Original Research ARTICLE

Front. Microbiol., 09 August 2012 | doi: 10.3389/fmicb.2012.00280

Gene expression correlates with process rates quantified for sulfate- and Fe(III)-reducing bacteria in U(VI)-contaminated sediments

  • 1 Florida State University, Tallahassee, FL, USA
  • 2 Department of Biology, Georgia State University, Atlanta, GA, USA
  • 3 Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
  • 4 Oak Ridge National Laboratory, Oak Ridge, TN, USA

Though iron- and sulfate-reducing bacteria are well known for mediating uranium(VI) reduction in contaminated subsurface environments, quantifying the in situ activity of the microbial groups responsible remains a challenge. The objective of this study was to demonstrate the use of quantitative molecular tools that target mRNA transcripts of key genes related to Fe(III) and sulfate reduction pathways in order to monitor these processes during in situ U(VI) remediation in the subsurface. Expression of the Geobacteraceae-specific citrate synthase gene (gltA) and the dissimilatory (bi)sulfite reductase gene (dsrA), were correlated with the activity of iron- or sulfate-reducing microorganisms, respectively, under stimulated bioremediation conditions in microcosms of sediments sampled from the U.S. Department of Energy’s Oak Ridge Integrated Field Research Challenge (OR-IFRC) site at Oak Ridge, TN, USA. In addition, Geobacteraceae-specific gltA and dsrA transcript levels were determined in parallel with the predominant electron acceptors present in moderately and highly contaminated subsurface sediments from the OR-IFRC. Phylogenetic analysis of the cDNA generated from dsrA mRNA, sulfate-reducing bacteria-specific 16S rRNA, and gltA mRNA identified activity of specific microbial groups. Active sulfate reducers were members of the Desulfovibrio, Desulfobacterium, and Desulfotomaculum genera. Members of the subsurface Geobacter clade, closely related to uranium-reducing Geobacter uraniireducens and Geobacter daltonii, were the metabolically active iron-reducers in biostimulated microcosms and in situ core samples. Direct correlation of transcripts and process rates demonstrated evidence of competition between the functional guilds in subsurface sediments. We further showed that active populations of Fe(III)-reducing bacteria and sulfate-reducing bacteria are present in OR-IFRC sediments and are good potential targets for in situ bioremediation.

Keywords: transcript level, uranium reduction, active sulfate-reducing bacteria, active metal-reducing bacteria

Citation: Akob DM, Lee SH, Sheth M, Küsel K, Watson DB, Palumbo AV, Kostka JE and Chin K-J (2012) Gene expression correlates with process rates quantified for sulfate- and Fe(III)-reducing bacteria in U(VI)-contaminated sediments. Front. Microbio. 3:280. doi: 10.3389/fmicb.2012.00280

Received: 18 May 2012; Accepted: 18 July 2012;
Published online: 09 August 2012.

Edited by:

Paul Bodelier, Netherlands Institute of Ecology, Netherlands

Reviewed by:

Steffen Kolb, University of Bayreuth, Germany
Dimitry Y. Sorokin, Delft University of Technology, Netherlands

Copyright: © 2012 Akob, Lee, Sheth, Küsel, Watson, Palumbo, Kostka and Chin. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.

*Correspondence: Kuk-Jeong Chin, Department of Biology, Georgia State University, 100 Piedmont Avenue, Atlanta, GA 30303, USA. e-mail: kchin@gsu.edu

Present address: Denise M. Akob, Institute of Ecology, Friedrich Schiller University Jena, 07743 Jena, Germany; Joel E. Kostka, Schools of Biology and Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.

Denise M. Akob and Sang Hyon Lee have contributed equally to this work.

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