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Microbial Ecology

, Volume 52, Issue 2, pp 159–175 | Cite as

Microarray Applications in Microbial Ecology Research

  • T. J. Gentry
  • G. S. Wickham
  • C. W. Schadt
  • Z. He
  • J. Zhou
Mini-review

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.

Keywords

Clone Library Oligonucleotide Probe Methanotrophs Ribosomal Database Project Polymerase Chain Reaction Amplicon 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

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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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • T. J. Gentry
    • 1
    • 2
  • G. S. Wickham
    • 1
  • C. W. Schadt
    • 1
  • Z. He
    • 1
    • 3
  • J. Zhou
    • 1
    • 3
  1. 1.Environmental Sciences DivisionOak Ridge National LaboratoryOak RidgeUSA
  2. 2.Department of Soil & Crop SciencesTexas A&M UniversityCollege StationUSA
  3. 3.Institute for Environmental Genomics (IEG), Department of Botany and MicrobiologyUniversity of OklahomaNormanUSA

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