Gene Expression Correlates with Process Rates Quantified for Sulfate- and Fe(III)-Reducing Bacteria in U(VI)-Contaminated Sediments

Denise M. Akob,Mili Sheth,Anthony V. Palumbo,Joel E. Kostka,Kirsten Küsel,David B. Watson,Sang Hyon Lee,Kuk-Jeong Chin

doi:10.3389/fmicb.2012.00280

Abstract

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.

Highlights

Mining and milling of uranium for nuclear weapons production has resulted in widespread uranium contamination in subsurface environments across North America, South America, and Eastern Europe (Abdelouas et al, 1998)
We further showed that active populations of Fe(III)-reducing bacteria and sulfate-reducing bacteria are present in Oak Ridge Integrated Field Research Challenge (OR-IFRC) sediments and are good potential targets for in situ bioremediation
SITE AND SEDIMENT SAMPLE DESCRIPTION The study was conducted at the Oak Ridge Integrated Field Research Challenge (OR-IFRC) site of the U.S Department of Energy’s (DOE) Subsurface Biogeochemistry Research program, which is located adjacent to the Y-12 industrial complex within the Oak Ridge National Laboratory (ORNL) reservation in Oak Ridge, Tennessee

Summary

Introduction

Mining and milling of uranium for nuclear weapons production has resulted in widespread uranium contamination in subsurface environments across North America, South America, and Eastern Europe (Abdelouas et al, 1998). Dissimilatory Fe(III)-reducing bacteria (FeRB) and sulfatereducing bacteria (SRB) comprise two major groups which are capable of U(VI) reduction (Tebo and Obraztsova, 1998; Lovley et al, 2004; Sani, 2004; DiChristina, 2005b; Payne and DiChristina, 2006; Wall and Krumholz, 2006). Both FeRB and SRB can directly reduce U(VI) by using it as an electron acceptor, and a subset of these groups have been shown to conserve energy for growth via U(VI) reduction (Lovley et al, 2004). Prior research has linked the activity of these functional guilds to U(VI) immobilization in contaminated www.frontiersin.org

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