Genomics and transcriptomics approaches to understanding function in the environment

Our goal is to understand the molecular underpinnings of diatom success in the diverse ocean environment and how ancient and extant interactions with other organisms such as bacteria, archaea and viruses have shaped and continue to shape diatom genomes. We also use comparative transcriptomics to understand the responses of diatoms to nutrient gradients and other biological, chemical and physical drivers in the ocean environment. We explore these responses in both the lab with single species or co-cultures and the field using metatranscriptomics to gain a larger picture of the role of diatoms in ocean communities. Finally, we use metagenomics to interrogate species diversity and potential functional roles of the microbial “uncultured majority” in ocean ecosystems. Among the standard molecular approaches we use for all of these projects, we include deep short-read sequencing with an AB SOLiD and extensive bioinformatics (see Research Support link, left).
(Shown right: Calm, stratified waters in the North Pacific onboard the R/V Thomas G. Thompson.)