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Berlin Brandenburg

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  • 1
    Language: English
    In: Science (New York, N.Y.), 08 August 2014, Vol.345(6197), pp.673-6
    Description: Anaerobic microbial degradation of hydrocarbons, typically occurring at the oil-water transition zone, influences the quality of oil reservoirs. In Pitch Lake, Trinidad and Tobago--the world's largest asphalt lake--we found that microorganisms are metabolically active in minuscule water droplets (1 to 3 microliters) entrapped in oil. Pyrotag sequencing of individual droplet microbiomes revealed complex methanogenic microbial communities actively degrading the oil into a diverse range of metabolites, as shown by nuclear magnetic resonance and Fourier transform ion cyclotron resonance mass spectrometry. High salinity and water-stable isotopes of the droplets indicate a deep subsurface origin. The 13.5% water content and the large surface area of the droplets represent an underestimated potential for biodegradation of oil away from the oil-water transition zone.
    Keywords: Water Microbiology ; Archaea -- Metabolism ; Bacteria -- Metabolism ; Lakes -- Microbiology ; Microbiota -- Genetics ; Petroleum -- Metabolism
    ISSN: 00368075
    E-ISSN: 1095-9203
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  • 2
    Language: English
    In: PLoS ONE, 2012, Vol.7(7), p.e40467
    Description: The characterization of microbial community structure via 16S rRNA gene profiling has been greatly advanced in recent years by the introduction of amplicon pyrosequencing. The possibility of barcoding gives the opportunity to massively screen multiple samples from environmental or clinical sources for community details. However, an on-going debate questions the reproducibility and semi-quantitative rigour of pyrotag sequencing, similar to the early days of community fingerprinting. In this study we demonstrate the reproducibility of bacterial 454 pyrotag sequencing over biological and technical replicates of aquifer sediment bacterial communities. Moreover, we explore the potential of recovering specific template ratios via quantitatively defined template spiking to environmental DNA. We sequenced pyrotag libraries of triplicate sediment samples taken in annual sampling campaigns at a tar oil contaminated aquifer in Düsseldorf, Germany. The abundance of dominating lineages was highly reproducible with a maximal standard deviation of ∼4% read abundance across biological, and ∼2% across technical replicates. Our workflow also allows for the linking of read abundances within defined assembled pyrotag contigs to that of specific ‘ in vivo ’ fingerprinting signatures. Thus we demonstrate that both terminal restriction fragment length polymorphism (T-RFLP) analysis and pyrotag sequencing are capable of recovering highly comparable community structure. Overall diversity was roughly double in amplicon sequencing. Pyrotag libraries were also capable of linearly recovering increasing ratios (up to 20%) of 16S rRNA gene amendments from a pure culture of Aliivibrio fisheri spiked to sediment DNA. Our study demonstrates that 454 pyrotag sequencing is a robust and reproducible method, capable of reliably recovering template abundances and overall community structure within natural microbial communities.
    Keywords: Research Article ; Biology ; Microbiology ; Ecology ; Marine And Aquatic Sciences
    E-ISSN: 1932-6203
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  • 3
    Language: English
    In: Applied and environmental microbiology, January 2013, Vol.79(2), pp.543-52
    Description: The detection of anaerobic hydrocarbon degrader populations via catabolic gene markers is important for the understanding of processes at contaminated sites. Fumarate-adding enzymes (FAEs; i.e., benzylsuccinate and alkylsuccinate synthases) have already been established as specific functional marker genes for anaerobic hydrocarbon degraders. Several recent studies based on pure cultures and laboratory enrichments have shown the existence of new and deeply branching FAE gene lineages, such as clostridial benzylsuccinate synthases and homologues, as well as naphthylmethylsuccinate synthases. However, established FAE gene detection assays were not designed to target these novel lineages, and consequently, their detectability in different environments remains obscure. Here, we present a new suite of parallel primer sets for detecting the comprehensive range of FAE markers known to date, including clostridial benzylsuccinate, naphthylmethylsuccinate, and alkylsuccinate synthases. It was not possible to develop one single assay spanning the complete diversity of FAE genes alone. The enhanced assays were tested with a range of hydrocarbon-degrading pure cultures, enrichments, and environmental samples of marine and terrestrial origin. They revealed the presence of several, partially unexpected FAE gene lineages not detected in these environments before: distinct deltaproteobacterial and also clostridial bssA homologues as well as environmental nmsA homologues. These findings were backed up by dual-digest terminal restriction fragment length polymorphism diagnostics to identify FAE gene populations independently of sequencing. This allows rapid insights into intrinsic degrader populations and degradation potentials established in aromatic and aliphatic hydrocarbon-impacted environmental systems.
    Keywords: Bacteria -- Enzymology ; Enzymes -- Genetics ; Fumarates -- Metabolism ; Hydrocarbons -- Metabolism ; Metabolic Networks and Pathways -- Genetics ; Metagenomics -- Methods
    E-ISSN: 1098-5336
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  • 4
    Language: English
    In: Analytical chemistry, 07 July 2015, Vol.87(13), pp.6622-30
    Description: Raman microspectroscopy is a prime tool to characterize the molecular and isotopic composition of microbial cells. However, low sensitivity and long acquisition times limit a broad applicability of the method in environmental analysis. In this study, we explore the potential, the applicability, and the limitations of stable isotope Raman microspectroscopy (SIRM), resonance SIRM, and SIRM in combination with surface-enhanced Raman scattering (SERS) for the characterization of single bacterial cells. The latter two techniques have the potential to significantly increase sensitivity and decrease measurement times in SIRM, but to date, there are no (SERS-SIRM) or only a limited number (resonance SIRM) of studies in environmental microbiology. The analyzed microorganisms were grown with substrates fully labeled with the stable isotopes (13)C or (2)H and compounds with natural abundance of atomic isotopes ((12)C 98.89% or (1)H 99.9844%, designated as (12)C or (1)H, respectively). Raman bands of bacterial cell compounds in stable isotope-labeled microorganisms exhibited a characteristic red-shift in the spectra. In particular, the sharp phenylalanine band was found to be an applicable marker band for SIRM analysis of the Deltaproteobacterium strain N47 growing anaerobically on (13)C-naphthalene. The study of G. metallireducens grown with (13)C- and (2)H-acetate showed that the information on the chromophore cytochrome c obtained by resonance SIRM at 532 nm excitation wavelength can be successfully complemented by whole-organism fingerprints of bacteria cells achieved by regular SIRM after photobleaching. Furthermore, we present here for the first time the reproducible SERS analysis of microbial cells labeled with stable isotopes. Escherichia coli strain DSM 1116 cultivated with (12)C- or (13)C-glucose was used as a model organism. Silver nanoparticles synthesized in situ were applied as SERS media. We observed a reproducible red-shift of an adenine-related marker band from 733 to 720 cm(-1) in SERS spectra for (13)C-labeled cells. Additionally, Raman measurements of (12)C/(13)C-glucose and -phenylalanine mixtures were performed to elucidate the feasibility of SIRM for nondestructive quantitative and spatially resolved analysis. The performed analysis of isotopically labeled microbial cells with SERS-SIRM and resonance SIRM paves the way toward novel approaches to apply Raman microspectroscopy in environmental process studies.
    Keywords: Spectrum Analysis, Raman -- Methods
    ISSN: 00032700
    E-ISSN: 1520-6882
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  • 5
    Language: English
    In: Soil Biology and Biochemistry, Feb, 2014, Vol.69, p.187(10)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.soilbio.2013.10.040 Byline: Dorte Dibbern, Andreas Schmalwasser, Tillmann Lueders, Kai Uwe Totsche Abstract: Plants introduce abundant carbon into soils, where it is mineralised and sequestered. Proportions of this fresh organic carbon introduced to top soils can be relocated to deeper soil layers and even to groundwater by event-driven transport upon heavy rainfalls or after snowmelt. It is assumed that a significant fraction of this flux involves biocolloids and possibly microbial biomass itself. However, the nature of such transported microbes, their origin and the mechanisms of their mobilisation are still poorly understood. Here, we provide primary evidence that specific microbial populations are exported from top soils upon seepage events. At an experimental maize field, we have analysed the composition of mobilised bacterial communities collected in seepage water directly after snowmelt in winter at different depths (35 and 65 cm), and compared them to the corresponding bulk soil microbiota. Using T-RFLP fingerprinting and pyrotag sequencing, we reveal that mostly members of the Betaproteobacteria (Methylophilaceae, Oxalobacteraceae, Comamonadaceae), the Alphaproteobacteria (Sphingomonadaceae, Bradyrhizobiaceae), the Gammaproteobacteria (Legionellaceae) and the Bacteroidetes (Sphingobacteriaceae) were mobilised, all characteristic taxa for the rhizoplane. This highlights the importance of preferential flow along root channels for the vertical mobilisation and transport of microbes. Although the estimated quantitative fluxes of bacterial biomass carbon appeared low, our study allows for an improved understanding of the links between top soil, subsoil, and groundwater microbiota, as well as carbon fluxes between soil compartments. Author Affiliation: (a) Institute of Groundwater Ecology, Helmholtz Zentrum Munchen - German Research Center for Environmental Health, Ingolstadter Landstr. 1, 85764 Neuherberg, Germany (b) Institute of Geosciences, Department of Hydrogeology, Friedrich-Schiller-Universitat Jena, Burgweg 11, 07749 Jena, Germany Article History: Received 19 August 2013; Revised 16 October 2013; Accepted 17 October 2013
    Keywords: Hydrogeology ; Soil Microbiology ; Groundwater ; Soils ; Soil Carbon
    ISSN: 0038-0717
    Source: Cengage Learning, Inc.
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  • 6
    Language: English
    In: Soil Biology and Biochemistry, September 2018, Vol.124, pp.168-178
    Description: Substantial amounts of organic matter are mobilized from upper soil layers during extreme precipitation events. This results in considerable fluxes of carbon from plant-associated topsoil to deeper mineral soil and to groundwater. Microbes constitute an important part of this mobile organic matter (MOM) pool. Previous work has shown that specific bacteria associated with the rhizosphere of decaying maize roots were selectively transported with seepage water upon snowmelt in winter. However, effective mechanisms of mobilization and also possible distinctions to microbial transport for living root systems remain poorly understood. In the present study, bacteria in seepage water were sampled from lysimeters at an experimental maize field after extreme rain events in summer. We show that a distinctive subset of rhizoplane-associated bacterial populations was mobilized after summer rain, especially including abundant members of the , representing a microbial conduit for fresh plant-derived carbon inputs into deeper soil layers. Marked distinctions of seepage communities were not observed between lysimeters with a different relative contribution of preferential vs. matrix flow. Time-resolved analyses of seepage water during an artificial rain event revealed temporal patterns in the mobilization of certain lineages, with members of the , , and preferentially mobilized in early and late seepage fractions, and members of the candidate phyla and mobilized mostly in intermediate fractions. While average bacterial cell counts were at ∼10  ml in seepage water, the recovery of amended fluorescently labeled cells of was low (0.2–0.6%) over seepage events. Still, mobilized bacteria clearly have the potential to influence bacterial activities and communities in subsoils. These findings demonstrate that dynamic hydraulic events must be considered for a better understanding of the connectivities between microbial populations and communities in soil, as well as of the links between distinct carbon pools over depth.
    Keywords: Natural Rain ; Artificial Rain ; Preferential Flow ; Seepage Water ; Soil Bacterial Communities ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
    Source: ScienceDirect Journals (Elsevier)
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  • 7
    In: FEMS Microbiology Ecology, 2016, Vol. 93(1)
    Description: The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly responsible for the anaerobic degradation of BTEX hydrocarbons in situ and to unravel their ecology in contaminated aquifers. Here, recent advances in our knowledge of the identity, diversity and ecology of microbes involved in these important ecosystem services are discussed. At several sites, distinct lineages within the Desulfobulbaceae , the Rhodocyclaceae and the Gram-positive Peptococcaceae have been shown to dominate the degradation of different BTEX hydrocarbons. Especially for the functional guild of anaerobic toluene degraders, specific molecular detection systems have been developed, allowing researchers to trace their diversity and distribution in contaminated aquifers. Their populations appear enriched in hot spots of biodegradation in situ . 13 C-labelling experiments have revealed unexpected pathways of carbon sharing and obligate syntrophic interactions to be relevant in degradation. Together with feedback mechanisms between abiotic and biotic habitat components, this promotes an enhanced ecological perspective of the anaerobic degradation of BTEX hydrocarbons, as well as its incorporation into updated concepts for site monitoring and bioremediation. This review summarises recent advances into the identity, diversity and ecology of anaerobic degraders of monoaromatic hydrocarbons in contaminated aquifers.
    Keywords: Toluene ; Benzene ; Groundwater ; Fumarate - Adding Enzymes ; Stable Isotope Probing ; Degrader Diversity
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 8
    Language: English
    In: Applied and Environmental Microbiology, 2011, Vol.77(11), p.3749(8)
    Description: Active microbes responsible for methane formation in samples were collected from abandoned coal mines for over 6 months to identify the microbes involved in the processes leading to methane formation in which acetate acts as the main precursor of methane. Active methanogens, closely affiliated with Methanosarcina barkeri, which utilized the readily available acetate rather than the thermodynamically more favorable hydrogen indicated that the methanogenic microbial community were highly adapted to the low-[H.sub.2] conditions found in coal mines.
    Keywords: Acetates – Chemical Properties ; Coal Industry – Environmental Aspects ; Methane – Environmental Aspects ; Methanogens – Physiological Aspects ; Microbial Metabolism – Research
    ISSN: 0099-2240
    Source: Cengage Learning, Inc.
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  • 9
    Language: English
    In: Applied and environmental microbiology, June 2011, Vol.77(11), pp.3749-56
    Description: In abandoned coal mines, methanogenic archaea are responsible for the production of substantial amounts of methane. The present study aimed to directly unravel the active methanogens mediating methane release as well as active bacteria potentially involved in the trophic network. Therefore, the stable-isotope-labeled precursors of methane, [(13)C]acetate and H(2)-(13)CO(2), were fed to liquid cultures from hard coal and mine timber from a coal mine in Germany. Guided by methane production rates, samples for DNA stable-isotope probing (SIP) with subsequent quantitative PCR and denaturing gradient gel electrophoretic (DGGE) analyses were taken over 6 months. Surprisingly, the formation of [(13)C]methane was linked to acetoclastic methanogenesis in both the [(13)C]acetate- and the H(2)-(13)CO(2)-amended cultures of coal and timber. H(2)-(13)CO(2) was used mainly by acetogens related to Pelobacter acetylenicus and Clostridium species. Active methanogens, closely affiliated with Methanosarcina barkeri, utilized the readily available acetate rather than the thermodynamically more favorable hydrogen. Thus, the methanogenic microbial community appears to be highly adapted to the low-H(2) conditions found in coal mines.
    Keywords: Soil Microbiology ; Bacteria -- Isolation & Purification ; Methane -- Metabolism ; Methanosarcinales -- Isolation & Purification
    ISSN: 00992240
    E-ISSN: 1098-5336
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  • 10
    Language: English
    In: Soil Biology and Biochemistry, February 2014, Vol.69, pp.187-196
    Description: Plants introduce abundant carbon into soils, where it is mineralised and sequestered. Proportions of this fresh organic carbon introduced to top soils can be relocated to deeper soil layers and even to groundwater by event-driven transport upon heavy rainfalls or after snowmelt. It is assumed that a significant fraction of this flux involves biocolloids and possibly microbial biomass itself. However, the nature of such transported microbes, their origin and the mechanisms of their mobilisation are still poorly understood. Here, we provide primary evidence that specific microbial populations are exported from top soils upon seepage events. At an experimental maize field, we have analysed the composition of mobilised bacterial communities collected in seepage water directly after snowmelt in winter at different depths (35 and 65 cm), and compared them to the corresponding bulk soil microbiota. Using T-RFLP fingerprinting and pyrotag sequencing, we reveal that mostly members of the ( , , ), the ( , ), the ( ) and the ( ) were mobilised, all characteristic taxa for the rhizoplane. This highlights the importance of preferential flow along root channels for the vertical mobilisation and transport of microbes. Although the estimated quantitative fluxes of bacterial biomass carbon appeared low, our study allows for an improved understanding of the links between top soil, subsoil, and groundwater microbiota, as well as carbon fluxes between soil compartments.
    Keywords: Bacterial Transport ; Biocolloids ; Preferential Flow ; Particulate Organic Matter ; Soil Organic Matter ; Lysimeter ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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