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      Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany

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          Abstract

          Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signature of methane measured in groundwater and coal-rich sediment samples indicated methanogenic activity. Analysis of 16S rRNA gene sequences showed the presence of methanogenic Archaea, predominantly belonging to the orders Methanosarcinales and Methanomicrobiales, capable of acetoclastic or hydrogenotrophic methanogenesis. Furthermore, we identified fermenting, sulfate-, nitrate-, and metal-reducing, or acetogenic Bacteria clustering within the phyla Proteobacteria, complemented by members of the classes Actinobacteria, and Clostridia. The indigenous microbial communities found in the groundwater as well as in the coal-rich sediments are able to degrade coal-derived organic components and to produce methane as the final product. Lignite-bearing sediments may be an important nutrient and energy source influencing larger compartments via groundwater transport.

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          Archaea in coastal marine environments.

          E Delong (1992)
          Archaea (archaebacteria) are a phenotypically diverse group of microorganisms that share a common evolutionary history. There are four general phenotypic groups of archaea: the methanogens, the extreme halophiles, the sulfate-reducing archaea, and the extreme thermophiles. In the marine environment, archaeal habitats are generally limited to shallow or deep-sea anaerobic sediments (free-living and endosymbiotic methanogens), hot springs or deep-sea hydrothermal vents (methanogens, sulfate reducers, and extreme thermophiles), and highly saline land-locked seas (halophiles). This report provides evidence for the widespread occurrence of unusual archaea in oxygenated coastal surface waters of North America. Quantitative estimates indicated that up to 2% of the total ribosomal RNA extracted from coastal bacterioplankton assemblages was archaeal. Archaeal small-subunit ribosomal RNA-encoding DNAs (rDNAs) were cloned from mixed bacterioplankton populations collected at geographically distant sampling sites. Phylogenetic and nucleotide signature analyses of these cloned rDNAs revealed the presence of two lineages of archaea, each sharing the diagnostic signatures and structural features previously established for the domain Archaea. Both of these lineages were found in bacterioplankton populations collected off the east and west coasts of North America. The abundance and distribution of these archaea in oxic coastal surface waters suggests that these microorganisms represent undescribed physiological types of archaea, which reside and compete with aerobic, mesophilic eubacteria in marine coastal environments.
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            Biogenic methane formation in marine and freshwater environments: CO2 reduction vs. acetate fermentation—Isotope evidence

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              Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set.

              The design and evaluation of a set of universal primers and probe for the amplification of 16S rDNA from the Domain Bacteria to estimate total bacterial load by real-time PCR is reported. Broad specificity of the universal detection system was confirmed by testing DNA isolated from 34 bacterial species encompassing most of the groups of bacteria outlined in Bergey's Manual of Determinative Bacteriology. However, the nature of the chromosomal DNA used as a standard was critical. A DNA standard representing those bacteria most likely to predominate in a given habitat was important for a more accurate determination of total bacterial load due to variations in 16S rDNA copy number and the effect of generation time of the bacteria on this number, since rapid growth could result in multiple replication forks and hence, in effect, more than one copy of portions of the chromosome. The validity of applying these caveats to estimating bacterial load was confirmed by enumerating the number of bacteria in an artificial sample mixed in vitro and in clinical carious dentine samples. Taking these parameters into account, the number of anaerobic bacteria estimated by the universal probe and primers set in carious dentine was 40-fold greater than the total bacterial load detected by culture methods, demonstrating the utility of real-time PCR in the analysis of this environment.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                20 March 2015
                2015
                : 6
                : 200
                Affiliations
                [1] 1Resource Geochemistry, Geomicrobiology, Federal Institute for Geosciences and Natural Resources, Hannover Germany
                [2] 2Federal Institute for Geosciences and Natural Resources, Hannover Germany
                [3] 3Institute of Groundwater Ecology, Helmholtz Center for Environmental Health, Neuherberg Germany
                [4] 4Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig Germany
                Author notes

                Edited by: Mark Alexander Lever, Eidgenössische Technische Hochschule Zürich, Switzerland

                Reviewed by: Hiroyuki Imachi, Japan Agency for Marine-Earth Science and Technology, Japan; Aude Picard, Harvard University, USA

                *Correspondence: Martin Krüger, Resource Geochemistry, Geomicrobiology, Federal Institute for Geosciences and Natural Resources, Stilleweg 2, D-30655 Hannover, Germany martin.krueger@ 123456bgr.de

                Present address: Friederike Gründger, Department of Geology, Centre for Arctic Gas Hydrate, Environment and Climate, The Arctic University of Norway, Tromsø, Norway

                This article was submitted to Extreme Microbiology, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2015.00200
                4367440
                25852663
                005c48f1-6cc1-4585-8c56-9b8b51ce14ed
                Copyright © 2015 Gründger, Jiménez, Thielemann, Straaten, Lüders, Richnow and Krüger.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 11 December 2014
                : 24 February 2015
                Page count
                Figures: 5, Tables: 3, Equations: 0, References: 81, Pages: 17, Words: 0
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                methanogenesis,cenozoic sediments,fluvial deposits,stable isotope fractionation,methanogenic hydrocarbon degradation,methanogenic archaea,coal

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