Transcriptomic and metatranscriptomic analyses of marine microbial communities
Poretsky, Rachel Susan
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47Bacteria are abundant (10-10 cells/ml), diverse organisms and are responsible for much of the nutrient cycling in aquatic systems. Advances in molecular techniques have made it possible to examine the composition of marine microbial communities and there is a growing interest in understanding the linkage between microbial structure and function. The work described herein investigates gene expression by bacteria from a variety of aquatic ecosystems in order to assess their functional roles. Initially, a method for analyzing mRNA from environmental samples, i.e., metatranscriptomics was developed. Gene expression in bacterioplankton communities of the Sapelo Island and the Mono Lake Microbial Observatories was analyzed using this method. Transcripts were found for genes from a variety of microbial taxonomic groups. Many of the expressed genes were involved in central intermediary metabolism or were unclassified or unidentified. About 5% of the genes were responsible for ecologically important processes, such as sulfur oxidation and cellulose degradation. Improving upon the metatranscriptomics method and applying it to bacterioplankton at the Hawaii Ocean Time-Series, gene expression was examined over a day/night cycle. Taxonomic binning of mRNAs suggested that Cyanobacteria might represent the most metabolically active cells in surface seawater. The composition of the transcriptome was consistent with models of prokaryotic gene expression. Statistical comparisons between the day vs. night transcriptomes revealed preferential biosynthesis of vitamins, membrane components and amino acids at night, and photosynthesis, heterotrophic C1 metabolism, and oxidative phosphorylation in the day. In a final study, bacterial expression patterns were characterized in response to dissolved organic matter from phytoplankton, using pure cultures of a model marine bacterium and a diatom in a microarray-based analysis. Several genes were upregulated in the presence of diatom DOM, including some involved in transport and utilization of amino acids, protocatechuate catabolism, and transcriptional regulation. These results provided a novel method for examining bacterial-phytoplankton associations on the level of gene expression and have implications for our understanding of phytoplankton/bacterial interactions. Together, the results of these gene expression characterizations contributed to our understanding of how microbial communities function, how microbial processes are regulated, and how microbes interact with each other and with their environment.