Marine phytoplankton are central players in the global carbon cycle, responsible for nearly half of primary production. The identification of the factors controlling phytoplankton ecology, physiology, and, ultimately, bloom dynamics has been a central problem in the field of biological oceanography for the past century. Molecular approaches, such as metatranscriptomics, enable the direct examination of species-specific metabolic profiles in mixed, natural communities, a task which was previously intractable. I am interested in the development and application of novel analytical tools and bioinformatic pipelines to characterize the physiological response of microscopic organisms to their environment. Here I present two studies from the oligotrophic ocean that demonstrate the insights that can be gained from these types of approaches. In the first study, metatranscriptomics was used to tease apart the physiological responses of the diatom, haptophyte, and dinoflagellate functional groups during simulated blooms to characterize the traits that govern the magnitude and timing of phytoplankton blooms in the oligotrophic ocean. The results indicated that blooms form when phytoplankton are released from limitation by resources and that the mechanistic basis for the success of one functional group over another may be driven by how efficiently the transcriptome is modulated following a nutrient pulse. The second study looked at the sub-species level, examining the balance of phenotypic plasticity and strain diversity in the success of the coccolithophore Emiliania huxleyi. Results indicated strong control of nitrogen on the species complex and showed that nutrient resupply shifted the strain composition as well as transcript abundance of key biogeochemical genes involved in nutrient acquisition and the life stage of the population. These tools, I believe, might be applied to the deeper and more dilute mesopelagic microbial community to assess not only the diversity, but the ecological and physiological functioning of protists. I am interested to work with other scientists and engineers at NAKFI to bring the tools that I developed in the surface ocean to the mesopelagic.