Genomics and transcriptomics approaches to understanding function in the environment

Our goal is to understand the molecular basis for how phytoplankton respond to the diverse conditions of different ocean environments. We explore how ancient and extant interactions between phytoplankton and other organisms including grazers, bacteria, and viruses influence these responses. We evaluate these responses in the lab with single species (primarily model diatoms) and with co-cultures between phytoplankton and bacteria. In the natural environment, we use metatranscriptomics to understand how different members of the community behave in situ. Among the standard molecular approaches we use for all of these projects, we include deep short-read sequencing and extensive bioinformatics. We recently developed a machine learning approach that uses metatranscriptomic data to predict in situ trophic modes of different protists (see Research Support).

Using a CTD at sunset to collect water samples onboard the R/V Thomas G. Thompson in the equatorial Pacific