Analysis of Microbial Gene Transcripts in Environmental Samples†

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 hybrid-ization of rRNA, was reverse transcribed, amplified with random primers, and cloned. Approximately 400 clones were analyzed, of which80 % were unambiguously mRNA derived. mRNAs appeared to be from diverse taxonomic groups, including both Bacteria (mainly - and -Proteobacteria) and Archaea (mainly Euryarcha-eota). 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. The technology of environmental genomics is based on se-quence analysis of fragments of environmental DNA and re-trieves genes without any previous sequence information and with relatively little apparent bias (1, 18, 21). An analogous method for environmental mRNA (i.e., environmental tran