Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments

Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA.
The ISME Journal (Impact Factor: 9.3). 11/2008; 3(2):216-30. DOI: 10.1038/ismej.2008.89
Source: PubMed


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.

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Available from: Lucie N'Guessan, Jul 08, 2015
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    • "GSU 1648 (MacC) is predicted to be periplasmic. The gene encoding a MacC homologue was more highly expressed in G. uraniireducens grown in a U(VI)-contaminated subsurface than in culture medium (Holmes et al., 2009). "
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    ABSTRACT: Geobacter species often play an important role in the in situ bioremediation of uranium-contaminated groundwater, but little is known about how these microbes avoid uranium toxicity. To evaluate this further, the proteome of G. sulfurreducens exposed to 100 µM U(VI) acetate was compared with control cells not exposed to U(VI). Of the 1363 proteins detected from these cultures, 203 proteins had higher abundance during exposure to U(VI) compared to the control cells and 148 proteins had lower abundance. U(VI)-exposed cultures expressed lower levels of proteins involved in growth, protein and amino acid biosynthesis, as well as key central metabolism enzymes as a result of the deleterious effect of U(VI) in the growth of G. sulfurreducens. In contrast, proteins involved in detoxification, such as several efflux pumps belonging to the RND family, and protection of membrane and proteins, such as chaperons and proteins involved in secretion systems, were in higher abundance in cells exposed to U(VI). Exposing G. sulfurreducens to U(VI) resulted in higher abundance of many proteins associated with the oxidative stress response, such as superoxide dismutase and superoxide reductase. A strain in which the gene for superoxide dismutase was deleted grew slower than the wild-type strain in the presence U(VI), but not in its absence. The results suggest that there is not one specific mechanism for uranium detoxification. Rather, multiple general stress responses are induced, which presumably enable Geobacter species to tolerate high uranium concentrations.
    Microbiology 10/2014; 160(Pt_12). DOI:10.1099/mic.0.081398-0 · 2.56 Impact Factor
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    • "Readiness to withstand oxidative stress It has been shown previously that Geobacter species can be oxidatively stressed in batch incubations with insoluble oxides of Fe(III) and Mn(IV) [1], in chemostats with soluble Fe(III) citrate [25] [26], and in natural sediments containing Fe(III) oxides [15]. The current study also revealed an oxidative stress response of G. metallireducens in retentostats with soluble Fe(III) citrate. "
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    ABSTRACT: The strict anaerobe Geobacter metallireducens was cultivated in retentostats under acetate and acetate plus benzoate limitation in the presence of Fe(III) citrate in order to investigate its physiology under close to natural conditions. Growth rates below 0.003 h−1 were achieved in the course of cultivation. A nano-liquid chromatography–tandem mass spectrometry-based proteomic approach (nano-LC–MS/MS) with subsequent label-free quantification was performed on proteins extracted from cells sampled at different time points during retentostat cultivation. Proteins detected at low (0.002 h−1) and high (0.06 h−1) growth rates were compared between corresponding growth conditions (acetate or acetate plus benzoate). Carbon limitation significantly increased the abundances of several catabolic proteins involved in the degradation of substrates not present in the medium (ethanol, butyrate, fatty acids, and aromatic compounds). Growth rate-specific physiology was reflected in the changed abundances of energy-, chemotaxis-, oxidative stress-, and transport-related proteins. Mimicking natural conditions by extremely slow bacterial growth allowed to show how G. metallireducens optimized its physiology in order to survive in its natural habitats, since it was prepared to consume several carbon sources simultaneously and to withstand various environmental stresses.
    Systematic and Applied Microbiology 06/2014; 37(4). DOI:10.1016/j.syapm.2014.02.005 · 3.28 Impact Factor
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    • "The response to uranium exposure of environmental bacteria such as Caulobacter crescentus [16], Geobacter uraniireducens [21], and Shewanella oneidensis [22] was previously analysed at the transcription level. In the uranium tolerant species C. crescentus, response to uranium did not overlap substantially with other heavy metal stresses [16] and this specific response was used subsequently to develop a whole cell uranyl biosensor [23]. "
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    ABSTRACT: Better understanding of uranyl toxicity in bacteria is necessary to optimize strains for bioremediation purposes or for using bacteria as biodetectors for bioavailable uranyl. In this study, after different steps of optimization, Escherichia colicells were exposed to uranyl at low pH to minimize uranyl precipitation and to increase its bioavailability. Bacteria were adapted to mid acidic pH before exposure to 50 or 80 µM uranyl acetate for two hours at pH≈3. To evaluate the impact of uranium, growth in these conditions were compared and the same rates of cells survival were observed in control and uranyl exposed cultures. Additionally, this impact was analyzedby two-dimensional differential gel electrophoresis proteomics to discover protein actors specifically present or accumulated in contact with uranium.Exposure to uranium resulted in differential accumulation of proteins associated with oxidative stress and in the accumulation of the NADH/quinone oxidoreductase WrbA. This FMN dependent protein performs obligate two-electron reduction of quinones, and may be involved in cells response to oxidative stress. Interestingly, this WrbA protein presents similarities with the chromate reductase from E. coli, which was shown to reduce uranyl in vitro.
    PLoS ONE 02/2014; 9(2):e89863. DOI:10.1371/journal.pone.0089863 · 3.23 Impact Factor
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