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Chapter 12 : Transcriptome Analysis of Metal-Reducing Bacteria
Category: Applied and Industrial Microbiology; Environmental Microbiology
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This chapter focuses on transcriptomic studies in the more well-studied systems of metal-reducing bacteria represented by Shewanella, Geobacter and Desulfovibrio that have both genome sequence data and postgenomic tools available. This review compares available data for more commonly studied bacteria that can transfer electrons to different metals in the context of carbon flow, electron flow, oxidative stress, and physiological states of the cell. A goal of the comparison is to identify similarities and differences in molecular mechanisms used by different metal-reducing bacteria to interact with metals and thus optimize their metabolism accordingly in order to tolerate “stressful” substrates. Microarrays have been a powerful tool for monitoring dynamic gene expression under various conditions and have been widely used for genome-wide transcriptional analyses in microorganisms. One important aspect to consider when investigating the metal-reduction mechanisms within a given species is the organization of vectoral electron transport. Transcriptome analysis indicated that increased oxygen levels upexpressed genes involved in cell-cell and cell-surface interactions, and the aggregated cells also upexpressed genes associated with anaerobic growth. Based upon the many different transcriptomic studies of stress and growth responses in three model metal-reducing bacteria, some similarities and differences can be discerned. Metal-reducing bacterias contain genes with homology to typical metalresponsive regulators. However, more work is needed to elucidate the respective regulatory networks for these regulators in anaerobic microorganisms and how the regulatory networks are coordinated.
Transmission electron micrograph of D. vulgaris Hildenborough after 24 h of incubation with 200 mM U(VI). The cells are unstained and show the extracellular nature of U(IV), whereas none was present inside the cells (D. Elias, unpublished data). 10.1128/9781555817190.ch12.f1