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SHORT REPORT

Analysis of Microbial Gene Transcripts in Environmental Samples

Department of Marine Sciences, University of Georgia, Athens, Georgia 30602,¹ Department of Molecular, Cellular, and Developmental Biology, P.O. Box 208103, Yale University, New Haven, Connecticut 06520,² Institute of Terrestrial Ecology, Swiss Federal Institute of Technology Zurich, CH-8952 Schlieren, Switzerland³

Received 12 August 2004/ Accepted 21 January 2005

We analyzed gene expression in marine and freshwater bacterioplankton communities by the direct retrieval and analysis of microbial transcripts. Environmental mRNA, obtained from total RNA by subtractive hybridization of rRNA, was reverse transcribed, amplified with random primers, and cloned. Approximately 400 clones were analyzed, of which 80% were unambiguously mRNA derived. mRNAs appeared to be from diverse taxonomic groups, including both Bacteria (mainly - and -Proteobacteria) and Archaea (mainly Euryarchaeota). Many transcripts could be linked to environmentally important processes such as sulfur oxidation (soxA), assimilation of C1 compounds (fdh1B), and acquisition of nitrogen via polyamine degradation (aphA). Environmental transcriptomics is a means of exploring functional gene expression within natural microbial communities without bias toward known sequences, and provides a new approach for obtaining community-specific variants of key functional genes.

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