Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1123586 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29410332.fastq.gz | Fastqsanger.gz | |||
| SRR29410333.fastq.gz | Fastqsanger.gz | |||
| SRR29410334.fastq.gz | Fastqsanger.gz | |||
| SRR29410335.fastq.gz | Fastqsanger.gz | |||
| SRR29410336.fastq.gz | Fastqsanger.gz |
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Project description:Investigation of comprehensive information about the transcripts (boundary, level, etc.) across the entire G. sulfurreducens genome in mulitple growth conditions, including in biofilm and on electrode. A five array study using total RNA recovered from two separate culture conditions of G. sulfurreducens. G. sulfurreducens were harvested one week after growth on electrode or to form biofilm. The high-density oligonucleotide tiling arrays used consisted of 381,174 oligonucleotide probes spaced 20 bp apart (30-bp overlap between two probes) across the G. sulfurreducens genome (NimbleGen). Experiments were conducted as two (electrode) or three (biofilm) biological replicates (different cultures).
2010-07-01 | E-GEOD-22497 | biostudies-arrayexpress
Project description:Anode-associated multi-species exoelectrogenic biofilms are essential to the function of bioelectrochemical systems (BESs). The investigation of electrode-associated biofilms is critical to advance understanding of the function of individual members within communities that thrive using an electrode as the terminal electron acceptor. This study focusses on the analysis of a model biofilm community consisting of Shewanella oneidensis, Geobacter sulfurreducens and Geobacter metallireducens. The conducted experiments revealed that the organisms can build a stable biofilm on an electrode surface that is rather resilient to changes in the redox potential of the anode surface. The community operated at maximum electron transfer rates with electrode potentials of 0.04 V versus normal hydrogen electrode. Current densities decreased gradually with lower potentials and reached half-maximal values at -0.08 V. A positive interaction of the individual strains could be observed in our experiments. At least S. oneidensis and G. sulfurreducens show an upregulation of their central metabolism as a response to cultivation under mixed-species conditions. Interestingly, G. sulfurreducens was detected in the planktonic phase of the bioelectrochemical reactors only in mixed-culture experiments but not when it was grown in the absence of the other two organisms. It is possible that G. sulfurreducens cells used flavins which were released by S. oneidensis cells as electron shuttles. This would allow the organism to broaden its environmental niche. To the best of our knowledge, this is the first study describing the dynamics of biofilm formation of a model exoelectrogenic community, the resilience of the biofilm, and the molecular responses towards mixed-species conditions.
2017-01-18 | GSE79750 | GEO
Project description:There is a wide diversity of potential applications for direct electron transfer from electrodes to microorganisms, which might be better optimized if the mechanisms for this novel electrode-biofilm interaction were better understood. Geobacter sulfurreducens is one of the few microorganisms available in pure culture that is known to be capable of directly accepting electrons from a negatively poised electrode. A microarray comparison of cells accepting electrons from the electrode versus cells donating electrons to the electrode reveals that the genes previously observed to be upregulated in current-producing biofilms are not highly expressed in current-consuming biofilms.
2010-11-23 | GSE19150 | GEO
Project description:Investigation of comprehensive information about the transcripts (boundary, level, etc.) across the entire G. sulfurreducens genome in mulitple growth conditions, including in biofilm and on electrode.
2010-07-01 | GSE22497 | GEO
Project description:G. sulfurreducens can generate electricity from the oxidation of organic compounds. This is because it can take electrons from organic compounds and ship them out to the outer surface of the cell where they can then be deposited on various insoluble electron acceptors including electrodes. Cells attatched to the surface of an electrode oxidize acetate and and deposit the electrons derived from acetate onto the surface of the electrode after which they can travel through an electrical circuit, producing a current. Microbial fuel cells powered by acetate oxidation by Geobacter species are called Geobatteries. In this experiment we compared gene expression in a biofilm of the wild type strain growing on the surface of an electrode within a current-producing Geobattery to gene expression in a wild type biofilm that is not producing current, but is growing on the surface of an electrode. In both cases, the cells were growing in a flow-through two chambered H-cell Geobattery setup. This consists of two glass chambers, an anoxic anode chamber containing G. sulfurreducens, a graphite electrode, a reference electrode and growth medium and an oxic chamber containing the counter electrode. The two chambers are connected by a cation selective membrane and a wire connected to a potentionstat. A potentiostat is an instrument which maintains the redox potential of the anode at a fixed value relative to a reference electrode. Media continuously flowed through the anoxic anode chamber at a dilution rate of 0.15. In the experimental condition, the Geobattery was operational. The circuit was closed and G. sulfurreducens attached to the electrode generated current as it oxidized acetate. The redox potential at the anode was poised at 300 mV by the potentiostat. In the control condition, everything was the same, except that the medium in the anode chamber contained fumarate as electron acceptor, and the anode was not hooked up to the potentiostat i.e. the circuit was open. This prevented the anode from serving as an electron acceptor. Nevertheless a thick G. sulfurreducens biofilm grew on the surface of the electrode. The control and experimental geobatteries were harvested when current in the operational/experimental Geobatteries reached 10 mA. Keywords: two condition comparison
2009-06-03 | GSE8012 | GEO
Project description:There is a wide diversity of potential applications for direct electron transfer from electrodes to microorganisms, which might be better optimized if the mechanisms for this novel electrode-biofilm interaction were further understood. Geobacter sulfurreducens is one of the few microorganisms available in pure culture that is known to be capable of directly accepting electrons from a negatively poised electrode. Gene transcript abundance in cells of G. sulfurreducens using electrons delivered from a graphite electrode as the sole electron donor for fumarate reduction was compared with transcript abundance in cells growing on the same graphite material, but without an electrical connection and acetate as the electron donor.
2010-11-23 | GSE19149 | GEO
Project description:The gene expression profile of wild-type Desulfovibrio vulgaris grown on cathodic hydrogen, generated at an iron electrode surface with an imposed negative potential of -1.1 V (cathodic protection conditions). The gene expression profile of cells grown on cathodic hydrogen was compared to that of cells grown with gaseous hydrogen bubbling through the culture. Relative to the latter, the electrode-grown cells over-expressed two hydrogenases, the hyn1 genes for [NiFe] hydrogenase-1, and the hyd genes, encoding [Fe] hydrogenase. The hmc genes for the high molecular weight cytochrome (Hmc) complex, which allows electron flow from the hydrogenases across the cytoplasmic membrane, were also over-expressed. In contrast, cells grown on gaseous hydrogen over-expressed the hys genes for [NiFeSe] hydrogenase. Cells growing on the electrode also over-expressed genes encoding proteins which promote biofilm formation. Although the gene expression profiles for these two modes of growth were distinct, they were more closely related to each other than to that for cells grown in a lactate- and sulfate-containing medium. Electrochemically measured corrosion rates were lower for iron electrodes covered with hyn1-, hyd-, and hmc-mutant biofilms, as compared to wild-type biofilms. This confirms the importance, suggested by the gene expression studies, of the corresponding gene products in D. vulgaris-mediated iron corrosion. Keywords: Growth on Iron Electrode and Biofilm formation For each condition 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference.
2010-05-26 | E-GEOD-10388 | biostudies-arrayexpress
Project description:The gene expression profile of wild-type Desulfovibrio vulgaris grown on cathodic hydrogen, generated at an iron electrode surface with an imposed negative potential of -1.1 V (cathodic protection conditions). The gene expression profile of cells grown on cathodic hydrogen was compared to that of cells grown with gaseous hydrogen bubbling through the culture. Relative to the latter, the electrode-grown cells over-expressed two hydrogenases, the hyn1 genes for [NiFe] hydrogenase-1, and the hyd genes, encoding [Fe] hydrogenase. The hmc genes for the high molecular weight cytochrome (Hmc) complex, which allows electron flow from the hydrogenases across the cytoplasmic membrane, were also over-expressed. In contrast, cells grown on gaseous hydrogen over-expressed the hys genes for [NiFeSe] hydrogenase. Cells growing on the electrode also over-expressed genes encoding proteins which promote biofilm formation. Although the gene expression profiles for these two modes of growth were distinct, they were more closely related to each other than to that for cells grown in a lactate- and sulfate-containing medium. Electrochemically measured corrosion rates were lower for iron electrodes covered with hyn1-, hyd-, and hmc-mutant biofilms, as compared to wild-type biofilms. This confirms the importance, suggested by the gene expression studies, of the corresponding gene products in D. vulgaris-mediated iron corrosion. Keywords: Growth on Iron Electrode and Biofilm formation
2008-02-13 | GSE10388 | GEO