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Applied and Environmental Microbiology, September 2006, p. 6288-6298, Vol. 72, No. 9
0099-2240/06/$08.00+0     doi:10.1128/AEM.00246-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation{dagger}

Eoin L. Brodie,1,2* Todd Z. DeSantis,2 Dominique C. Joyner,2 Seung M. Baek,1 Joern T. Larsen,2 Gary L. Andersen,2 Terry C. Hazen,2 Paul M. Richardson,3 Donald J. Herman,1 Tetsu K. Tokunaga,2 Jiamin M. Wan,2 and Mary K. Firestone1

Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720,1 Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720,2 Department of Energy, Joint Genome Institute, Walnut Creek, California 945983

Received 1 February 2006/ Accepted 28 June 2006

Reduction of soluble uranium U(VI) to less-soluble uranium U(IV) is a promising approach to minimize migration from contaminated aquifers. It is generally assumed that, under constant reducing conditions, U(IV) is stable and immobile; however, in a previous study, we documented reoxidation of U(IV) under continuous reducing conditions (Wan et al., Environ. Sci. Technol. 2005, 39:6162-6169). To determine if changes in microbial community composition were a factor in U(IV) reoxidation, we employed a high-density phylogenetic DNA microarray (16S microarray) containing 500,000 probes to monitor changes in bacterial populations during this remediation process. Comparison of the 16S microarray with clone libraries demonstrated successful detection and classification of most clone groups. Analysis of the most dynamic groups of 16S rRNA gene amplicons detected by the 16S microarray identified five clusters of bacterial subfamilies responding in a similar manner. This approach demonstrated that amplicons of known metal-reducing bacteria such as Geothrix fermentans (confirmed by quantitative PCR) and those within the Geobacteraceae were abundant during U(VI) reduction and did not decline during the U(IV) reoxidation phase. Significantly, it appears that the observed reoxidation of uranium under reducing conditions occurred despite elevated microbial activity and the consistent presence of metal-reducing bacteria. High-density phylogenetic microarrays constitute a powerful tool, enabling the detection and monitoring of a substantial portion of the microbial population in a routine, accurate, and reproducible manner.

* Corresponding author. Mailing address: Ecology Department, Earth Sciences Division, Lawrence Berkeley National Lab, 1 Cyclotron Rd., MS 70A-3317, Berkeley, CA 94720. Phone: (510) 486-6584. Fax: (510) 486-7152. E-mail: elbrodie{at}lbl.gov.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, September 2006, p. 6288-6298, Vol. 72, No. 9
0099-2240/06/$08.00+0     doi:10.1128/AEM.00246-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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