Geotalea uraniireducens Rf4
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ABSTRACT:
PROVIDER: PRJNA107223 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Geobacteraceae transfer electrons from a donor such as acetate to an electron acceptor such as Fe(III) or U(VI). Geobacter uraniireducens is found in uranium-contaminated sites and plays an important role in in situ bioremediation. In this experiment, gene expression was compared between G. uraniireducens cultures grown in sediments from a uranium contaminated site amended with acetate and cultures grown in acetate/fumarate medium. Keywords: two-condition comparison
2008-10-20 | GSE10920 | GEO
Project description:G. uraniireducens was isolated from a subsurface site in Rifle, CO undergoing in situ uranium bioremediation. Sediments from the Rifle site were heat-sterilized, amended with acetate to simulate in situ bioremediation conditions, and inoculated with G. uraniireducens. Gene transcript abundance in these cells using sediment Fe(III) and Mn(IV) oxides as the electron acceptor were compared with transcript levels in cells grown with fumarate as the electron acceptor. Additional comparisons were made between cells grown on synthetic Fe(III) or Mn(IV) oxides and cells grown on fumarate. 3 biological replicates hybridized in duplicate
2010-07-21 | E-GEOD-12874 | biostudies-arrayexpress
Project description:G. uraniireducens was isolated from a subsurface site in Rifle, CO undergoing in situ uranium bioremediation. Sediments from the Rifle site were heat-sterilized, amended with acetate to simulate in situ bioremediation conditions, and inoculated with G. uraniireducens. Gene transcript abundance in these cells using sediment Fe(III) and Mn(IV) oxides as the electron acceptor were compared with transcript levels in cells grown with fumarate as the electron acceptor. Additional comparisons were made between cells grown on synthetic Fe(III) or Mn(IV) oxides and cells grown on fumarate.
2010-07-22 | GSE12874 | GEO
Project description:Gene expression patterns under conditions of oxidative stress in Geobacter uraniumreducens
| PRJNA113015 | ENA
Project description:Iron- and uranium-reducing bacterium
| PRJNA15768 | ENA
Project description:Differential Gene Expression in G. uraniireducens during Growth on Iron or Manganese Oxide as Electron Acceptor
| PRJNA111053 | ENA
Project description:Previous analysis of gene transcript levels of Geobacter species in groundwater during in situ bioremediation of a uranium-contaminated aquifer detected expression of genes encoding superoxide dismutase (sodA) and cytochrome d ubiquinol oxidase (cydA), proteins known to be involved in the response to oxidative stress in other microorganisms. In order to further elucidate gene expression patterns that could be attributed to oxygen exposure, G. uraniumreducens was grown with acetate as the electron donor and fumarate as the electron acceptor in the presence of oxygen and compared to non-oxygen treated cultures.
2009-06-04 | GSE12455 | GEO
Project description:Mahadevan2006 - Genome-scale metabolic
network of Geobacter sulfurreducens (iRM588)
This model is described in the article:
Characterization of
metabolism in the Fe(III)-reducing organism Geobacter
sulfurreducens by constraint-based modeling.
Mahadevan R, Bond DR, Butler JE,
Esteve-Nuñez A, Coppi MV, Palsson BO, Schilling CH, Lovley
DR.
Appl. Environ. Microbiol. 2006 Feb;
72(2): 1558-1568
Abstract:
Geobacter sulfurreducens is a well-studied representative of
the Geobacteraceae, which play a critical role in organic
matter oxidation coupled to Fe(III) reduction, bioremediation
of groundwater contaminated with organics or metals, and
electricity production from waste organic matter. In order to
investigate G. sulfurreducens central metabolism and electron
transport, a metabolic model which integrated genome-based
predictions with available genetic and physiological data was
developed via the constraint-based modeling approach.
Evaluation of the rates of proton production and consumption in
the extracellular and cytoplasmic compartments revealed that
energy conservation with extracellular electron acceptors, such
as Fe(III), was limited relative to that associated with
intracellular acceptors. This limitation was attributed to lack
of cytoplasmic proton consumption during reduction of
extracellular electron acceptors. Model-based analysis of the
metabolic cost of producing an extracellular electron shuttle
to promote electron transfer to insoluble Fe(III) oxides
demonstrated why Geobacter species, which do not produce
shuttles, have an energetic advantage over shuttle-producing
Fe(III) reducers in subsurface environments. In silico analysis
also revealed that the metabolic network of G. sulfurreducens
could synthesize amino acids more efficiently than that of
Escherichia coli due to the presence of a pyruvate-ferredoxin
oxidoreductase, which catalyzes synthesis of pyruvate from
acetate and carbon dioxide in a single step. In silico
phenotypic analysis of deletion mutants demonstrated the
capability of the model to explore the flexibility of G.
sulfurreducens central metabolism and correctly predict mutant
phenotypes. These results demonstrate that iterative modeling
coupled with experimentation can accelerate the understanding
of the physiology of poorly studied but environmentally
relevant organisms and may help optimize their practical
applications.
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MODEL1507180000.
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2015-07-30 | MODEL1507180000 | BioModels
Project description:Members of the bacterial phylum Spirochaetes are primarily studied for their commensal and pathogenic roles in animal hosts. However, Spirochaetes are also frequently detected in anoxic hydrocarbon-contaminated environments but their ecological role in such ecosystems has so far remained unclear. Here we provide a functional trait to these frequently detected organisms with an example of a sulfate-reducing, naphthalene-degrading enrichment culture consisting of a sulfate-reducing deltaproteobacterium Desulfobacterium naphthalenivorans and a novel spirochete Rectinema cohabitans. Using a combination of genomic, proteomic, and physiological studies we show that R. cohabitans grows by fermentation of organic compounds derived from biomass from dead cells (necromass). It recycles the derived electrons in the form of H2 to the sulfate-reducing D. naphthalenivorans, thereby supporting naphthalene degradation and forming a simple microbial loop. We provide metagenomic evidence that equivalent associations between Spirochaetes and hydrocarbon-degrading microorganisms are of general importance in hydrocarbon- and organohalide-contaminated ecosystems. We propose that environmental Spirochaetes form a critical component of a microbial loop central to nutrient cycling in subsurface environments. This emphasizes the importance of necromass and H2-cycling in highly toxic contaminated subsurface habitats such as hydrocarbon-polluted aquifers.
2018-05-17 | PXD005624 | Pride