Ecological insights into marine microbial communities via expression analyses
Gifford, Scott Michael
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In the oceans, the transfer of energy and cycling of elements is predominantly controlled by bacterioplankton, such that any understanding of marine ecosystems requires knowledge about bacterial activities and functional capabilities. Metatranscriptomics, the direct retrieval and sequencing of environmental RNA, is a powerful tool that can identify active community members and their expressed functional capabilities. This dissertation is composed of three studies that used metatranscriptomics to gain fundamental insights into the ecology and biogeochemistry of coastal microbial communities. In the first study, an internal standard approach was developed to make absolute (per liter) estimates of transcript numbers, a significant advantage over proportional estimates. Expression levels of genes diagnostic for transformations in the marine nitrogen, phosphorus and sulfur cycles were determined, as well as the total size of the mRNA pool. By representing expression in absolute units, metatranscriptomics extends beyond relative comparisons, allowing for direct comparisons with other biogeochemical measurements. In the second study, a metatranscriptomic dataset revealed an unexpected abundance of transcripts to ‘Candidatus Nitrosopumilus maritimus’, an ammonia oxidizing Archaea whose presence has significant implications in the carbon and nitrogen cycles. Reads assigned to genes for ammonia uptake and oxidation accounted for 37% of N. maritimus transcripts. In contrast, transcripts from co-occurring ammonia oxidixing Bacteria were in much lower abundance, with no transcripts related to ammonia oxidation or carbon fixation. This study suggests that these two members of the ammonia oxidizing functional guild respond differently to the same environmental cues. The third study used metatranscriptomics to examine how differences in expression among taxa can be indicative of niche diversification. The sequencing of transcripts from four coastal bacterial communities revealed the expression and activity of thousands of different taxa. The genes carried by these taxa have extensive overlap, and the majority of highly expressed genes were for redundant functions. To identify unique ecological roles for these taxa, a method was developed to classify genes both by their expression level and their frequency in genomes. The results show clear functional delineations across broad phylogenetic groupings and provide insights into the diversity of lifestyle strategies that supports complex microbial assemblages.