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Microarray Applications in Microbial Ecology Research

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Abstract

Microarray technology has the unparalleled potential to simultaneously determine the dynamics and/or activities of most, if not all, of the microbial populations in complex environments such as soils and sediments. Researchers have developed several types of arrays that characterize the microbial populations in these samples based on their phylogenetic relatedness or functional genomic content. Several recent studies have used these microarrays to investigate ecological issues; however, most have only analyzed a limited number of samples with relatively few experiments utilizing the full high-throughput potential of microarray analysis. This is due in part to the unique analytical challenges that these samples present with regard to sensitivity, specificity, quantitation, and data analysis. This review discusses specific applications of microarrays to microbial ecology research along with some of the latest studies addressing the difficulties encountered during analysis of complex microbial communities within environmental samples. With continued development, microarray technology may ultimately achieve its potential for comprehensive, high-throughput characterization of microbial populations in near real time.

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Notes

  1. The latest issues at the time of this writing were the March 2006, January 2006, and February 2006 issues of Environmental Microbiology, Microbial Ecology, and Applied and Environmental Microbiology, respectively.

  2. For the remainder of the review, when we refer to the rRNA, we will be referring specifically to the ssu rRNA.

  3. ProbeBase also contains complete probe lists for a number of other published POAs.

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Acknowledgments

The authors would like to thank E. Hollister for valuable comments on this manuscript. The authors' efforts in preparing this review were supported by the United States Department of Energy Office of Science as part of its Environmental Research Programs in Natural and Accelerated Bioremediation Research, Biotechnology Investigations Ocean Margins Program, Microbial Genome Program, Genomics:GTL program, and Carbon Sequestration [as part of the consortium on research to enhance Carbon Sequestration in Terrestrial Ecosystems (CSiTE)]. Oak Ridge National Laboratory is managed by UT-Battelle LLC for the Department of Energy under contract DE-AC05-00OR22725.

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  1. Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA

    T. J. Gentry, G. S. Wickham, C. W. Schadt, Z. He & J. Zhou

  2. Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843, USA

    T. J. Gentry

  3. Institute for Environmental Genomics (IEG), Department of Botany and Microbiology, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK, 73019, USA

    Z. He & J. Zhou

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  1. T. J. Gentry
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  5. J. Zhou
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Correspondence to J. Zhou.

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Gentry, T.J., Wickham, G.S., Schadt, C.W. et al. Microarray Applications in Microbial Ecology Research. Microb Ecol 52, 159–175 (2006). https://doi.org/10.1007/s00248-006-9072-6

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