The high diversity and uneven representation of genes in metatranscriptomes of natural microbial communities presents challenges for analysis. In this study, we are examining the effect of coverage depth on detection and interpretation of biogeochemically-relevant gene expression in metatranscriptomic sequence datasets. Two replicate samples were collected off the coast of Sapelo Island, in shallow coastal waters of the southeastern United States. The environment is characterized by well mixed and turbid waters that can have dynamic ranges in temperature, salinity, inorganic nutrient concentrations, and dissolved organic matter (DOM) concentrations. Sampling was carried out in collaboration with the The Sapelo Island Microbial Observatory (SIMO), an NSF project investigating how microbes respond to and transform the diversity of DOM compounds that enter this shallow coastal system.
RNA samples were obtained on the night of August 8, 2008 by capturing microbial cells in the 0.2-3.0 micron size range from 10 liters of water. Two replicate water samples were processed. The RNA was converted to cDNA and sequenced with FLX pyrosequencing (two runs per replicate) (Poretsky et al. 2009; Env. Microbiol. Rev.). These are the initial samples from a metatranscriptomic study that will provide baseline microbial expression data for all four seasons at this coastal site.
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