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  • 1
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    Deep Subsurface Microbiology (2015)
    Lausanne : Frontiers
    Details
    Keywords: deep subsurface ; marine sediment ; deep biosphere ; ocean crust ; subseafloor sediment ; Methane ; Peru margin ; Hydrogen ; acetogenesis ; sulfate reduction ; microbiology
    Description / Table of Contents: Deep subsurface microbiology is a highly active and rapidly advancing research field at the interface of microbiology and the geosciences; it focuses on the detection, identification, quantification, cultivation and activity measurements of bacteria, archaea and eukaryotes that permeate the subsurface biosphere of deep marine sediments and the basaltic ocean and continental crust. The deep subsurface biosphere abounds with uncultured, only recently discovered and – at best - incompletely understood microbial populations. In spatial extent and volume, Earth’s subsurface biosphere is only rivaled by the deep sea water column. So far, no deep subsurface sediment has been found that is entirely devoid of microbial life; microbial cells and DNA remain detectable at sediment depths of more than 1 km; microbial life permeates deeply buried hydrocarbon reservoirs, and is also found several kilometers down in continental crust aquifers. Severe energy limitation, either as electron acceptor or donor shortage, and scarcity of microbially degradable organic carbon sources are among the evolutionary pressures that have shaped the genomic and physiological repertoire of the deep subsurface biosphere. Its biogeochemical role as long-term organic carbon repository, inorganic electron and energy source, and subduction recycling engine continues to be explored by current research at the interface of microbiology, geochemistry and biosphere/geosphere evolution. This Research Topic addresses some of the central research questions about deep subsurface microbiology and biogeochemistry: phylogenetic and physiological microbial diversity in the deep subsurface; microbial activity and survival strategies in severely energy-limited subsurface habitats; microbial activity as reflected in process rates and gene expression patterns; biogeographic isolation and connectivity in deep subsurface microbial communities; the ecological standing of subsurface biospheres in comparison to the surface biosphere – an independently flourishing biosphere, or mere survivors that tolerate burial (along with organic carbon compounds), or a combination of both? Advancing these questions on Earth’s deep subsurface biosphere redefines the habitat range, environmental tolerance, activity and diversity of microbial life.
    Pages: Online-Ressource (303 Seiten)
    ISBN: 9782889195367
    URL: https://doi.org/10.3389/978-2-88919-536-7
    Language: English
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  • 2
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    Solid phase geochemistry of sediments from ROV push cores during Pourquoi Pas ? cruise INDEX2016, Hydrothermal Vent Outlet in the Kairei Field (2021)
    PANGAEA
    Details
    Publication Date: 2023-04-24
    Description: Deep-sea sediment samples were taken from the (wider) Kairei hydrothermal field area (25°S, 70°E) as well as a remote site (26°S, 71°E) in the Indian Ocean during the INDEX cruise 2016 with the N/O Pourquoi pas? (Ifremer, France). Push core samples from different areas of the Kairei vent field, as well as a sample from the remote site (~200 km south-east from the Kairei), were recovered with the help of the ROV VICTOR 6000 (Ifremer, France). All subsampling steps were carried out shipboard at 4 °C. With sterile syringes (nozzles removed) 3 ml of 2 cm layers of sediment were transferred into sterile falcon tubes for DNA extraction and stored at –80 °C. The remaining sediment was cut into 2 cm slices, freeze-dried, and partially milled to 〈75 mm for geochemical analyses. The sediment was analyzed for carbon chemistry, i.e. total organic carbon (TOC) and total inorganic carbon (TIC) with routine standard methods (IR-detection after combustion, ISO 10694, LECO CS 230 analyzer). Elemental composition of Kairei sediments was estimated by the accredited Actlab Laboratories, Canada (Multimethod mix called Ultratrace 3 program, using INAA, 4-Acid Digestion, ICP-OES, and ICP-MS). Sediments from the remote station were analyzed by routine WD-XRF after fusion with Li-Metaborate/Li-Bromide (XRF spectrometers Philips PW 2400 und Philips PW 1480).
    Keywords: 16S rRNA gene tags; Aluminium oxide; Area/locality; Calcium oxide; Carbon, carbonate; Carbon, organic; Carbon, total; Depth, bottom/max; DEPTH, sediment/rock; Depth, top/min; Element Analyser CS, LECO CS 230; Event label; geochemistry of porewaters; hydrothermal vent; INDEX2016; INDEX2016_12ROV; INDEX2016_20ROV; Indian Ocean; Iron oxide, Fe2O3; Kairei field; Magnesium oxide; Manganese oxide; metalliferous sediments; Phosphorus pentoxide; Potassium oxide; Pourquoi Pas ? (2005); Sample code/label; Silicon dioxide; Sodium oxide; Sulfur, total; Titanium dioxide; VICTOR; Victor6000 ROV
    Type: Dataset
    Format: text/tab-separated-values, 628 data points
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  • 3
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    Porewater geochemistry of sediments from ROV push cores during Pourquoi Pas ? cruise INDEX2016, Hydrothermal Vent Outlet in the Kairei Field (2021)
    PANGAEA
    Details
    Publication Date: 2023-03-02
    Description: Deep-sea sediment samples were taken from the (wider) Kairei hydrothermal field area (25°S, 70°E) as well as a remote site (26°S, 71°E) in the Indian Ocean during the INDEX cruise 2016 with the N/O Pourquoi pas? (Ifremer, France). Push core samples from different areas of the Kairei vent field, as well as a sample from the remote site (~200 km south-east from the Kairei), were recovered with the help of the ROV VICTOR 6000 (Ifremer, France). All subsampling steps were carried out shipboard at 4 °C. Porewater from push cores was extracted with rhizons (CSS, 5 cm Rhizosphere Research Products B.V., Netherlands) at a resolution of 2-3 cm, fixed with 1% HNO3 for trace element analyses and stored at 4 °C. With sterile syringes (nozzles removed) 3 ml of 2 cm layers of sediment were transferred into sterile falcon tubes for DNA extraction and stored at –80 °C. Concentrations of minor and trace elements Li, Al, Rb, Cs, Sr, Ba, V, Mn, Fe, Co, Ni, Cu, Zn, Ag, Cd, Tl, Pb, In, Sn, Sb, Bi, W, Mo, U, Au, As, and L were determined by highresolution ICP-SF-MS (Element XR, Thermo Scientific) after 25-fold dilution and spiking with Y and Re for internal standardization using appropriate mass resolution settings.
    Keywords: 16S rRNA gene tags; Aluminium; Antimony; Area/locality; Arsenic; Barium; Cadmium; Caesium; Cerium; Cobalt; Copper; DEPTH, sediment/rock; Europium; Event label; geochemistry of porewaters; hydrothermal vent; ICP-OES; ICP-SF-MS, Thermo Scientific, Element XR; INDEX2016; INDEX2016_12ROV; INDEX2016_20ROV; Indian Ocean; Ion chromatography; Iron; Kairei field; Lanthanum; Lead; Manganese; metalliferous sediments; Molybdenum; Neodymium; Nickel; Nitrate; Pourquoi Pas ? (2005); Praseodymium; Samarium; Sample code/label; Silica, dissolved; Silver; Thallium; Tin; Tungsten; Uranium; Vanadium; VICTOR; Victor6000 ROV; Zinc
    Type: Dataset
    Format: text/tab-separated-values, 942 data points
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    DATA PANGAEA
  • 4
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    Mineral composition of hydrothermal chimneys sampled with ROV during Pourquoi Pas ? cruise INDEX2016 (2021)
    PANGAEA
    Details
    Publication Date: 2023-03-02
    Description: Hydrothermal chimneys were collected by a ROV in 2016 from the Kairei and Pelagia vent fields along the Indian Ridge. Major element compositions of the chimney samples were determined by a combination of ICP emission and mass spectrometry. For semi-quantitative analysis of sulfide mineral distribution polished sections of the chimneys were investigated by optical and scanning electron microscopy and electron microprobe analyses. The abundance of bacterial and archaeal taxa was determined by sequencing of the 16S rRNA gene by Illumina MiSeq.
    Keywords: Accession number, genetics; Anhydrite; Area/locality; bacterial community composition; Chalcopyrite; chimney structure; Comment; Copper; deep sea mining; Event label; hydrothermal vent; INDEX2016; INDEX2016_06ROV; INDEX2016_12ROV; INDEX2016_16ROV; INDEX2016_20ROV; Indian Ocean; Iron; Isocubanite; massive sulfide deposits; Pourquoi Pas ? (2005); Pyrite/Marcasite; Pyrrhotite; Sample code/label; South East Indian Ridge; Sphalerite; VICTOR; Victor6000 ROV; Zinc
    Type: Dataset
    Format: text/tab-separated-values, 95 data points
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  • 5
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    (Table T1) Total procaryotes, and living bacteria and archaea in black shales of ODP Leg 207 sites (2006)
    PANGAEA
    In:  Supplement to: Schippers, Axel; Neretin, Lev N (2006): Data report: Microbiological AODC and CARD-FISH analysis of black shale samples from the Demerara Rise, ODP Leg 207. In: Mosher, DC; Erbacher, J; Malone, MJ (eds.) Proceedings of the Ocean Drilling Program, Scientific Results, College Station, TX (Ocean Drilling Program), 207, 1-6, https://doi.org/10.2973/odp.proc.sr.207.105.2006
    Details
    Publication Date: 2024-01-09
    Description: Subseafloor sediments harbor over half of all prokaryotic cells on Earth (Whitman et al., 1998). This immense number is calculated from numerous microscopic acridine orange direct counts (AODCs) conducted on sediment cores drilled during the Ocean Drilling Program (ODP) (Parkes et al., 1994, doi:10.1038/371410a0, 2000, doi:10.1007/PL00010971). Because these counts cannot differentiate between living and inactive or even dead cells (Kepner and Pratt, 1994; Morita, 1997), the population size of living microorganisms has recently been enumerated for ODP Leg 201 sediment samples from the equatorial Pacific and the Peru margin using ribosomal ribonucleic acid targeting catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) (Schippers et al., 2005, doi:10.1038/nature03302). A large fraction of the subseafloor prokaryotes were alive, even in very old (16 Ma) and deep (〉400 m) sediments. In this study, black shale samples from the Demerara Rise (Erbacher, Mosher, Malone, et al., 2004, doi:10.2973/odp.proc.ir.207.2004) were analyzed using AODC and CARD-FISH to find out if black shales also harbor microorganisms.
    Keywords: 207-1257C; 207-1258B; 207-1259C; 207-1261B; Acridine Orange Direct Counting (AODC); Archaea; Bacteria, abundance; Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH); DEPTH, sediment/rock; DRILL; Drilling/drill rig; DSDP/ODP/IODP sample designation; Event label; Joides Resolution; Leg207; Ocean Drilling Program; ODP; Prokaryotes, abundance as single cells; Sample code/label; Sample comment; South Atlantic Ocean; Walvis Ridge, Southeast Atlantic Ocean
    Type: Dataset
    Format: text/tab-separated-values, 90 data points
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  • 6
    Electronic Resource
    Electronic Resource
    Quantification of Microorganisms Involved in Cemented Layer Formation in Sulfidic Mine Waste Tailings (Freiberg, Saxony, Germany) (2007)
    s.l. ; Stafa-Zurich, Switzerland
    Advanced materials research Vol. 20-21 (July 2007), p. 481-484 
    Details
    ISSN: 1662-8985
    Source: Scientific.Net: Materials Science & Technology / Trans Tech Publications Archiv 1984-2008
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Cemented layers predominantly consisting of gels/poorly crystalline mineral phases havebeen formed as a consequence of mineral weathering in sulfidic tailings near Freiberg, Saxony,Germany. These layers function as natural attenuation barrier for toxic compounds and reduceoxidation and erosion processes of tailings surfaces. Quantitative molecular biological andcultivation methods were applied to investigate the role of microorganisms for mineral weatheringand cemented layer formation. High resolution depth profiles of numbers of microorganismsshowed maximal cell numbers in the oxidation zone where cemented layers had been formed.Highest total cell numbers of 〉109 cells g-1 dry weight (dw) were detected by SybrGreen directcounting. Using quantitative real-time PCR (Q-PCR) between 107 and 109 Bacteria g-1 dw and up to108 Archaea g-1 dw were determined. As well high numbers of cultivable and living Bacteria couldbe detected by MPN (most probable number) for Fe(II)- and S-oxidizers and CARD-FISH(catalyzed reporter deposition - fluorescence in situ hybridization). Overall, the high numbers ofmicroorganisms determined with various quantification techniques argue for a significant role ofmicroorganisms in cemented layer formation due to microbial mineral weathering. It ishypothesized that EPS (extracellular polymeric substances) mediate the formation of secondarymineral phases
    Type of Medium: Electronic Resource
    URL: http://www.tib-hannover.de/fulltexts/2011/0528/01/39/transtech_doi~10.4028%252Fwww.scientific.net%252FAMR.20-21.481.pdf
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  • 7
    Electronic Resource
    Electronic Resource
    Biooxidation and Cyanidation for Gold and Silver Recovery from Acid Mine Drainage Generating Tailings (Ticapampa, Peru) (2007)
    s.l. ; Stafa-Zurich, Switzerland
    Advanced materials research Vol. 20-21 (July 2007), p. 91-94 
    Details
    ISSN: 1662-8985
    Source: Scientific.Net: Materials Science & Technology / Trans Tech Publications Archiv 1984-2008
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The acid mine drainage (AMD) generating sulfidic tailings have a total mass of1,639,130 t containing 1.65 g/t Au, 34.5 g/t Ag, 7.74 % Fe, 5.91 % S, 3.2 % As, 0.75 % Zn and 0.05% Cu. The precious metals Au and Ag are enriched in the fine fractions. Approximately 35 % of thematerial is below 25 /m in size and 53 % below 63 /m. Electron microprobe analysis of a sulfideconcentrate of the tailings, produced by gravity separation, proved the occurrence of pyrite andarsenopyrite with appreciable sphalerite and galena. Refractory gold (up to 316 g/t) is hosted in Asrichzones of some arsenopyrites. Approximately 200 g of the sulfide concentrate of the tailings wasbiooxidized in laboratory shake flasks using an adapted mixed culture of Acidithiobacillusferrooxidans (Ram 6F), Acidithiobacillus thiooxidans (Ram 8T) and Leptospirillum ferrooxidans(R3). During biooxidation, arsenopyrite was preferentially dissolved and the secondary mineraltooeleite (Fe8(AsO4)6(OH)5·H2O) precipitated. The following cyanidation of the biooxidized sulfideconcentrate showed a recovery of 97 % and 50 % for Au and Ag, respectively. The values were 56% and 18 % for the untreated concentrate. The recovery of Au and Ag from the tailingssignificantly reduces the costs for the tailings remediation to mitigate AMD release
    Type of Medium: Electronic Resource
    URL: http://www.tib-hannover.de/fulltexts/2011/0528/01/39/transtech_doi~10.4028%252Fwww.scientific.net%252FAMR.20-21.91.pdf
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  • 8
    Electronic Resource
    Electronic Resource
    Iron Isotope Fractionation by Biogeochemical Processes in Mine Tailings (2007)
    s.l. ; Stafa-Zurich, Switzerland
    Advanced materials research Vol. 20-21 (July 2007), p. 237-237 
    Details
    ISSN: 1662-8985
    Source: Scientific.Net: Materials Science & Technology / Trans Tech Publications Archiv 1984-2008
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Type of Medium: Electronic Resource
    URL: http://www.tib-hannover.de/fulltexts/2011/0528/01/39/transtech_doi~10.4028%252Fwww.scientific.net%252FAMR.20-21.237.pdf
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  • 9
    Electronic Resource
    Electronic Resource
    Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria (2005)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 433 (2005), S. 861-864 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Chemical analyses of the pore waters from hundreds of deep ocean sediment cores have over decades provided evidence for ongoing processes that require biological catalysis by prokaryotes. This sub-seafloor activity of microorganisms may influence the surface Earth by changing the chemistry of ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature03302
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  • 10
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    Deep subsurface microbiology : a guide to the research topic papers (2014)
    Frontiers Media
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 4 (2013): 122, doi:10.3389/fmicb.2013.00122.
    Description: Deep subsurface microbiology is a rising field in geomicrobiology, environmental microbiology and microbial ecology that focuses on the molecular detection and quantification, cultivation, biogeographic examination, and distribution of bacteria, archaea, and eukarya that permeate the subsurface biosphere. The deep biosphere includes a variety of subsurface habitats, such as terrestrial deep aquifer systems or mines, deeply buried hydrocarbon reservoirs, marine sediments and the basaltic ocean crust. The deep subsurface biosphere abounds with uncultured, only recently discovered and—at best—incompletely understood microbial populations. So far, microbial cells and DNA remain detectable at sediment depths of more than 1 km and life appears limited mostly by heat in the deep subsurface. Severe energy limitation, either as electron acceptor or donor shortage, and scarcity of microbially degradable organic carbon sources are among the evolutionary pressures that may shape the genomic and physiological repertoire of the deep subsurface biosphere. Its biogeochemical importance in long-term carbon sequestration, subsurface elemental cycling and crustal aging, is a major focus of current research at the interface of microbiology, geochemistry, and biosphere/geosphere evolution.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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