase gene cluster (encoding the hydrogen converting enzyme and its maturation/assembly machinery) detected on the first sequenced H. crunogenus strain (XCL-2) suggested that hydrogen conversion may also play a role in this organism. Yet, numerous experiments have underlined XCL-2’s inability to consume hydrogen under the tested conditions. A recent study showed that the closely related strain SP-41 contains a homolog of the XCL-2 hydrogenase (a group 1b [NiFe]-hydrogenase), but that it can indeed use hydrogen. Hence, the question remained unresolved, why SP-41 is capable of using hydrogen, while XCL-2 is not. Results Here, we present the genome sequence of the SP-41 strain and compare it to that of the XCL-2 strain. We show that the chromosome of SP-41 codes for a further hydrogenase gene cluster, including two additional hydrogenases: the first appears to be a group 1d periplasmic membrane-anchored hydrogenase, and the second a group 2b sensory hydrogenase. The region where these genes are located was likely acquired horizontally and exhibits similarity to other Hydrogenovibrio species (H. thermophilus MA2-6 and H. marinus MH-110 T) and other hydrogen oxidizing Proteobacteria (Cupriavidus necator H16 and Ghiorsea bivora TAG-1 T). The genomes of XCL-2 and SP-41 show a strong conservation in gene order. However, several short genomic regions are not contained in the genome of the other strain. These exclusive regions are often associated with signs of DNA mobility, such as genes coding for transposases. They code for transport systems and/or extend the metabolic potential of the strains. Conclusions Our results suggest that horizontal gene transfer plays an important role in shaping the genomes of these strains, as a likely mechanism for habitat adaptation, including, but not limited to the transfer of the hydrogen conversion ability.
    Type: Article , PeerReviewed
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