ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
Collection
Keywords
Publisher
Years
  • 1
    facet.materialart.
    Unknown
    Diversity and metabolism of the JTB255 clade in deep-sea sediments (2018)
    PANGAEA
    In:  Supplement to: Hoffmann, Katy; Bienhold, Christina; Buttigieg, Pier Luigi; Knittel, Katrin; Laso-Pérez, Rafael; Rapp, Josephine Z; Boetius, Antje; Offre, Pierre (2020): Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities. The ISME Journal, 14(4), 1042-1056, https://doi.org/10.1038/s41396-020-0588-4
    Details
    Publication Date: 2023-01-13
    Description: The present study aimed at a first characterization of the enigmatic JTB255 marine benthic group in deep-sea sediments, by: i) confirming the abundance and ubiquitous distribution of JTB255 in deep-sea sediments globally, ii) refining the phylogenetic positioning of the JTB255 clade within the \u03b3-Proteobacteria, iii) distinguishing potential ecotypes within the JTB255 clade, iv) providing first insights into the metabolic potential of deep-sea representatives of this clade. Therefore, two single cell genomes from Arctic HAUSGARTEN deep-se surface sediments were obtained and CARD-FISH counts of total cells, y-Proteobacteria and the JTB255 marine benthic group performed.
    Type: Dataset
    Format: application/zip, 2 datasets
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    DATA PANGAEA
  • 2
    facet.materialart.
    Unknown
    Abundance of Prokaryotes in deep-sea sediments analyzed by CARD-FISH (2017)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    Description: We fixed 0.5 g aliquots of sediment with a 4% formaldehyde solution for 2-4 h, washed the fixed sediments three times with 1x phosphate-buffered saline (PBS), before storing them in 50% ethanol/PBS at -20°C. For water samples, we fixed 10 ml (for samples from the deep chlorophyll maximum and 100 m water depth) and 30 ml (for meso- and bathypelagic samples) with formaldehyde to a final concentration of 2-4% for 2-4 h, then filtered over a 0.22 µm polycarbonate filter, and stored samples at -20°C. We performed total cell counts as described by Schauer et al. (2011, doi:10.1111/j.1462-2920.2011.02530.x) using the nucleic acid dye 4'-6-diamidino-2-phenylindole (DAPI). A minimum of 1,000 cells in 20 independent grids were counted using a Zeiss Axio Imager M1 epifluorescence microscope equipped with a 100x/1.25 oil plan-apochromat objective. We used Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization (CARD-FISH) according to Ishii et al. (2004) to count Gammaproteobacteria and JTB255 cells. We used the GAM42a oligonucleotide probe and the BET42a competitor probe to target members of the Gammaproteobacteria (Manz et al., 1992, doi:10.1016/S0723-2020(11)80121-9). We designed the JTB819a and JTB897 probes to target 16S rRNA gene sequences assigned to JTB255 in SILVA release 128 and the cJTB897 competitor probe to target all non-JTB255 16S sequences in SILVA release 128 that have a single mismatch to JTB819a and JTB897 probes. We obtained total gammaproteobacterial and JTB255 cell counts from duplicate filters derived from each sampling site.
    Keywords: ABYSS; Analytical method; ANT-XXIX/8; ANT-XXV/3; ANT-XXVIII/3; Arctic Ocean; ARK-XXIX/2.2; ARK-XXVII/3; ARK-XXVIII/2; Assessment of bacterial life and matter cycling in deep-sea surface sediments; AT26-23-05; AT26-23-12; Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH); Comment; Date/Time of event; Depth, bottom/max; DEPTH, sediment/rock; Depth, top/min; EGI; Elevation of event; Environmental feature; Epifluorescence microscopy after DAPI staining; Event label; Gammaproteobacteria; Gammaproteobacteria, cells; GeoB12202-1; GeoB12202-2; HGI; HGIV; HGIX; HGVI; HYDROMAR-III; J2-255; J2-258; J2-261; Japan Trench Bacteria clone 255 marine benthic group; JPI-OCEANS; Latitude of event; Longitude of event; M74/2; M74/2_962-1; M74/2_962-2; Maria S. Merian; Meteor (1986); MSM04/3; MSM04/3_251-ROV; MSM04/3_259-ROV; MSM04/3_271-ROV; MUC; MultiCorer; Multicorer with television; North Greenland Sea; PC; Piston corer; PLA; Plankton net; Polarstern; Prokaryotes; PS73/127-7; PS73 LOHAFEX; PS79; PS79/086-28; PS79/141-9; PS79/177-3; PS80/225-1; PS80/350-1; PS80 IceArc; PS81; PS81/606-1; PS85; PS85/436-1; PS85/454-3; PS85/460-4; PS85/464-1; PS85/465-4; PS85/470-3; PS93/067-2; PS93.2; Reference/source; Remote operated vehicle; Replicates; ROV; Sample ID; Sample type; SO242/2; SO242/2_147-148; SO242/2_194-1; SO242/2_198_MUC; Sonne_2; South Atlantic Ocean; South Pacific Ocean, Peru Basin; tropical/subtropical North Atlantic; TVMUC
    Type: Dataset
    Format: text/tab-separated-values, 648 data points
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    DATA PANGAEA
  • 3
    facet.materialart.
    Unknown
    Overview of sampling sites, site characteristics, and experiments to explore diversity and metabolism of the JTB255 clade (2018)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    Keywords: Accession number, genetics; Analysis; ANT-XXIX/8; ANT-XXV/3; ANT-XXVIII/3; Arctic Ocean; ARK-XXIX/2.2; ARK-XXVII/3; ARK-XXVIII/2; ARK-XXX/1.2; AT26-23-05; AT26-23-12; BC; Box corer; Carbon, organic, total; Chlorophyll a; Comment; CTD, towed system; CTD/Rosette; CTD/Rosette with Underwater Vision Profiler; CTD-RO; CTD-RO_UVP; CTD-twoyo; Date/Time of event; Depth, bottom/max; DEPTH, sediment/rock; Depth, top/min; EG_IV; EGI; Elevation of event; Environment; Event label; GC; GeoB12202-1; GeoB12202-2; GeoB18801-6; GeoB18805-18; GeoB18811-3; Grab; GRAB; Gravity corer; HE432; HE432/01-6; HE432/05-18; HE432/11-3; Heincke; HG_I; HG_IV; HG_IX; HGI; HGIV; HGIX; HGVI; HYDROMAR-III; J2-255; J2-258; J2-261; JPI-OCEANS; Latitude of event; Longitude of event; M74/2; M74/2_962-1; M74/2_962-2; Maria S. Merian; Meteor (1986); MSM04/3; MSM04/3_251-ROV; MSM04/3_259-ROV; MSM04/3_271-ROV; MUC; MultiCorer; Multicorer with television; North Greenland Sea; North Sea; Number; PC; Piston corer; PLA; Plankton net; Polarstern; PS73/127-7; PS73 LOHAFEX; PS79; PS79/086-28; PS79/141-9; PS79/177-3; PS80/225-1; PS80/350-1; PS80/361-1; PS80 IceArc; PS81; PS81/606-1; PS81/626-1; PS81/631-1; PS81/639-1; PS81/653-1; PS81/656-1; PS81/657-1; PS81/659-1; PS81/661-1; PS81/663-1; PS85; PS85/436-1; PS85/454-3; PS85/460-4; PS85/464-1; PS85/465-4; PS85/470-3; PS93/050-5; PS93/050-6; PS93/067-2; PS93.2; PS99/042-1; PS99/042-11; PS99/048-1; PS99/048-11; PS99/059-2; PS99/060-3; PS99/066-2; PS99/066-5; PS99.2; Reference/source; Remote operated vehicle; ROV; Sample comment; Sample ID; SO242/2; SO242/2_146_MUC-1; SO242/2_147-148-151; SO242/2_194-1; SO242/2_198_MUC; Sonne_2; South Atlantic Ocean; South Pacific Ocean, Peru Basin; tropical/subtropical North Atlantic; TVMUC; Uniform resource locator/link to source data file
    Type: Dataset
    Format: text/tab-separated-values, 926 data points
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    DATA PANGAEA
  • 4
    facet.materialart.
    Unknown
    Establishing anaerobic hydrocarbon-degrading enrichment cultures of microorganisms under strictly anoxic conditions (2018)
    Springer Nature
    Details
    Publication Date: 2018-05-17
    Print ISSN: 1754-2189
    Electronic ISSN: 1750-2799
    Topics: Natural Sciences in General
    Published by Springer Nature
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 5
    facet.materialart.
    Unknown
    Thermophilic archaea activate butane via alkyl-coenzyme M formation (2016)
    Springer Nature
    Details
    Publication Date: 2016-10-17
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Springer Nature
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 6
    facet.materialart.
    Unknown
    Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities (2020)
    Springer Nature
    Details
    Publication Date: 2020-01-27
    Print ISSN: 1751-7362
    Electronic ISSN: 1751-7370
    Topics: Biology
    Published by Springer Nature
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 7
    facet.materialart.
    Unknown
    “Candidatus Ethanoperedens,” a Thermophilic Genus of Archaea Mediating the Anaerobic Oxidation of Ethane (2020)
    American Society for Microbiology
    In:  EPIC3mBio, American Society for Microbiology, 11(2), pp. 1-18, ISSN: 2150-7511
    Details
    Publication Date: 2021-01-26
    Description: Cold seeps and hydrothermal vents deliver large amounts of methane and other gaseous alkanes into marine surface sediments. Consortia of archaea and partner bacteria thrive on the oxidation of these alkanes and its coupling to sulfate reduction. The inherently slow growth of the involved organisms and the lack of pure cultures have impeded the understanding of the molecular mechanisms of archaeal alkane degradation. Here, using hydrothermal sediments of the Guaymas Basin (Gulf of California) and ethane as the substrate, we cultured microbial consortia of a novel anaerobic ethane oxidizer, “Candidatus Ethanoperedens thermophilum” (GoM-Arc1 clade), and its partner bacterium “Candidatus Desulfofervidus auxilii,” previously known from methane-oxidizing consortia. The sulfate reduction activity of the culture doubled within one week, indicating a much faster growth than in any other alkane-oxidizing archaea described before. The dominance of a single archaeal phylotype in this culture allowed retrieval of a closed genome of “Ca. Ethanoperedens,” a sister genus of the recently reported ethane oxidizer “Candidatus Argoarchaeum.” The metagenome-assembled genome of “Ca. Ethanoperedens” encoded a complete methanogenesis pathway including a methyl-coenzyme M reductase (MCR) that is highly divergent from those of methanogens and methanotrophs. Combined substrate and metabolite analysis showed ethane as the sole growth substrate and production of ethyl-coenzyme M as the activation product. Stable isotope probing demonstrated that the enzymatic mechanism of ethane oxidation in “Ca. Ethanoperedens” is fully reversible; thus, its enzymatic machinery has potential for the biotechnological development of microbial ethane production from carbon dioxide.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 8
    facet.materialart.
    Unknown
    Establishing anaerobic hydrocarbon-degrading enrichment cultures of microorganisms under strictly anoxic conditions (2018)
    Nature Publishing Group
    In:  EPIC3Nature Protocols, Nature Publishing Group, 13(6), pp. 1310-1330, ISSN: 1754-2189
    Details
    Publication Date: 2020-02-23
    Description: Traditionally, the description of microorganisms starts with their isolation from an environmental sample. Many environmentally relevant anaerobic microorganisms grow very slowly, and often they rely on syntrophic interactions with other microorganisms. This impedes their isolation and characterization by classic microbiological techniques. We developed and applied an approach for the successive enrichment of syntrophic hydrocarbon-degrading microorganisms from environmental samples. We collected samples from microbial mat-covered hydrothermally heated hydrocarbon-rich sediments of the Guaymas Basin and mixed them with synthetic mineral medium to obtain sediment slurries. Supplementation with defined substrates (i.e., methane or butane), incubation at specific temperatures, and a regular maintenance procedure that included the measurement of metabolic products and stepwise dilutions enabled us to establish highly active, virtually sediment-free enrichment cultures of actively hydrocarbon-degrading communities in a 6-months to several-years' effort. Using methane as sole electron donor shifted the originally highly diverse microbial communities toward defined mixed cultures dominated by syntrophic consortia consisting of anaerobic methane-oxidizing archaea (ANME) and different sulfate-reducing bacteria. Cultivation with butane at 50 °C yielded consortia of archaea belonging to Candidatus Syntrophoarchaeum and Candidatus Desulfofervidus auxilii partner bacteria. This protocol also describes sampling for further molecular characterization of enrichment cultures by fluorescence in situ hybridization (FISH), and transcriptomics and metabolite analyses, which can provide insights into the functioning of hydrocarbon metabolism in archaea and resolve important mechanisms that enable electron transfer to their sulfate-reducing partner bacteria.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 9
    facet.materialart.
    Unknown
    Anaerobic Degradation of Non-Methane Alkanes by “Candidatus Methanoliparia” in Hydrocarbon Seeps of the Gulf of Mexico (2019)
    American Society for Microbiology
    In:  EPIC3mBio, American Society for Microbiology
    Details
    Publication Date: 2021-01-26
    Description: Crude oil and gases in the seabed provide an important energy source for subsurface microorganisms. We investigated the role of archaea in the anaerobic degradation of non-methane alkanes in deep-sea oil seeps from the Gulf of Mexico. We identified microscopically the ethane and short-chain alkane oxidizers “Candidatus Argoarchaeum” and “Candidatus Syntrophoarchaeum” forming consortia with bacteria. Moreover, we found that the sediments contain large numbers of cells from the archaeal clade “Candidatus Methanoliparia,” which was previously proposed to perform methanogenic alkane degradation. “Ca. Methanoliparia” occurred abundantly as single cells attached to oil droplets in sediments without apparent bacterial or archaeal partners. Metagenome-assembled genomes of “Ca. Methanoliparia” encode a complete methanogenesis pathway including a canonical methyl-coenzyme M reductase (MCR) but also a highly divergent MCR related to those of alkane-degrading archaea and pathways for the oxidation of long-chain alkyl units. Its metabolic genomic potential and its global detection in hydrocarbon reservoirs suggest that “Ca. Methanoliparia” is an important methanogenic alkane degrader in subsurface environments, producing methane by alkane disproportionation as a single organism.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 10
    facet.materialart.
    Unknown
    Thermophilic archaea activate butane via alkyl-CoM formation (2016)
    In:  EPIC3Nature, (539), pp. 396-401
    Details
    Publication Date: 2017-01-30
    Description: The anaerobic formation and oxidation of methane involve unique enzymatic mechanisms and cofactors, all of which are believed to be specific for C1-compounds. Here we show that an anaerobic thermophilic enrichment culture composed of dense consortia of archaea and bacteria apparently uses partly similar pathways to oxidize the C4 hydrocarbon butane. The archaea, proposed genus ‘Candidatus Syntrophoarchaeum’, show the characteristic autofluorescence of methanogens, and contain highly expressed genes encoding enzymes similar to methyl-coenzyme M reductase. We detect butyl-coenzyme M, indicating archaeal butane activation analogous to the first step in anaerobic methane oxidation. In addition, Ca. Syntrophoarchaeum expresses the genes encoding β-oxidation enzymes, carbon monoxide dehydrogenase and reversible C1 methanogenesis enzymes. This allows for the complete oxidation of butane. Reducing equivalents are seemingly channelled to HotSeep-1, a thermophilic sulfate-reducing partner bacterium known from the anaerobic oxidation of methane. Genes encoding 16S rRNA and methyl-coenzyme M reductase similar to those identifying Ca. Syntrophoarchaeum were repeatedly retrieved from marine subsurface sediments, suggesting that the presented activation mechanism is naturally widespread in the anaerobic oxidation of short-chain hydrocarbons.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...