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Accession: PRJNA118497 ID: 118497

Potential Differences in the Metabolic Status of Geobacter sulfurreducens at Different Depths in Anode Biofilms

See Genome Information for Geobacter sulfurreducens
Microtoming Coupled with Microarray Analysis to Evaluate Potential Differences in the Metabolic Status of Geobacter sulfurreducens at Different Depths in Anode Biofilms Differences in the Metabolic Status of Geobacter sulfurreducens at Different Depths in A Current Producing Biofilm Further insight into the metabolic status of cells within anode biofilms is essential for understanding the functioning of microbial fuel cells and developing strategies to optimize their power output. In order to further compare the metabolic status of cells growing close to the anode versus cells in the outer portion of the anode biofilm, mature anode biofilms were treated to stop turnover over of mRNA and then encased in resin which was sectioned into 100 nm shavings with a diamond knife and pooled into inner (0-20 µm from anode surface) and outer (30-60 µm) fractions. Whole genome DNA microarray analysis of RNA extracted from the shavings revealed that, at a 2-fold lower threshold, there were 146 genes that had significant (p<0.05), differences in transcript abundance between the inner and outer portions of the biofilm. Only 1 gene, GSU0093, a hypothetical ABC transporter, had significantly higher transcript abundances in the outer biofilm. Genes with lower transcript abundance in the outer biofilm included genes for ribosomal proteins and NADH dehydrogenase, suggesting that cells in the outer biofilm had lower metabolic rates. However, the differences in transcript abundance were relatively low (<3-fold) and the outer biofilm did not have significantly lower expression of the genes for TCA cycle enzymes which previous studies have demonstrated are sensitive indicators of changes in rates of metabolism in G. sulfurreducens. There also was no significant difference in the transcript levels for outer-surface cell components thought to be important in electron transfer in anode biofilms. Lower expression of genes involved in stress responses in the outer biofilm may reflect the development of low pH near the surface of the anode. The results of the metabolic staining and gene expression studies suggest that cells throughout the biofilm are metabolically active and can potentially contribute to current production. The microtoming/microarray strategy described here may be useful for evaluating gene expression with depth in a diversity of microbial biofilms. Overall design: Three biological replicates were hybridized in triplicate on a coustom affimetrix tilling array using prokaryotic protocol (p69Affy, p75 Adobe) for labeling, hybridization and scanning.
AccessionPRJNA118497; GEO: GSE17591
Data TypeTranscriptome or Gene expression
ScopeMultiisolate
OrganismGeobacter sulfurreducens[Taxonomy ID: 35554]
Bacteria; Proteobacteria; Deltaproteobacteria; Desulfuromonadales; Geobacteraceae; Geobacter; Geobacter sulfurreducens
PublicationsFranks AE et al., "Microtoming coupled to microarray analysis to evaluate the spatial metabolic status of Geobacter sulfurreducens biofilms.", ISME J, 2009 Dec 24;4(4):509-19
SubmissionRegistration date: 22-Jun-2010
D. R. Lovley, Microbiology, University of Massachusetts Amherst
RelevanceEnvironmental
Project Data:
Resource NameNumber
of Links
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PubMed1
Other datasets
GEO DataSets1
GEO Data Details
ParameterValue
Data volume, Spots7094
Data volume, Processed Mbytes1
Data volume, Supplementary Mbytes23

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