Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments

Abstract

To learn more about the physiological state of Geobacter species living in subsurface sediments, heat-sterilized sediments from a uranium-contaminated aquifer in Rifle, Colorado, were inoculated with Geobacter uraniireducens, a pure culture representative of the Geobacter species that predominates during in situ uranium bioremediation at this site. Whole-genome microarray analysis comparing sediment-grown G. uraniireducens with cells grown in defined culture medium indicated that there were 1084 genes that had higher transcript levels during growth in sediments. Thirty-four c-type cytochrome genes were upregulated in the sediment-grown cells, including several genes that are homologous to cytochromes that are required for optimal Fe(III) and U(VI) reduction by G. sulfurreducens. Sediment-grown cells also had higher levels of transcripts, indicative of such physiological states as nitrogen limitation, phosphate limitation and heavy metal stress. Quantitative reverse transcription PCR showed that many of the metabolic indicator genes that appeared to be upregulated in sediment-grown G. uraniireducens also showed an increase in expression in the natural community of Geobacter species present during an in situ uranium bioremediation field experiment at the Rifle site. These results demonstrate that it is feasible to monitor gene expression of a microorganism growing in sediments on a genome scale and that analysis of the physiological status of a pure culture growing in subsurface sediments can provide insights into the factors controlling the physiology of natural subsurface communities.

Microtoming coupled to microarray analysis to evaluate the spatial metabolic status of Geobacter sulfurreducens biofilms

“…For example, transcript levels for gltA, which encodes a subunit of citrate synthase in G. sulfurreducens (Bond et al, 2005), is directly related to metabolic rates, including electron transfer to electrodes (Holmes et al, 2005). A similar response is expected for other TCA cycle enzyme genes (Holmes et al, , 2009). In general, values for transcript abundance of TCA cycle genes seemed to be lower in the samples from the outer layer of the biofilm, but the differences were small (otwo-fold) and not statistically significant.…”

“…Greater ribosome production is associated with faster growth rates in many microorganisms (Wagner, 1994;Hua et al, 2004;Beste et al, 2005;Boccazzi et al, 2005) and there was more ribosomal protein in faster growing cultures of G. sulfurreducens (Ding et al, 2006). In the closely related G. uraniireducnes, transcript abundance for ribosomal protein genes was related Spatial metabolic status of Geobacter sulfurreducens biofilms AE Franks et al to growth rate (Holmes et al, 2009). Thus, the slightly lower abundance of ribosomal protein gene transcripts in the outer layer of the biofilm suggests that those cells might be growing slower.…”

Extracellular reduction of uranium via Geobacter conductive pili as a protective cellular mechanism

“…required to design effective in situ bioremediation strategies. Analyses of transcript abundance for key Geobacteraceae genes are useful tools to predict the metabolic and physiological state of Geobacter bacteria during in situ bioremediation (26,(47)(48)(49), yet provide no information about the mechanism of U bioreduction. However, similar tools could be applied to monitor the activity of conserved components of Geobacter's pilus apparatus to assess the effectiveness of in situ bioremediation schemes.…”

Field-Based Detection and Monitoring of Uranium in Contaminated Groundwater using Two Immunosensors

“…Both the site and the field bioremediation research have been described extensively elsewhere [5][6][7] and a more complete description of the ongoing work at the Old Rifle UMTRA site may be found at http://www.pnl.gov/nabir-umtra/intro.stm. In the summer of 2008, much of the research activity was focused upon the collection of samples for proteomic analyses [5,[8][9][10][11], and timely information about the extent of uranium immobilization or remobilization in groundwater samples was useful to the research team in the timing of sample collection.…”