Research

The Armbrust group uses lab- and field-based approaches to understand the complexities surrounding diatoms, their environment and their interactions with other microbes. We work at the cellular, population, and community scale to understand how these organisms shape and are shaped by environmental conditions.

In the lab, we use molecular, physiological, and chemical measurements to examine intra- and inter-species relationships among diatoms, bacteria and archaea. Complete genomes and whole-cell transcriptomes allow us to interrogate diatoms as they respond to nutrient limitation, interact with other microbes, and adapt to projected environmental changes such as increased carbon dioxide levels. We also develop a suite of bioinformatics and flow cytometric software to address current challenges in large-scale data acquisition and analysis. These data encompass DNA/transcript sequence obtained from our in-house high-throughput SOLiD sequencer and underway analyses of flow cytometric phytoplankton distributions.

In the field, we collect temporal and spatial samples across environmental gradients to better understand the impacts of community-wide interactions on biogeochemical cycles. Metagenomes, metatranscriptomes and our custom-made underway flow cytometer (SeaFlow) enable high-resolution insight into the abundance and distribution of these microscopic organisms. Measurements are coupled to classic oceanographic parameters (e.g. biogenic silica, nutrients, chlorophyll) to help us assess the biogeochemical ramifications of the impact of diatoms and their interactions with others on the marine environment.


Jenny

Ginger

Jarred
Former UW undergraduate Jenny Lai counting cells of the diatom, Thalassiosira pseudonana Ginger collecting a net tow sample onboard the R/V Thomas G. Thompson in the North Pacific Micaela and Jarred during the poster session at the 2009 ASLO conference in Nice, France

Click on a research theme in the panel on the left to learn more about specific projects.

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).

Phytoplankton ecology and physiology along environmental gradients


Our goal is to understand how nutrient and physico-chemical gradients shape the distribution, abundance and activity of environmentally and biogeochemically important phytoplankton groups, such as cyanobacteria and diatoms. We combine molecular tools, microscopy and flow cytometry to investigate the physiological and ecological responses of these organisms across a wide range of environmental conditions, using both laboratory cultures and natural populations of phytoplankton. Ultimately, this information will help us to predict to response of phytoplankton to future ocean conditions.
(Shown right: A phytoplankton hotspot (in red) localized at the intersection (yellow line) of offshore waters and coastal waters of the Northeast Pacific Ocean.)

Specific projects include:
  1. Distribution, abundance and activity of phytoplankton communities across oceanic fronts and characterization of the selective forces and mechanisms that shape these patterns (led by Francois Ribalet).
  2. Molecular and physiological responses of diatoms to increasing carbon dioxide levels in the atmosphere (led by Gwenn Hennon).

Phytoplankton inter-kingdom interactions


Microbial interactions are at the core of species success or failure. These interactions constitute an important component of microbial communities, where synergism, competition or grazing among species can drive the diversity of an ecosystem. The Armbrust lab is interested in understanding how interactions between phytoplankton and prokaryotes (bacteria and archaea) shape the distribution of microorganisms across diverse marine habitats. Of particular interest is the role of interspecies communication in mediating these interactions. We use a combination of techniques in the laboratory and in the field including microbiological and co-culturing techniques, next-gen sequencing (transcriptomics and metagenomics), metabolomics, flow cytometry and computer engineering and development to achieve this goal.

(Shown above: Examples of bacterial interactions with diatoms, categorized as Competitive (purple), Synergistic (orange), and Parasitic (blue). An example of horizontal gene transfer (HGT) as evidence for past associations between diatoms and bacteria is also shown (green).)

Specific projects include:
  1. Characterization of the molecular basis of diatom-bacterial signaling and interactions using environmentally-relevant model systems (led by Shady Amin).
  2. Utilization of metabolomics to characterize the chemical currencies shared between diatoms and associated bacteria (led by Helena van Tol).
  3. Understanding of community-level interactions between microbial species using metagenomics (led by Vaughn Iverson).
  4. Characterization of the selective forces and mechanisms that drive the coupling between cyanobacteria and their protist grazers using flow cytometry and molecular tools (led by Francois Ribalet).

Research Support: Innovation, engineering and data analysis


Rhonda

Thompson

Gwenn
Rhonda displaying the results of a successful incubation experiment at Station Papa SeaFlow data collected along the Pacific Northwest showing Synechococcus distributions in surface waters Gwenn tending to her Thalassiosira pseudonana chemostats, grown under high and low carbon dioxide levels

In the Armbrust lab, we have a team of research scientists, engineers, bioinformaticists and software developers who work on data acquisition and analysis, from extensive lab culturing projects to bioinformatics pipelines and instrumentation. Over the past several years, our lab has tackled the ongoing challenge of processing, managing and interpreting large-scale data sets, including (e.g.): SOLiD sequence reads, assembled for (meta)genomic and (meta)transcriptomic analysis, basin-wide flow cytometry data that maps temporal and spatial variability in phytoplankton communities, and additional sequence databases generated from various EST and tiling array projects, as well as collaborations with external lab groups.

Specific areas of innovation:
  1. Bioinformatics analysis pipelines and cluster computing infrastructure (led by Chris Berthiaume).
  2. Mathematical/Statistical modeling of diatom genomes and mathematical graph-based representation of
    metagenomic data (led by Tony Chiang).
  3. Development of in-house tools for SOLiD read assembly and analysis (led by Vaughn Iverson).
  4. Management of laboratory procedures and SOLiD sequencing engineer, including preparation of SOLiD sequencing libraries and instrument operation (led by Rhonda Morales).
  5. R software development for real-time analysis of flow cytometry data (led by Francois Ribalet).
  6. Development of the SeaFlow instrumentation (led by Jarred Swalwell).
  7. Culture maintenance and support for laboratory experiments (led by Irina Oleinikov).
  8. Office management and herder of cats (led by Rita Peterson).
In-house tools:
  1. SEAStAR for quantifying SOLiD read coverage in metagenomes and (meta)transcriptomes.
  2. The R package flowPhyto used to analyze high-throughout SeaFlow data.
  3. MANTA, an R package for conducting comparative metatranscriptomics.