Expression Analysis of Geobacter sulfurreducens Current-Consuming Biofilm versus Current-Producing Biofilm
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ABSTRACT:
ORGANISM(S): Geobacter sulfurreducens
PROVIDER: GSE19150 | GEO | 2010/11/23
SECONDARY ACCESSION(S): PRJNA123753
REPOSITORIES: GEO
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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:Is there a universal genetically programmed defense providing tolerance to antibiotics when bacteria grow as biofilms? A comparison between biofilms of three different bacterial species by transcriptomic and metabolomic approaches uncovered no evidence of one. Single-species biofilms of three bacterial species (Pseudomonas aeruginosa, Staphylococcus aureus, and Acinetobacter baumannii) were grown in vitro for three days then challenged with respective antibiotics (ciprofloxacin, daptomycin, tigecycline) for an additional 24 h. All three microorganisms displayed reduced susceptibility in biofilms compared to planktonic cultures. Global transcriptomic profiling of gene expression comparing biofilm to planktonic and antibiotic-treated biofilm to untreated biofilm was performed. Extracellular metabolites including 18 amino acids, glucose, lactate, acetate, formate, and ethanol were measured to characterize the utilization of carbon sources between biofilms, treated biofilms, and planktonic cells. While all three bacteria exhibited a species-specific signature of stationary phase, no conserved gene, gene set, or common functional pathway could be identified that changed consistently across the three microorganisms. Across the three species, glucose consumption was increased in biofilms compared to planktonic cells and alanine and aspartic acid utilization were decreased in biofilms compared to planktonic cells. The reasons for these changes were not readily apparent in the transcriptomes. No common shift in the utilization pattern of carbon sources was discerned when comparing untreated to antibiotic-exposed biofilms. Overall, our measurements do not support the existence of a common genetic or biochemical basis for biofilm tolerance against antibiotics. Rather, there are likely myriad genes, proteins, and metabolic pathways that influence the physiological state of microorganisms in biofilms contributing to antibiotic tolerance. The Staphylococcus aureus microarray data from the study described above is deposited here.
2021-10-18 | GSE185864 | GEO
Project description:Is there a universal genetically programmed defense providing tolerance to antibiotics when bacteria grow as biofilms? A comparison between biofilms of three different bacterial species by transcriptomic and metabolomic approaches uncovered no evidence of one. Single-species biofilms of three bacterial species (Pseudomonas aeruginosa, Staphylococcus aureus, and Acinetobacter baumannii) were grown in vitro for three days then challenged with respective antibiotics (ciprofloxacin, daptomycin, tigecycline) for an additional 24 h. All three microorganisms displayed reduced susceptibility in biofilms compared to planktonic cultures. Global transcriptomic profiling of gene expression comparing biofilm to planktonic and antibiotic-treated biofilm to untreated biofilm was performed. Extracellular metabolites including 18 amino acids, glucose, lactate, acetate, formate, and ethanol were measured to characterize the utilization of carbon sources between biofilms, treated biofilms, and planktonic cells. While all three bacteria exhibited a species-specific signature of stationary phase, no conserved gene, gene set, or common functional pathway could be identified that changed consistently across the three microorganisms. Across the three species, glucose consumption was increased in biofilms compared to planktonic cells and alanine and aspartic acid utilization were decreased in biofilms compared to planktonic cells. The reasons for these changes were not readily apparent in the transcriptomes. No common shift in the utilization pattern of carbon sources was discerned when comparing untreated to antibiotic-exposed biofilms. Overall, our measurements do not support the existence of a common genetic or biochemical basis for biofilm tolerance against antibiotics. Rather, there are likely myriad genes, proteins, and metabolic pathways that influence the physiological state of microorganisms in biofilms contributing to antibiotic tolerance. The Acinetobacter baumannii microarray data from the study described above is deposited here.
2021-10-18 | GSE186041 | GEO
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:electrode biofilms sequencing of MFCs with Fe3+
| PRJNA343570 | ENA
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:Application of 200 µA of direct current to bacterial biofilms leads to cellular death. We hypothesize that bacterial death is caused, in part, by the generation of reactive oxygen species. We used microarray analysis to determine the effects at a cellular level following 60 minutes of exposure of bacterial biofilms to 200 µA direct current.
2016-12-02 | GSE90757 | GEO
Project description:Shewanella oneidensis MR-1 exhibits extracellular electron transfer (EET) activity that is influenced by various cellular components, including outer-membrane cytochromes, cell-surface polysaccharides (CPS), and regulatory proteins. Here, a random transposon-insertion mutant library of S. oneidensis MR-1 was screened after extended cultivation in electrochemical cells (ECs) with a working electrode poised at +0.2 V (vs. Ag/AgCl) to isolate mutants that adapted to electrode-respiring conditions and identify as-yet-unknown EET-related factors. Several mutants isolated from the enrichment culture exhibited rough morphology and extraordinarily large colonies on agar plates compared to wild-type MR-1. One of the isolated mutants, designated strain EC-2, produced 90% higher electric current than wild-type MR-1 in ECs and was found to have a transposon inserted in the SO_1860 (uvrY) gene, which encodes a DNA-binding response regulator of the BarA/UvrY two-component regulatory system. However, an in-frame deletion mutant of SO_1860 (∆SO_1860) did not exhibit a similar level of current generation as that of EC-2, suggesting that the enhanced current-generating capability of EC-2 was not simply due to the disruption of SO_1860. In both EC-2 and ∆SO_1860, the transcription of genes related to CPS synthesis was decreased compared to wild-type MR-1, suggesting that CPS negatively affects current generation. In addition, transcriptome analyses revealed that a number of genes, including those involved in biofilm formation, were differentially expressed in EC-2 compared to those in ∆SO_1860. The present results indicate that the altered expression of the genes related to CPS biosynthesis and biofilm formation is associated with the distinct morphotype and high current-generating capability of strain EC-2, suggesting an important role of these genes in determining the EET activity of S. oneidensis.
2014-07-14 | GSE50443 | GEO
Project description:Geobacter sulfurreducens is a dissimilatory metal-reducing bacterium capable of forming thick electron-conducting biofilms on solid electrodes in the absence of alternative electron acceptors. The remarkable ability of such biofilms to transfer electrons, liberated from soluble organic electron donors, over long distances has attracted scientific interest as to the mechanism for this process, and technological interest for application to microbial fuel and electrolysis cells and sensors. Here, we employ comparative proteomics to identify key metabolic pathways involved in G. sulfurreducens respiration by planktonic cells versus electron-conducting biofilms, in an effort to elucidate long-range electron transfer mechanisms.
2018-02-16 | PXD002667 | Pride