Main Goals

• to describe the genetic potential of marine diatom species (Genomics)

• to systematically quantify genes expressed within a diatom cell under different environmental conditions (Transcriptomics)

The combination of genomics and transcriptomics allows us to identify genes involved in short-term response and long-term acclimation to changing environmental conditions and to evaluate the potential of these genes as indicators of physiological status. This work will improve our understanding of diatom evolution and physiology, and reveal insights into how different diatoms are adapted to different environmental niches in the marine system.

Specific topics of interest include:

• Whole genome sequences for diatom: Thalassiosira pseudonana (completed, led by E. Virginia Armbrust), Phaeodactylum tricornutum (completed, external collaboration with Dr. Chris Bowler), Pseudo-nitzschia multiseries (sequencing underway, led by Micaela S. Parker and E. Virginia Armbrust), Fragilariopsis cylindrus (external collaboration with Dr. Thomas Mock)


• Expressed sequence tag (EST) libraries for Pseudo-nitzschia australis (led by Micaela S. Parker) and Thalassiosira pseudonana (external collaboration with Dr. Thomas Mock)


• Tiling and gene-specific microarrays for Thalassiosira pseudonana (external collaboration with Dr. Thomas Mock)


• Single nucleotide polymorphisms in Thalassiosira pseudonana (led by Vaughn Iverson)

Additional people involved in these projects include Ellen Lin (molecular biology), Rhonda Marohl (molecular biology), Chris Berthiaume (bioinformatics), , and Tiffany Truong (undergraduate).

Main Goals

Our goal is to understand how different groups of organisms persist over time and space in the marine environment. We conduct field studies in estuaries, coastal regions, and the open ocean, and we complement our field studies with laboratory experiments. We use molecular tools, microscopy and flow cytometry to investigate the spatial and temporal diversity at a range of scales, including the individual, population, species, genus and community. Our targets are environmentally important planktonic organisms that range in size from phytoplankton (e.g. cyanobacteria, diatoms, including harmful algal species) to macrozooplankton (e.g. copepods).

Specific topics of interest include:

• Mechanisms of and genetic and physiological consequences of population divergence in the diatom Ditylum brightwellii (led by Julie Koester)


• Identification of mechanisms that lead to structure in genetically distinct (but morphologically similar) populations of Calanus on a global scale (led by Mikelle Nuwer)


• Response of pico- and nano-phytoplankton populations in various nutrient regimes to fluxes of organic and inorganic nitrogen, and the effect of these nitrogen sources on phytoplankton community structure (led by Sara Bender and Micaela S. Parker)


• Environmental forces that shape inter- and intra-specific community diversity in the genus Pseudo-nitzschia (led by Kate Hubbard and Adrian Marchetti)

Additional people involved in these projects include Ellen Lin (molecular biology), Rhonda Marohl (flow cytometry), Claire Ellis (undergraduate), Rachelle Lambert (undergraduate), and April Bailey (undergraduate).

Main Goals

Microorganisms in the marine environment live in close association with one another. Traditionally in the laboratory, we go to great lengths to maintain pure cell cultures—a very unnatural act—so that we may study phytoplankton in isolation from all other types of organisms. This reductionist approach has shed light on the roles these organisms individually play in the environment; but the behaviors observed as cells adjust to a sterile lab environment are skewed, and simplified, by the absence of interaction with members of the natural communities these organisms have co-evolved with over many millions of years. Our goal is to understand interactions between diatoms and associated heterotrophic bacteria.

Specific topics of interest include:

• Interactions between diatoms and bacteria mediated through vitamins (led by Vaughn Iverson)


• Role of domoic acid in bacterial associations with Pseudo-nitzschia species (led by Micaela S. Parker)

Main Goals

We are interested in understanding fundamental metabolic differences between major phytoplankton functional groups in the ocean. Our focus is mainly on diatoms and their adaptations to coastal and open ocean environments. Using a combination of molecular tools and physiological manipulations, we are investigating the responses of genes involved in photorespiration, the urea cycle, iron storage, chitin synthesis and oxylipin production to changing environmental conditions. We generate and test hypotheses on the cycling of major and minor elements in diatom cells and extend our findings to a global biogeochemistry context.

Specific topics of interest include:

• Photorespiration as an energy-dissipation pathway and its role in carbon and nitrogen cycling in marine diatoms (led by Micaela S. Parker)


• The role of the urea cycle in nitrogen-uptake, cellular metabolism, and photosynthesis in diatoms (led by Sara Bender)


• The ecological and functional significance of chitin synthesis in marine diatoms (led by Colleen Durkin)


• The use and regulation of ferritin for iron sequestration in marine pennate diatoms (led by Adrian Marchetti and Micaela Parker)

• The involvement of oxylipin metabolism in response to stress in diatoms (led by Francois Ribalet)

Additional people involved in these projects include Ellen Lin (molecular biology), Rhonda Marohl (molecular biology and flow cytometry), and Audrey Djunaedi (undergraduate).