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  • 1
    Online Resource
    Online Resource
    Cham :Springer International Publishing AG,
    Keywords: Marine chemical ecology. ; Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (204 pages)
    Edition: 1st ed.
    ISBN: 9783030348274
    Series Statement: Springer Oceanography Series
    Language: English
    Note: Intro -- Foreword -- Acknowledgements -- Contents -- 1 Microbial Communities and Metabolisms at Hydrocarbon Seeps -- Abstract -- Life at Hydrocarbon Seeps -- Life Styles at Hydrocarbon Seeps -- Aerobic Methanotrophy -- Anaerobic Methanotrophy Coupled to Sulfate Reduction -- Anaerobic Methanotrophy Coupled to Nitrate, Nitrite, and Metal Oxides -- Aerobic and Anaerobic Oxidation of Non-methane Hydrocarbons -- Thiotrophy -- Heterotrophy -- Microbial Community Assembly and Biogeography -- References -- 2 Anaerobic Hydrocarbon-Degrading Sulfate-Reducing Bacteria at Marine Gas and Oil Seeps -- Abstract -- Characteristics of Habitats Suitable for Microbial Hydrocarbon Degradation -- In Situ Evidence for Anaerobic Hydrocarbon Degradation by Sulfate-Reducing Bacteria -- Anaerobic Hydrocarbon-Degrading Microorganisms -- Anaerobic Hydrocarbon-Degrading Sulfate-Reducing Bacteria -- Detection and In Situ Quantification of Hydrocarbon-Degrading Sulfate-Reducing Bacteria -- SCA1 -- SCA2 -- LCA1 -- LCA2 -- Desulfatiglans anilini and Relatives -- Seep-Endemic Sulfate-Reducing Bacteria -- Pathways for Anaerobic Hydrocarbon Degradation -- Diversity and Distribution of Fumarate-Adding Marker Genes -- Outlook -- References -- 3 Guaymas Basin, a Hydrothermal Hydrocarbon Seep Ecosystem -- Abstract -- General Characteristics of Guaymas Basin -- Microbial Communities of Guaymas Basin Sediments -- Sulfur-Oxidizing Mat-Forming Bacteria in Guaymas Basin -- Microbial Nitrogen Cycling in Surficial Sediments and Mats of Guaymas Basin -- Microbial Cycling of Methane and Other Hydrocarbons in Guaymas Basin -- Microbial Communities of Guaymas Basin Hydrothermal Mounds, and Chimneys -- Methanogens and Methane Oxidizers in Guaymas Basin -- Alkane-Oxidizing Bacteria and Archaea in Guaymas Basin -- Genomic Surveys of Guaymas Basin Microbial Communities. , Challenging Conditions for Microbial Life in Guaymas Basin Hydrothermal Sediments -- References -- 4 The Gulf of Mexico: An Introductory Survey of a Seep-Dominated Seafloor Landscape -- Abstract -- Bathymetry and Fluid Geochemistry in the Gulf of Mexico -- Microbial Communities and Their Environmental Constraints in Gulf of Mexico Sediments -- Microbial Communities at Selected Northern Gulf of Mexico Seep Sites -- Alaminos Canyon 601 -- Garden Banks 425 -- Garden Banks 697 -- Green Canyon 246 -- Green Canyon 600 -- Mississippi Canyon 118 -- Mississippi Canyon 252 -- References -- 5 Benthic Deep-Sea Life Associated with Asphaltic Hydrocarbon Emissions in the Southern Gulf of Mexico -- Abstract -- Introduction -- The Hydrocarbon Province in the Southern Gulf of Mexico -- The Chapopote Asphalt Volcano -- Asphalt Geochemistry and Compositional Changes Related to Biodegradation -- Asphalt-Derived Hydrocarbons Induce Increased Microbial Activity -- Microorganisms Associated to Asphalt Volcanism -- Chemosynthetic and Grazing Macrofauna -- Summary and Outlook -- Acknowledgements -- References -- 6 Archaea in Mediterranean Sea Cold Seep Sediments and Brine Pools -- Abstract -- Introduction -- Geological Structures in Cold Seeps -- Geochemical Conditions in Cold Seeps -- Mud Volcanoes in the Mediterranean Sea -- Microorganisms in the Center of the Amsterdam Mud Volcano -- Microorganisms in the Center of the Napoli Mud Volcano -- Microorganisms in Microbial Mats Associated with the Napoli Mud Volcano -- Microorganisms in Pockmark Sediments of the Nile Deep Sea Fan -- References -- 7 The Microbial Communities of the East Mediterranean Sea Mud Volcanoes and Pockmarks -- Abstract -- Introduction -- The Eastern Mediterranean Sea Mud Volcanoes and Pockmarks: Sites and Methods Used -- Bacterial Diversity -- Archaeal Diversity -- Future Perspectives -- References. , 8 Large Sulfur-Oxidizing Bacteria at Gulf of Mexico Hydrocarbon Seeps -- Abstract -- Initial Surveys -- Pigmented and Unpigmented Filamentous Beggiatoaceae -- Unicellular Thiomargarita -- Sessile Filamentous "Candidatus Marithrix" -- New Findings of Beggiatoaceae Types in the Gulf of Mexico -- Discovery of Thioploca-like Organisms -- Macroscopic Aggregates of Curled Filamentous Sulfide Oxidizers -- Enriching Thiomargarita-Like Organisms -- Conclusions -- Acknowledgements -- References -- 9 Growth Patterns of Giant Deep Sea Beggiatoaceae from a Guaymas Basin Vent Site -- Abstract -- Autotrophic CO2 Fixation in Beggiatoaceae: Gaps in the Evidence -- Experiments with Filamentous Beggiatoaceae from Guaymas Basin, Gulf of California -- Inorganic Carbon Assimilation by Giant Guaymas Beggiatoaceae -- Acknowledgements -- References -- 10 Uncovering Microbial Hydrocarbon Degradation Processes: The Promise of Stable Isotope Probing -- Abstract -- Introduction -- SIP Methodology -- DNA-SIP -- RNA-SIP -- Coupling DNA-/RNA-SIP with Other Techniques -- Applications to Benthic Systems -- Aerobic SIP -- Anaerobic SIP -- Summary -- References.
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  • 2
    Online Resource
    Online Resource
    Cham : Springer International Publishing | Cham : Imprint: Springer
    Keywords: Geobiology. ; Geoecology. ; Environmental geology. ; Microbial ecology. ; Bioorganic chemistry.
    Description / Table of Contents: Diversity and assembly of seep-associated microbial communities -- Anaerobic hydrocarbon-degrading sulfate-reducing bacteria at marine gas and oil seeps -- Guaymas Basin, a hydrothermal hydrocarbon seep ecosystem -- The Gulf of Mexico: An introductory survey of a seep-dominated seafloor landscape -- Benthic deep-sea life associated with asphaltic hydrocarbon emissions at Chapopote, southern Gulf of Mexico -- Archaea in Mediterranean Sea cold seep sediments and brine pools -- The microbial communities of the East Mediterranean Sea mud volcanoes and pockmarks -- Large sulfur-oxidizing bacteria at Gulf of Mexico hydrocarbon seeps -- Growth patterns of giant deep-sea Beggiatoaceae from a Guaymas Basin vent site -- Uncovering microbial hydrocarbon degradation processes: the promise of stable isotope probing.
    Type of Medium: Online Resource
    Pages: 1 Online-Ressource(XII, 199 p. 55 illus., 49 illus. in color.)
    Edition: 1st ed. 2020.
    ISBN: 9783030348274
    Series Statement: Springer Oceanography
    Language: English
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  • 3
    Keywords: Microbiology ; Microbiology ; Science (General)
    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
    Type of Medium: Online Resource
    Pages: 1 Online-Ressource (1 electronic resource (303 p.))
    ISBN: 9782889195367
    Language: Undetermined
    Note: English
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  • 4
    Online Resource
    Online Resource
    s.l. : Frontiers Media SA
    Keywords: Science (General) ; Science (General) ; Microbiology
    Type of Medium: Online Resource
    Pages: 1 Online-Ressource (1 electronic resource (284 p.))
    ISBN: 9782889196821
    Language: Undetermined
    Note: English
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  • 5
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 47 (2000), S. 0 
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: . Eighteen strains of flagellated protists representing nine species were isolated and cultured from four deep-sea hydrothermal vents: Juan de Fuca Ridge (2,200 m), Guaymas Basin (2,000 m), 21° N (2,550 m) and 9° N (2,000 m). Light and electron microscopy were used to identify flagellates to genus and, when possible, species. The small subunit ribosomal RNA genes of each vent species and related strains from shallow-waters and the American Type Culture Collection were sequenced then used for comparative analysis with database sequences to place taxa in an rDNA tree. The hydrothermal vent flagellates belonged to six different taxonomic orders: the Ancyromonadida, Bicosoecida, Cercomonadida, Choanoflagellida, Chrysomonadida, and Kinetoplastida. Comparative analysis of vent isolate and database sequences resolved systematic placement of some well-known species with previously uncertain taxonomic affinities, such as Ancyromonas sigmoides, Caecitellus parvulus and Maxxixteria marina. Many of these vent isolates are ubiquitous members of marine, freshwater, and terrestrial ecosystems worldwide, suggesting a global distribution of these flagellate species.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 45 (2003), S. 0 
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The prokaryotic community inhabiting the deep subsurface sediments in the Forearc Basin of the Nankai Trough southeast of Japan (ODP Site 1176) was analyzed by 16S rDNA sequencing. Sediment samples from 1.15, 51.05, 98.50 and 193.96 m below sea floor (mbsf) harbored highly diverse bacterial communities. The most frequently retrieved clones included members of the Green non-sulfur bacteria whose closest relatives come from deep subsurface environments, a new epsilon-proteobacterial phylotype, and representatives of a cluster of closely related bacterial sequences from hydrocarbon- and methane-rich sediments around the world. Archaeal clones were limited to members of the genus Thermococcus, and were only obtained from the two deepest samples.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: A number of strains of heterotrophic bacteria were isolated from various environments on the basis of their potential to oxidize inorganic sulfur compounds to tetrathionate. The isolates were screened for the ability to oxidize thiosulfate under denitrifying conditions. Many of them could grow anaerobically with acetate and nitrate, and eight strains could oxidize thiosulfate to tetrathionate under the same conditions. In batch cultures with acetate as carbon and energy source, most active anaerobic thiosulfate oxidation occurred with N2O as electron acceptor. The level of anaerobic thiosulfate-oxidizing activity in cultures and cell suspensions supplied with nitrate correlated with the activity of nitrite reductase in cell suspensions. Some strains converted thiosulfate to tetrathionate equally well with nitrite, nitrate and N2O as electron acceptors. Others functioned best with N2O during anaerobic thiosulfate oxidation. The latter strains appeared to have a lower level of nitrite reductase activity. Thiosulfate oxidation under anaerobic conditions was much slower than in the presence of oxygen, and was obviously controlled by the availability of organic electron donor. The strains had DNA-DNA similarity levels higher than 30%. Sequence analysis of the 16S rRNA gene of four selected isolates showed their affiliation to specific genomovars of Pseudomonas stutzeri and the proposed new species, Pseudomonas balearica. As shown by 16S rRNA sequence analysis and DNA-DNA hybridization, the previously misnamed ‘Flavobacterium lutescens’ (ATCC 27951) is also a P. stutzeri strain which can oxidize thiosulfate to tetrathionate aerobically and anaerobically in the presence of N2O. The data suggest that tetrathionate-forming heterotrophic bacteria, in particular those belonging to the P. stutzeri‘superspecies’, can play a much more significant role in the biogeochemical cycles than was previously recognized.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 25 (1998), S. 0 
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Most probable number (MPN) counts of sulfate-reducing bacteria in the upper 3 mm of a cyanobacterial mat of Solar Lake (Sinai, Egypt) were 20 times lower during the day under oxic conditions than at night in the absence of oxygen. In order to study the oxygen-dependent behaviour of the predominant sulfate reducers four strains were isolated from the highest dilutions of the MPN series. Strain D22 was obtained from a sample taken during the day, while the strains N13, N33 and N24 were dominant in the upper layer at night. All isolates belonged to the genus Desulfovibrio. Strain N24 and strain N13 could be identified as Desulfovibrio oxyclinae. In capillary tubes filled with cell suspensions strain N13, but not strain D22, showed a negative aerotactic response by forming bands around oxygen bubbles at the oxic/anoxic interface. All isolates respired with oxygen using H2, lactate or sulfide as electron donors. Ethanol, which could be used for sulfate reduction, was not metabolised with oxygen. Strain N13 grew with oxygen for 2 days. However, cell division was inhibited. While the protein content increased, the cell number remained constant and the cell length increased up to fivefold. Strain D22, which remained in the upper layer during the day, appeared not to be better adapted to oxic conditions than the strains isolated from the anoxic zone. It is concluded that possible strategies of sulfate-reducing bacteria to escape oxygen stress in a cyanobacterial mat include migration to deeper anoxic zones, formation of clumps, and oxygen removal by active respiration in bands.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 80 (1991), S. 0 
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract: The almost complete 16S rRNA sequence from Mycobacterium leprae was determined by direct sequencing of the chromosomal gene amplified by the polymerase chain reaction. The primary sequence revealed an insertion of 12 nucleotides at the 5′ end of the 16S rRNA gene, which consists of an A-T stretch and appears to be unique for M. leprae. Within the mycobacteria M. leprae branches off with a group of slow-growing species comprising M. scrofulaceum, M. kansasii, M. szulgai, M. malmoense, M. intracellulare and M. avium. A systematic comparison of the nucleotide sequence resulted in the characterization of oligonucleotide probes which are highly specific for M. leprae. The probes hybridized exclusively to 16S rRNA nucleic acids from M. leprae, but not to nucleic acids from 20 cultivable fast- and slow-growing mycobacteria.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1432-1432
    Keywords: Key words: Protozoa — Flagellate —Ancyromonas—Apusomonas— Opisthokont — 18S small subunit ribosomal DNA — Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Molecular and morphological evidence points to the ancyromonad Ancyromonas as a plausible candidate for the closest relative to the common ancestor of metazoans, fungi, and choanoflagellates (the Opisthokonta). Using 18S rDNA sequences from most of the major eukaryotic lineages, maximum-likelihood, minimum-evolution, and maximum-parsimony analyses yielded congruent phylogenies supporting this hypothesis. Combined with ultrastructural similarities between Ancyromonas and opisthokonts, the evidence presented here suggests that Ancyromonas may form an independent lineage, the Ancyromonadida Cavalier-Smith 1997, closer in its relationship to the opisthokonts than is its nearest protist relatives, the Apusomonadida. However, the very low bootstrap support for deep nodes and hypothesis testing indicate that the resolving power of 18S rDNA sequences is limited for examining this aspect of eukaryotic phylogeny. Alternate branching positions for the Ancyromonas lineage cannot be robustly rejected, revealing the importance of ultrastructure when examining the origins of multicellularity. The future use of a multigene approach may additionally be needed to resolve this aspect of eukaryotic phylogeny.
    Type of Medium: Electronic Resource
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