Poretsky, R. S., N. Bano, A. Buchan, G. LeCleir, M. Pickering, J. Kleikemper, M. A. Moran, and J. T. Hollibaugh. 2005. Analysis of microbial gene transcripts in environmental samples. Appl. Environ. Microbiol. 71: 4121-4126.

We analyzed gene expression in microbial communities at the Sapelo Island Microbial Observatory (SIMO) and the Mono Lake Microbial Observatory (MLMO) by the direct retrieval and analysis of mRNA from bacterioplankton. mRNA was obtained from total RNA by subtractive hybridization, reverse transcribed, PCR amplified with random primers and cloned. Approximately 400 clones were analyzed from MLMO and SIMO. Based on closest sequence matches in BLAST analyses, mRNAs appear to be from diverse taxonomic groups, including both Bacteria (mainly Proteobacteria) and Archaea (mainly Euryarchaeota). Many of the expressed genes had inferred functions in central intermediary metabolism (~20%), protein synthesis (~5%), energy metabolism (~4%), and transport (~4%). A significant fraction of the transcripts were from genes of unknown function, either hypothetical (~35%) or conserved hypothetical (~5%). The transcripts could be linked to environmentally important processes carried out by bacterioplankton communities, such as sulfur oxidation, use of C1 compounds, and amino acid and peptide uptake. Approximately 80% of the sequences obtained from cloned amplicons were unambiguously mRNA derived. This approach provides a means of exploring functional gene expression within complex natural microbial communities without bias toward known genes.