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.)

Specific projects include:
  1. Characterization of species composition and reconstruction of whole genome sequences from uncultured and poorly understood groups of organisms through development of novel metagenomic approaches. (led by Vaughn Iverson).
  2. Whole transcriptional responses of bacteria-diatom interactions, including cell-cell communication and establishment of mutualism (led by Shady Amin).
  3. Mathematical and statistical modeling of polymorphic regions in the whole genomes of seven separate strains of the cosmopolitan centric diatom, Thalassiosira pseudonana (led by Tony Chiang).
  4. Molecular and physiological responses of diatoms to increasing carbon dioxide levels in the atmosphere and its effect on the biological pump (led by Gwenn Hennon).