Lab Retreat March 2015 (Image Credit: Megan Schatz)
armbrust at uw.edu
Phytoplankton are the main focus of research in our lab. These organisms are responsible for about 50% of the total amount of photosynthesis that occurs on our planet. They play a critical role in the global carbon cycle and ultimately in global climate. Because much of the organic carbon generated by phytoplankton is used by bacteria and archaea, we also study phytoplankton interactions with other microbes.
My areas of focus are building and running a computing infrastructure for bioinformatics research and writing software tools that allow users to scale an analysis from 1 core to hundreds of cores. Our computing environment is mostly Linux (CentOS) servers networked together to operate as a single cluster using the Rocks cluster management toolkit (http://www.rocksclusters.org/). The specific resource manager/scheduler combination is Torque/Maui. Much of software that I write for this system could be considered pipelines that split, distribute, and merge the analysis of large genomic data sets across the cluster. Basically wrappers for common third party bioinformatics tools (e.g. BLAST, Interproscan, HMMER, BWA, Velvet) and in-house custom software, taking advantage of the embarrassingly parallel nature of many problems in genome research. Specific areas of research interest are the quality processing, alignment, and assembly of next-gen sequencing data, with a focus on color space sequencing technology (SOLiD).
Email: sclayton at u.washington.edu
I am broadly interested in understanding the role of ocean physics in setting patterns of phytoplankton diversity and community structure. I use a combination of approaches to explore this question: numerical modelling, data analysis and seagoing research. Most recently I have been working with the UW's eScience Institute to develop pipelines for analysing oceanographic "big data".
Here are a couple of links to outreach projects that I have been involved with recently:
Short Documentary about Darwin Project Research, by MIT Student Helen Hou
Synergy Art exhibit at the Boston Museum of Science
PhD Physical Oceanography (2013), MIT/WHOI Joint Program in Oceanography, USA
BSc(Hons) Ocean Sciences (2007), Bangor University, UK
BA(Hons) Fine Art (2001), Middlesex University, UK
Nagai, T. and Clayton, S. Nutrient interleaving below the mixed layer of the Kuroshio Extension Front. (submitted to Ocean Dynamics).
Clayton, S., Jahn, O., Dutkiewicz, S., Heimbach, P., Hill, C., Follows, M. J. (2016) Biogeochemical versus ecological consequences of increased model resolution. Biogeosciences Discussions (under review)
Clayton, S., Lin, Y. C., Follows, M. J., Worden, A. Z. (2016) Co-existence of distinct Ostreococcus ecotypes at an oceanic front. Limnology & Oceanography, doi:10.1002/lno.10373
Hyrkas, J., Clayton, S., Ribalet, F., Halperin, D., Armbrust, E.V. and Howe, B. (2015) Scalable clustering algorithms for continuous environmental flow cytometry. Bioinformatics, doi:10.1093/bioinformatics/btv594
Ribalet, F., Swalwell, J., Clayton, S., Jimenez, V., Sudek, S., Lin, Y., Johnson, Z.I., Worden, A.Z. and Armbrust, E.V. (2015) Light-driven synchrony of Prochlorococcus cell growth and mortality in the subtropical Pacific gyre. Proceedings of the National Academy of Sciences USA, doi:10.1073/pnas.1424279112
Clayton, S., Nagai, T., Follows, M. J. (2014) Fine scale phytoplankton community structure across the Kuroshio Extension Front. Journal of Plankton Research, doi:10.1093/plankt/fbu020
Clayton, S., Dutkiewicz, S., Jahn, O., and M. J. Follows (2013) Dispersal, eddies, and the diversity of marine phytoplankton. Limnology & Oceanography: Fluids & Environments, 3, 182-197, doi:10.1215/21573689-2373515
Bracco A, Clayton S., Pasquero C. (2009) Horizontal advection, diffusion and plankton spectra at the sea surface. Journal of Geophysical Research – Oceans, 114, C02001, doi:10.1029/2007JC004671
coesel at uw.edu
Post-doctoral research associateDiatoms under the microscope
office: (206) 685-4196
Marine microbes are a critical component of the ocean ecosystem, principally through their influence on energy and nutrient flow. I am interested in interactions among marine microbes, specifically, how microbes use organic compounds as metabolic currencies and signaling molecules to form the basis for different trading alliances.
Oceanic primary production, carried out predominantly by unicellular phytoplankton, generates one of the largest reservoirs of carbon on Earth. About half of this fixed carbon is subsequently degraded by heterotrophic bacteria, a transfer that accounts for the largest flux of carbon through the ocean. The chemical makeup of this carbon pool is inherently complex, a product of the diversity of the hundreds of thousands of different planktonic organisms that make up seawater communities. Thus, compounds important in this trophic link are poorly known.
To explore metabolite exchange in bacterial-phytoplankton interactions, our lab has employed a model microbial system approach where we co-culture marine bacteria and diatoms together and use gene expression and metabolite analyses to assay for compounds passed between them (see Amin et al., 2015 & Durham et al., 2015). So far, we have detected exchange of sulfonated substrates and auxin-like signaling molecules between bacteria and diatoms. Genes for biosynthesis and degradation of these organic compounds have limited distribution among bacterioplankton, suggesting that these sulfonated substrates and signaling molecules underlie targeted interactions between mutualistic bacteria and diatoms.
I am currently using a combination of laboratory- and field-based measurements to study sulfonates and auxins in terms of their contribution to marine organic matter flux, their taxonomically driven spatiotemporal dynamics, and their roles in ecosystem interdependencies.
Collection of plankton onboard the UW's R/V Thomas G. ThompsonExtraction of plankton metabolites in the lab
Photo credit: Robyn Von Swank
Ph.D., Microbiology, University of Georgia, 2014
B.S., Biology, Virginia Tech, 2008
Amin SA, Hmelo LR, van Tol HM, Durham BP, Carlson LT, Heal KR, Morales RL, Berthiaume CT, Parker MS, Djunaedi B, Ingalls AE, Parsek MR, Moran MA, Armburst EV. 2015. Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature 522:98-101.
Varaljay VA, Robidart J, Preston CM, Gifford SM, Durham BP, Burns AS, Ryan JP, Marin R III, Kiene RP, Zehr JP, Scholin CA, Moran MA. 2015. Single-taxon field measurements of bacterial gene regulation controlling DMSP fate. ISME Journal 9:1677-1686.
Durham BP, Sharma S, Luo H, Smith CB, Amin SA, Bender SJ, Dearth SP, Van Mooy BAS, Campagna SR, Kujawinski EB, Armbrust EV, Moran MA. 2015. Cryptic carbon and sulfur cycling between surface ocean plankton. Proc Natl Acad Sci USA 112:453-457.
Durham BP, Grote J, Whittaker KA, Bender SJ, Luo H, Grim SL, Brown JM, Casey JR, Dron A, Florez-Leiva L, Krupke A, Luria CM, Mine AH, Pather S, Talarmin A, Wear EK, Weber TS, Wilson JM, Church MJ, DeLong EF, Karl DM, Steward GF, Eppley JM, Kyrpides NC, Schuster S, Rappé MS. 2014. Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing a remarkably small genome. Standards in Genomic Sciences 9:632-645.
Moran MA, Satinsky B, Gifford SM, Luo H, Rivers A, Chan LK, Meng J, Durham BP, Shen C, Varaljay VA, Smith CB, Yager PL, Hopkinson BM. 2013. Sizing up metatranscriptomics. ISME Journal 7:237-243.
Post-doctoral research associate
Research Interests and Current Projects:
Diatoms have an important role in the Earth’s carbon cycle, but they are not alone: the nature of their relationships with other marine microbes determines the fate of their fixed carbon. I aim to use modern molecular and informatics techniques to understand these complex relationships, using model diatom-bacteria associations.
Metagenomics and Metatranscriptomics of Ocean Communities
The advent of novel sequencing technologies has opened up new windows for investigation of community structure and function. Dramatic decreases in sequencing cost-per-base has allowed for the collection of massive community data sets, but the task of extracting meaningful information from these large data presents a challenge. I am developing pipelines for analysis of many environmental samples in order to improve our understanding of biological processes at the genetic and transcriptional levels.
B. S. magna cum laude in Molecular, Cellular & Developmental Biology with Minor in Oceanography, University of Washington (2016)
A.S. with honors, Seattle Central College (2013)
Groussman, Ryan D., Micaela S. Parker, and E. Virginia Armbrust. "Diversity and Evolutionary History of Iron Metabolism Genes in Diatoms." PloS one 10, no. 6 (2015).
Hennon, Gwenn MM, Justin Ashworth, Ryan D. Groussman, Chris Berthiaume, Rhonda L. Morales, Nitin S. Baliga, Mónica V. Orellana, and E. V. Armbrust. "Diatom acclimation to elevated CO2 via cAMP signalling and coordinated gene expression." Nature Climate Change 5, no. 8 (2015): 761-765.
Groussman, Ryan D., Gwenn M.M. Hennon, and E. Virginia Armbrust. "Regulation of Gene Networks by Cyclic AMP in the Diatom Thalassiosira pseudonana" (2016) UW Undergraduate Research Symposium, Seattle, WA, USA. Oral presentation.
Groussman, Ryan D., Gwenn M.M. Hennon, and E. Virginia Armbrust. "Investigating cyclic AMP as a mediator of CO2-sensing in the diatom Thalassiosira pseudonana" (2015) Molecular Life of Diatoms Conference, Seattle, WA, USA. Poster presentation.
Groussman, Ryan D., Gwenn M.M. Hennon, and E. Virginia Armbrust. "Investigating cyclic AMP as a mediator of CO2-Sensing in the diatom Thalassiosira pseudonana" (2015) UW Undergraduate Research Symposium, Seattle, WA, USA. Oral presentation.
Groussman, Ryan D., Micaela S. Parker, and E. Virginia Armbrust. "Diversity of Diatom Iron Metabolism Genes Revealed through Whole Transcriptome Sequencing" (2014) Ocean Sciences Meeting, Honolulu, HI, USA. Oral presentation.
Groussman, Ryan D., Micaela S. Parker, and E. Virginia Armbrust. "Evolutionary History and Environmental Expression of Iron Metabolism Genes in Diatoms: A High Resolution Investigation" (2014) UW Undergraduate Research Symposium, Seattle, WA, USA. Oral presentation.
Groussman, Ryan D., Micaela S. Parker, and E. Virginia Armbrust. "Recently Sequenced Transcriptomes Reveal Unexpected Diversity and Ancient Origin of Diatom Ferritin" (2013) UW Undergraduate Research Symposium, Seattle, WA, USA. Poster presentation.
Honors and Scholarships:
ARCS Foundation Fellow (2016)
WSGC Summer Undergraduate Research Program (Summer 2015)
Levinson Emerging Scholars Award (2014-15, 2015-16)
Mary Gates Endowed Scholarship (2013-14)
Broadway High School Alumni Endowed Scholarship for Transfer Students
The Boeing Company Endowed Scholarship (2012-13)
National Science Foundation S-STEM Scholarship (2012-13)
Washington State Opportunity Scholarship (2012-15)
Vaughn Iverson, Ph.D. vsi at uw.edu
I am interested in observing the complex interactions occurring within natural communities of microorganisms; as one would find in virtually any water sample taken from the environment. The approach I am developing uses biological sensing techniques capable of inferring the behaviors and interactions within natural microbial communities by identifying and quantifying genes and proteins used by specific members of the community.
Microorganisms in the environment are always found living in association with one another. For example, wherever there is a natural population of phytoplankton (e.g. diatoms), associated bacteria will also be present. The traditional way to study microbes is in the laboratory, by isolating and maintaining pure cell cultures which can be used to perform controlled experiments. This reductionist approach is a valuable tool to shed light on the roles these organisms may individually play in an ecosystem.
However, this approach is limited because a large majority of microscopic organisms we can detect in the environment are resistant to growth in a pure laboratory culture, which excludes most of the actual participants in natural ecosystems from study using this method. Even for those "model organisms" that do happen to grow under sterile laboratory conditions, our ability to observe their natural behaviors is limited by monoculture, which is simplified and skewed by the absence of interactions with the natural microbial communities within which these organisms have evolved.
Biological research has been revolutionized over the past several decades by the sequencing of whole genomes for many cultured organisms. Biological oceanography is being similarly transformed by the flood of genomic data now available for a wide variety of isolated marine microbes. Leveraging this information, together with astounding recent advances in massively parallel DNA sequencing technology, I am developing computational methods that allow us to effectively analyze data resulting from simultaneously sequencing the combined DNA of all members of a natural microbial community.
From these analyses, we can characterize the community composition (revealing who's there), while also reconstructing very long stretches of DNA sequence (revealing what they might be doing). These DNA sequences are often sufficient to produce whole genomes representing uncultured, poorly understood groups of organisms. Genome sequence allows us to reveal previously unknown roles such organisms play in maintaining healthy marine ecosystems, and may ultimately provide us with the necessary clues to isolate them into culture, further extending the reach of traditional laboratory methods.
As a Research Engineer in the Armbrust Lab, I get to participate in many different projects, and work with virtually everyone in the lab. Currently, my focus is creating DNA and RNA libraries to run on our high throughput sequencing machine, the SOLiD. The SOLiD is pretty amazing in that it can sequence a whole diatom genome in one run! This is done by breaking up the DNA or RNA into millions of short fragments, attaching these fragments to tiny beads, and attaching the beads to a microscope slide. The slide is put in the SOLiD sequencer where random fluorescent probes are washed over the DNA or RNA that is attached to the beads. These probes code for two bases, and when a certain probe finds its match in the sample, it attaches itself to the DNA/RNA. The SOLiD then takes a picture using certain light filters to determine which probe is sitting where and on what bead. This process happens over and over until the whole fragment is sequenced. Right now, the SOLiD generates about 700 million 50 -100 base-pair reads per run which is about 35-70 billion bases of data! Putting all of the bases in order, aligning them to a reference genome, and/or assembling the reads is extremely computationally intensive. We have a team of bioinformaticians (see the pages of Vaughn, Chris, and Dave) who develop tools and pipelines that aid in data analysis of SOLiD reads. We are using the SOLiD technology in our lab for a variety of different applications including genome re-sequencing, de-novo genome sequencing, environmental metagenomics, and experimental and environmental transcriptomics.
Another aspect of my job is to run the flow cytometer (affectionately called Leo). A flow cytometer records the size and fluorescence (chlorophyll, DNA, etc.) of sample particles below 70µm in size, and sorts the particles according to these parameters. It does this by creating a very thin stream of water and injecting sample particles into the middle of this stream. As the individual particles flow through the stream, they are hit with different wavelengths of laser light. This light is interrupted, or scattered, by the particles, and a computer records this scatter displaying the information in real time. Thus, you can see the size and fluorescence of your particles as they are going through the machine! Because the flow cytometer records data in real time, it is possible to select certain particles according to the parameters of your choice and sort them into 96 well plates, test tubes, or microscope slides. This is very useful for trying to make cultures axenic, isolating a certain population of interest to look at under the microscope (or culture), and “seeing” particles that are too small for the microscope to detect. We have also taken the flow cytometer out to sea to collect real time data looking at microscopic phytoplankton and bacteria in the field (Check out the pages of Jarred and Francois for information about a cool underway flow cytometer called the SeaFlow!).
I am the assistant to Dr. Armbrust. I work behind the scenes to facilitate administrative operations of our busy and dynamic lab. My role casts a wide net: From budget forecasting and scheduling to meeting coordination, purchasing and hospitality, it is all in an ever-changing day’s work. I also plan the quarterly seminar series jointly sponsored by the University of Washington and NOAA and their Centers for Oceans and Human Health. This series promotes dialogue among scientists, students and others who seek to understand the diverse and complex interactions of oceans and human health. In this age of global warming, I am privileged be part of this important research setting. It gives me joy to be a supportive presence to a wonderful group of talented, hard-working techs, students and scientists, known affectionately as the “Armbrusters.”
I am a marine ecologist studying how the environment shapes the distribution and abundance of plankton in the ocean. I am interested in where these organisms are found, how many occur there, and why.
last modified: December 2016
Senior Research Scientist
ribalet at uw.edu
I am interested predominantly in the physiology and ecology of marine microbes and their adaptation to different environments. As part of the Simons Collaboration on Ocean Process and Ecosystems project, I am investigating the coupling between cyanobacteria and their consumers and its effects on ecosystem stability.
I use SeaFlow, our underway flow cytometer developed in the Armbrust lab, to collect continuous information about the distribution and abundance of marine microbes and their activity at the single cell level. Since its launch in 2008, SeaFlow has collected over 100,000 km worth of data, equivalent to one sample every 1 km. I develop tools to process the high-volume of SeaFlow data and extract key information out of it. For more information about our cytometry facility and software tools, go to http://seaflow.ocean.washington.edu
Open Source Software
Email: dianer4 at u.washington.edu
M.S. in Biology, California State University, Los Angeles (2012)
B.A. in Biology, University of California, Santa Cruz (2000)
Two ecotypes of the diatom Ditylum brightwellii have been isolated from Puget Sound water samples. One of the ecotypes is globally distributed and blooms in Puget Sound in early spring. The second ecotype has only been identified in Puget Sound, where it blooms later in the year. Blooms of the two ecotypes correlate with distinct silicic acid concentrations and solar irradiance levels (Rynearson, Newton, & Armbrust, 2006). Since the second ecotype has approximately twice the DNA as the global ecotype, it is likely to have diverged as a result of a genome duplication event. I am interested in comparing gene sequences expressed by the two ecotypes to identify those genes responsible for the adaptive success of the second ecotype in Puget Sound.
Stauffer, BA, AG Gellene, D Rico, C Sur, DA Caron. Growth of the heterotrophic dinoflagellate Noctiluca scintillans on red tide-forming dinoflagellates and raphidophytes.
I am a research tech in the Armbrust lab which means I am fortunate to participate in many projects that the grad students and post docs are involved with. Along with caring for the lab’s phytoplankton culture collection, I am learning molecular methods, trace metal clean methods, and how to operate the lab’s flow cytometers, Influx and SeaFlow. It is a privilege to be a part of such a multifaceted group of people.
I come to the Armbrust lab with previous oceanography experience with microzooplankton. I have been a part of projects that have allowed me to gain quite a bit of sea time under my belt. The first project was Ecology and Oceanography of Harmful Algal Blooms - Pacific Northwest (ECOHAB-PNW). Here we determined growth and grazing rates of the diatom, Pseudo-nitzschia, which produces toxins and causes shellfish harvesting closures along the Washington coast. The second project was Riverine Influences on Shelf Ecosystems (RISE). The goal was to determine how the Columbia River influences the growth and grazing rates of the phytoplankton community along the Washington and Oregon coasts. The third project was the Bering Sea Ecosystem Study (BEST). For these cruises we conducted krill feeding experiments to determine feeding rates and what phytoplankton the krill are eating. All the cruises resulted in a large quantity of plankton samples and many hours with a microscope identifying and counting phytoplankton and microzooplankton.
H.R. Harvey, R.L. Pleuthner, E.J. Lessard, M.J. Bernhardt, and C.T. Shaw. 2012. Physical and biochemical properties of the euphausiids Thysanoessa inermis, Thysanoessa raschii, and Thysanoessa longipes in the eastern Bering Sea. Deep Sea Res II. 65-70: 173-183.
M.B. Olson, E.J. Lessard, C.H.J. Wong, and M.J. Bernhardt. 2006. Copepod feeding selectivity on microplankton, including the toxigenic diatoms Pseudo-nitzschia spp., in the coastal Pacific Northwest. Mar Eco Pro Ser. 326: 207-220.
Research engineer, firstname.lastname@example.org
I develop new instrumentation to study the complex structure of microbial communities in the oceans. My work spans the fields of optical, mechanical, software and electrical/electronic engineering. Instruments such as the SeaFlow sheathless flow cytometer are designed and built from the ground up in my laboratory and machine shop. SeaFlow is currently being operated monthly on Hawaii Ocean Time-Series cruises and annual SCOPE funded cruises. I am currently working on a new flow cytometer for autonomous platforms. This cytometer, named PipeCyte, uses an immersion primary optic combined with sheathless detection optics to perform in situ single cell measurements in any fluid scaled to any size. The first target platform will be on board a CTD to perform continuous depth profiles of the phytoplankton community.
Benjamin Hall IRB 323
M.Sc. Oceanography. University of Washington, Seattle, WA, 2015.
B.Sc. Environmental Science (Hon.), Biology minor. Mount Allison University, Sackville, NB, 2011.
For my Master's project I studied interactions between the flavobacterium Croceibacter atlanticus and diatoms. C. atlanticus was isolated from the pennate chain-forming diatom Pseudo-nitzschia multiseries, and was found to inhibit growth in many different diatoms. When C. atlanticus was grown with the centric diatom Thalassiosira pseudonana, we observed large polyploid cells with multiple plastids. These features indicate that C. atlanticus may inhibit cytokinesis in diatoms.
Epifluorescence microscopy image of T. pseudonana in mono-culture (left) and in co-culture (right) with C. atlanticus. Green = SYBR-stained DNA, red = plastid autofluorescence.
Former Lab Members.
Postdoctoral Research Fellow
How does the environment impact biodiversity? Specifically, how do differing oceanic regions affect the genotype - and potentially phenotype - of members of a given species.
My research focuses primarily on the mathematical and statistical modeling of polymorphic regions for seven separate oceanic strains of Thalassiosira pseudonana. Using data derived from next-generation sequencing technologies, I use simple statistical methods to model areas of significantly high or low variability such as single nucleotide polymorphisms (SNPs) or large-scale insertions or deletions. The ability to estimate regions of high variability gives clues to the adaptation mechanisms of the species for differing environments. Conversely, estimating regions of low to no variability across strains helps us determine essential genomic sequences.
I am also broadly interested in the role of theoretical computer science in biology. As data becomes larger and more abundant, it will be much more necessary to find efficient ways to store, query, and share data. My preliminary work in this area uses a graph theoretic framework to represent metagenomes. My collaborators and I are building a novel data structure for metagenomes so that we might be able to generalize the notion of comparative genomics.
Postdoctoral Research Fellow, School of Oceanography, University of Washington, 2011-Present
Affiliate Postdoctoral Fellow, Computer Science & Engineering, University of Washington, 2011-Present
Graduate Research Fellow - Computational Statistics, University of Cambridge, 2006-2010
Graduate Research Assistant - Pure Mathematics, University of California at Berkeley, 2001-2005
Doctor of Philosophy - King's College, University of Cambridge
Bachelor of Science - Massachusetts Institute of Technology
My primary affiliation is within the Oceanography department; I have a secondary affiliation with the Computer Science and Engineering group. I am co-mentored by Ginger Armbrust and Larry Ruzzo of Oceans and CSE respectively.
|7 Genomes Poster||3.92 MB|
Research Interests and Current Projects:
Phytoplankton are responsible for producing half of the oxygen we breathe everyday. They also fix carbon into organic matter, which not only drives the food chain for all marine life, but it also sinks into the deep in a process called the biological pump. The biological pump helps to shape the earth's response to increasing CO2 and warming climate. In order to understand what the future holds for earth's ecosystems we need to understand what factors drive the phytoplankton productivity and the biological pump and how these factors will change in the future.
Physiology and Gene expression of a Model Diatom acclimated to elevated CO2:
I am interested in how increasing carbon dioxide levels in the atmosphere will affect the physiology and gene expression of diatoms and the biological pump. Phytoplankton, including diatoms, have evolved to cope with relatively low CO2 by developing carbon concentrating mechanisms (CCMs). Now as CO2 levels are rising rapidly, these CCMs may down regulated, changing the fluxes of energy and carbon in diatom cells. I am interested in how diatoms will acclimate to higher CO2 levels and if there will be significant physiological changes that could effect the biological pump and ocean ecology.
I just published in Nature Climate Change on culturing experiments with the diatom Thalassiosira pseudonana under low, medium and high CO2 and nitrate limitation. Using gene expression data we found co-regulated CCM and photorespiration genes that are regulated by cyclic-AMP giving us insights into how diatoms acclimate to rising CO2 (http://www.nature.com/nclimate/journal/vaop/ncurrent/full/nclimate2683.html).
Gradients in Microbial Ecology and the Biological pump across the Western Tropical Atlantic:
It is thought that with increasing global temperature, the oceans will become more strongly stratified, resulting in changes in phytoplankton communities. Smaller phytoplankton might out-compete larger phytoplankton resulting in a shift in the ecosystem as well as the size of organic particles and the efficiency of the biological pump.
Using the SeaFlow underway flow cytometer I collected continuous data along the DeepDOM 2013 cruise to investigate gradients in phytoplankton community composition and growth rate. In collaboration with Evan Howard and Rachel Stanley of Woods Hole Oceanographic Institution as well as Francois Ribalet, I'm preparing a manuscript to on the apparent differences in inorganic nitrogen limitation between Prochlorococcus ecotypes in different biogeochemical provinces.
Ph. D. in Oceanography, University of Washington (2015)
M. S. in Oceanography, University of Washington (2012)
B. S. in Chemistry, Massachusetts Institute of Technology (2009)
Dean A. McManus Excellence in Teaching Award (2013)
NOAA Earnest F. Hollings Scholarship (2007-2009)
Presentations and Publications:
Hennon, G. M. M. ; Howard, E.; Stanley, R.; Ribalet, F..; Armbrust, E. V. . “In situ division rates of Prochlorococcus reveal different nitrogen-utilizing ecotypes across the tropical Atlantic” (in prep)
Hennon, G. M. M. ; Ashworth J.; Groussman, R.D.; Berthiaume, C.; Morales, R. L.; Baliga, N.S.; Orellana, M.V.; Armbrust, E. V. . “Diatom acclimation to elevated CO2 via cAMP signalling and coordinated gene expression” (2015) Nature Climate Change
Hennon, G. M. M. ; Quay, P.; Morales, R. L.; Swanson, L. M.; Armbrust, E. V. . “Acclimation conditions modify physiological response of the diatom Thalassiosira pseudonana to elevated CO2 concentrations in a nitrate-limited chemostat” (2014) Journal of Phycology
Hennon, G. M. ; Armbrust, E. V.; “Acclimated Physiology and Gene Expression of the Diatom Thalassiosira pseudonana under Elevated CO2” (2013) ASLO Aquatic Sciences Meeting, New Orleans, LA, USA
Hennon, G.M.; Armbrust, E.V.; Ashworth, J.; Lee, A.; Orellana, M.V.; Baliga, N.S.; “Acclimated Physiology of the Diatom Thalassiosira pseudonana under Pre-Industrial and Future Levels of CO2: Implications for Carbon Sequestration” (2011) PSA annual meeting. Seattle, WA, USA
Bowman, J; Chan, K. Y.; Durkin, C.; Hennon, G.; Smith, D.; Sullivan, B. “Is Diversity Related to Service Provision Across an Ecosystem?” (2011) World Conference on Marine Biodiversity, Aberdeen, Scotland
Wood, M; Strutton, PG; Eberhart, B; Foley, DG; Forster, Z; Hunter, M; McKibben, SM; Miller, G; O’Higgins, L; Peterson, WT; Peterson, TD; Trainer, V; Smith, D; Tweddle, JF; White, AE. (2010) “MOCHA: Monitoring Oregon Coastal Harmful Algae”, Ocean Sciences Meeting
McKibben, SM; Strutton, PG; Wood, M; Miller, G; Eberhart, B; Trainer, V. “Development of a Predictive Model for In Situ Domoic Acid Concentrations off the Oregon Coast”. (2010) Ocean Sciences Meeting
Miller, GM. “Investigating Humpback Whale (Megaptera novaeangliae) diets using fatty acid trophic markers”, NOAA Hollings Scholar Presentation Week, Silver Spring MD, July 2008
Antos, J.M.; Miller, G.M.; Grotenbreg, G.M.; Ploegh, H.L.. Lipid Modification of Proteins through Sortase-Catalyzed Transpeptidation. JACS. 2008
Ph.D., University of Georgia, Odum School of Ecology, 2010. Thesis adviser: Erin K. Lipp. Thesis title: Environmental factors and reservoir shifts contribute to the seasonality of pathogenic Vibrio species.
B.S., Mercer University, Chemistry, 1998.
If you've eaten raw seafood, especially bivalve mollusks such as oysters, or dipped a toe into the ocean, you've likely encountered Vibrio parahaemolyticus (Vp). Vp is a Gram-stain negative bacterium indigenous to coastal marine waters and the leading cause of seafood-borne bacterial gastroenteritis worldwide. Central to safeguarding the public from Vp is the ability to distinguish between virulent and avirulent strains of this bacterium. This distinction is based on the presence or absence of genes and or genetic elements, which are known to be associated with virulence. Seemingly straightforward, the control and prevention of this Vp is largely based on the screening of water and seafood for the presence or absence of a single virulence factor – the thermostable direct hemolysin (TDH). Unfortunately, not all clinical isolates elaborate TDH and additional virulence-associated factors, such as the thermostable related hemolysin (TRH) and proteins related to the type III secretion system (T3SS), can also contribute to pathogenesis.
In the Pacific Northwest (USA), traditional Vp virulence markers, such as TDH, are especially poor determinants of virulence. In a unique collaboration between Ginger Armbrust (UW’s Center for Environmental Genomics) and Mark Strom [NOAA’s West Coast Center for Oceans and Human Health (WCCOHH) at NOAA’s Northwest Fisheries Science Center], I am using sequencing by oligonucleotide ligation and detection (SOLiD) to sequence the genomes of 20 Vp strains. These strains originate from the Pacific Northwest and represent a diversity of environmental sources and include several clinical isolates. Genome – genome comparisons will aid in the identification of genes and genetic elements unique to pathogenic strains, which are locally endemic to the PNW. Once genetic features of pathogenesis are determined, future work can focus on the development of gene-specific assays to identify potentially virulent strains in environmental samples. These improved virulence assays will then be deployed onboard a marine biosensor (Environmental Sampling Processor, ESP), which will be integrated within a network of tools focused on the realization of a Vibrio early warning system.
Electron scanning microscopy of V. parahaemolyticus cells attached
to the shell of a crab. Photo courtesy of Carla Ster and Rohinee Paranjpye.
Environmental Sampling Processor (ESP) (minus instrument housing) for environmental monitoring of microbial pathogens and harmful algal blooms (HABs). The ESP was developed by the Monterey Bay Aquarium Research Institute (MBARI) and manufactured by SpyGlass Biosecurity.
Please follow these links below to learn more about NOAA's West Coast Center for Oceans and Human Health (WCCOHH) and NOAA's Oceans and Human Health Initiative (OHHI).
This research is funded by NOAA's Oceans and Human Health Initiative's (OHHI) Postdoctoral Traineeship, the National Research Council's (NRC) Research Associateship Program and NOAA's Marine Biosensor Program (see NOAA's Integrated Ocean Observing System, IOOS).
Turner, J. W., L. Malayil, D. Guadognoli, D. C. Cole and E. K. Lipp (2013). Detection of Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae with respect to seasonal fluctuations in temperature and plankton abundance. Environmental Microbiology doi:10.1111/1462-2920.12246.
Turner, J. W., R. N. Paranjpye, E. Landis, N. Gonzales-Escalona, W. B. Nilsson, S. V. Biryukov and M. S. Strom (2013). Population Structure of Clinical and Environmental Vibrio parahaemolyticus from the Pacific Northwest Coast of the United States. PLoS ONE 8 (2): e55726. doi:10.1371/journal.pone.0055726.
Strom, M. S., R. N. Paranjpye, W. B. Nilsson, J. W. Turner, and G. K. Yanagida (2013). Pathogen update: Vibrio species. In Advances in Microbial Food Safety. 1: 97-113. J Sofos (ed), Woodhead publishink, Cambridge, U.K.
Xu, J., J. W. Turner, M. Idso, S. V. Biryukov, L. Rognstad, H. Gong, M. S. Strom and Q. Yu (2013). In situ strain level distinction of Vibrio parahaemolyticus using surface enhanced Raman spectroscopy. Analytical Chemistry 85 (5): 2630–2637.
Mote, B. L., J. W. Turner and E. K. Lipp (2012). Persistence and growth of the fecal indicator bacteria, enterococci, in detritus and natural estuarine plankton communities. Applied and Environmental Microbiology 78: 2569-2577.
Malayil, L., J. W. Turner, B. L. Mote, K. Howe and E. K. Lipp (2011). Evaluation of enrichment media for improved detection of V. cholerae and V. vulnificus from estuarine water and plankton. Journal of Applied Microbiology 110 (6): 1470-1475.
Sutherland, K. P., J. W. Porter, J. W. Turner, M. K. Meyers, M. L. Griffith, J. C. Futch and E. K. Lipp (2010). Human sewage identified as likely source of white pox disease of the threatened Caribbean elkhorn coral, Acropora palmata. Environmental Microbiology 12 (3): 112-1131
Turner, J. W., B. Good, D. Cole and E. K. Lipp (2009). Plankton composition and environmental factors contribute to Vibrio seasonality. International Society of Microbial Ecology 3:1082-1092.
Tobin-D’Angelo, M., S. Thomas, D. Cole and J. W. Turner (2007). Vibrio in Georgia. Georgia Epidemiology Report 23: 1-4.
My diversity of research interests is unified by a central concept in that the status and health of our oceans is inextricably connected to human health. This central concept allows me to integrate my education as a chemist and an ecologist and work experience as an aquatic toxicologist with my research as a microbial ecologist. A common objective of my work has been to characterize the ecology of microorganisms in the marine environment, which adversely affect human health. Pathogenic species of the Vibrio genus, such as V. cholerae, V. parahaemolyticus and V. vulnificus, are often the focus of my research; however, my experience includes work with microbial indicators (Escherichia coli and Enterococcus faecalis) and microbial pathogens of corals (Serratia marcescens).
My dissertation research was primarily focused on describing how fluctuations in environmental factors (such as temperature and salinity) and shifts in the composition of the plankton reservoir affect the prevalence and seasonality of pathogenic Vibrio species. Results show that fluctuations in environmental factors alone were unable to account for the seasonal variation encountered in our field studies. Shifts in the abundance of plankton taxa were strong Vibrio drivers. In particular, seasonal variation in the abundance of diatoms, copepods and decapods appear to play a temperature-independent role in the observed Vibrio seasonality. In sum, this research suggests that future Vibrio predictive models could be improved through characterizing Vibrio prevalence in the context of environmental factors as well as bloom formation and shifts in the abundance and life history of specific plankton taxa.
The focus of my research is to find connections between genes, phenotypes and the environmental forces of natural selection. Diatoms are my test-organisms of choice.
Two populations of the planktonic diatom Ditylum brightwellii co-occur in Puget Sound, but are differentiated by genome size (Koester et al. 2010); they are hypothesized to be cryptic species. Species Dbr2 has a 2-folder larger genome size than Dbr1, and likely arose from Dbr1 via whole genome duplication because its distribution is restriction to the northeastern Pacific Ocean, whereas Dbr1 has a circum-global distribution. Duplicated genes tend to accumulate mutations that are masked by working copies. These mutations may be selected for and sweep through a population providing adaptive benefit.
Seven percent of the protein coding genes in Thalassiosira pseudonana were determined to be positively selected (i.e. adaptively beneficial) by comparing homologous genes from seven strains of T. pseudonana. These genes disproportionately code for transcriptional regulators and protein-binding proteins. In addition, five positively selected genes that are putatively associated with the cell wall are up-regulated under iron and silicate limitation (Koester et al. in prep).
Left to right 1-3: 1) Two gametic valves and one large valve from a sexual clone of Ditylum brightwellii from the Gulf of Maine, 2-3) Ditylum brightwellii: a large clone from Puget Sound and small clone from New Zealand.
Ph.D. University of Washington, 2012
M.S., University of Maine, 2005
B.Sc. Honours, University of British Columbia, 1991
Microbial interactions are likely as old as life itself and will continue to play an integral role in shaping microbial diversity. Can we use a combination of culturing and molecular techniques (e.g. next-gen sequencing) to understand how these interactions evolved, how important are they today, and how will they respond to climate change?
Email: shadyam at u.washington.edu
Ph.D. in Bioinorganic Chemistry, University of California, San Diego/San Diego State University (2010)
M.A. in Inorganic Chemistry, San Diego State University (2005)
B.Sc. in Biochemistry, University of California, Santa Barbara (2003)
I'm interested in how marine microbes talk to each other. These types of interactions are mostly uncharacterized yet they play a critical role in the physiology of interacting organisms, which leads to a change in the chemical environment surrounding those cells and subsequently to the whole ecosystem. Because diatoms are among the most important primary producers in the oceans, I am investigating inter-species interactions between diatoms (photosynthetic eukaryotes) and the two other domains of life (heterotrophic prokaryotes): 1) bacteria and 2) archaea.
1) Diatom-bacterial interactions are common in the oceans and can be beneficial or lethal. Only a small number of these interactions have been described. One possible mechanism for a diatom to detect and respond to beneficial or "pathogenic" bacteria is through detection of a molecule the bacteria produce. Many marine bacteria use hydrophobic signals to communicate with each other (i.e. quorum sensing). Similar to some plants, diatoms maybe able to detect beneficial vs lethal bacteria by differentiating between their excreted molecular signals. Currently, I'm using whole transcriptome analysis and metabolomics to study interactions between diatoms and their bacterial microflora. So far, evidence suggests there are an array of complex interactions that take place between the diatom and its many bacterial partners.
2) Archaea have been typically associated with extreme environments such as hydrothermal vents. However, we now know that marine archaea dominate many parts of the marine environment and influence global biogeochemical cycles. For example, Ammonia-oxidizing Archaea (AOA) play an important role in the nitrogen cycle by oxidizing ammonia to nitrite. Their dominance in many marine habitats and presence in the upper water column (e.g. chlorophyll a maxima where phytoplankton thrive) suggest that they are likely to interact with other microbes including diatoms. Currently, I'm studying trace metal limitation of the only cultured marine AOA isolate with wider implications to diatom metal availability. Recently published results from this study show that AOA may be strongly limited by Cu availability in many parts of the marine environment. Many oceanic diatoms also require a high Cu demand, suggesting that both taxa may be interacting/competing for Cu particularly in the open ocean.
1) Qin, W.; Amin, S.A.; Martens-Habbena, W.; Urakawa, H.; Devol, A.H.; Moffett, J.W.; Armbrust, E.V.; Ingalls, A.E.; Stahl, D.A. Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation. Proc. Natl. Acad. Sci. U.S.A., Early Access.
2) Jacquot, J.; Horak, R.E.; Amin, S.A.; Devol, A.; Ingalls, A.E.; Armbrust, E.V.; Stahl, D.A.; Moffett, J.W. Assessment of the potential for copper limitation of ammonia oxidation by Archaea in a dynamic estuary. Marine Chemistry, 162, 37-49.
3) Amin, S.A.; Moffett, J.W.; Martens-Habbena, W.; Jacquot, J.; Han, Y.; Devol, A.; Ingalls, A.; Stahl, D.A.; Armbrust, E.V. Copper requirements of the ammonia-oxidizing archaeon Nitrosopumilus maritimus SCM1 and implications to nitrification in the marine environment. Limnology and Oceanography, 2013, 58, 2037-2045.
4) Weerasinghe, A.;Amin, S.A.; Barker, R.; Othman, T.; Romano, A.; Siburt, C.P.; Tisnado, J.; Lambert, L.A.; Huxford, T.; Carrano, C.J.; Crumbliss, A.L. Borate as a synergistic anion for Marinobacter algicola ferric binding protein, FbpA: A role for boron in iron transport in marine life Journal of the American Chemical Society, 2013, 135, 14504-14507.
5) Gärdes, A.; Triana, C.; Amin, S.A.; Green, D.H.; Trimble, L.; Romano, A.; Carrano, C.J. Detection of a Photoactive Siderophore Biosynthetic Genes in the Marine Environment. BioMetals, 2013, 26, 507-516.
6) Romano, A.; Trimble, L.; Hobusch, A.; Schroeder, K.; Amin, S.A.; ; Hartnett, A.; Barker, R.A.; Crumbliss, A.; Carrano, C.J. Regulation of iron transport related genes by boron in the marine bacterium Marinobacter algicola DG893. Metallomics 2013, 5, 1025-1030.
8) Amin, S.A.; Green, D.H.; Gardes, A.; Romano, A.; Trimble, L.; Carrano, C.J. Siderophore-mediated iron uptake in two clades of Marinobacter spp. associated with phytoplankton: The role of light. BioMetals 2012, 25, 181-192.
9) Amin, S.A.; Green, D.H.; Al-Waheeb, D.; Gardes, A.; Carrano, C.J. Iron transport in the genus Marinobacter. BioMetals 2012,25,135-147.
10) Amin, S.A.; Green, D.H.; Kuepper, F.C.; Sunda, W.G.; Carrano, C.J. Photolysis of iron siderophore chelates promotes bacterial-algal mutualism. Proceedings of the National Academy of Sciences of the U.S.A. 2009, 106, 17071-17076.
11) Amin, S.A.; Green, D.H.; Kuepper, F.C.; Carrano, C.J. Vibrioferrin, an unusual marine siderophore: Iron binding, photochemistry and biological implications. Inorganic Chemistry 2009, 48, 11451-11458.
12) Zhang, G; Amin, S.A.; Kuepper, F.C.; Holt, P.D.; Carrano, C.J.; Butler, A. Ferric stability constants of representative marine siderophores: Marinobactins, Aquachelins, and Petrobactin. Inorganic Chemistry 2009, 48, 11466-11473.
13) Carrano, C.J.; Schellenberg, S.; Amin, S.A.; Green, D.H.; Kuepper, F.C. Boron and marine life: A new look at an enigmatic bioelement. Marine Biotechnology, 2009, 11, 431-440.
14) Harris, W.R.; Amin, S.A.; Kuepper, F.C.; Green, D.H.; Carrano, C.J. Borate binding to siderophores: Structure and stability. Journal of the American Chemical Society 2007, 129, 12263-12271.
15) Amin, S.A.; Kuepper, F.C.; Green, D.H.; Harris, W.R.; Carrano, C.J. Boron binding by a siderophore isolated from marine bacteria associated with the toxid dinoflagellate Gymnodinium catenatum. Journal of the American Chemical Society 2007, 129, 478-479.
Extensive diversity has been detected in phytoplankton communities, and while some organisms appear to be ubiquitously distributed throughout the marine environment, other organisms appear to be constrained to particular places or environments. I am interested in the connection between diversity and distribution across different environments, and more specifically, how physiology, dispersal, and (physical and chemical) environment may structure marine diatom communities. For my graduate studies, I am surveying genetic diversity in the harmful alga, Pseudo-nitzschia. Most of my research takes place in the coastal and estuarine waters of British Columbia and Washington, although I am interested in the global distribution of Pseudo-nitzschia (and welcome potential sampling collaborations). This research is being conducted as part of the Pacific Northwest Center for Human Health and Ocean Studies, a multi-disciplinary investigation to understand how harmful algae blooms are initiated in the marine environment, and the impacts they have on shellfish and humans (and vice versa). The genus Pseudo-nitzschia is comprised of some 30 species, and is perhaps best known because many species are able to produce the neurotoxin domoic acid. Diatoms in this genus also exhibit a cosmopolitan distribution, with species detected in all oceans including polar regions. Individual species, however, can be notoriously difficult to identify. For my master's research, I designed genus specific primers and developed a Pseudo-nitzschia Automated Intergenic Spacer Analysis (ARISA) to easily and accurately identify species in environmental samples (Hubbard et al. 2008). ARISA can be used in tandem with environmental clone libraries to identify diversity at the species and sub-species levels. For my PhD research, I am using these approaches to identify population structure (in toxic and non-toxic blooms), across coastal and estuarine environmental gradients (e.g. salinity). Ecological investigations of distribution patterns, coupled with circulation models, will be used to make predictions about the impact of physiology and physical oceanography on dispersal, which will be tested using Pseudo-nitzschia isolates in laboratory experiments. Education: M.S. in Oceanography, University of Washington, 2005. B.A. in Biology, New College of Florida, 2002. Recent publications: Hubbard, K.A., Rocap, G., and Armbrust, E.V. 2008. Inter- and intra-specific community structure within the diatom genus Pseudo-nitzschia (Bacillariophyceae). J. Phycol. 44 (3) 637-649. Marchetti, A., Lundholm, N., Kotaki, Y., Hubbard, K.A., Armbrust, E.V., and Harrison, P.J. 2007. Identification and assessment of domoic acid production in oceanic Pseudo-nitzschia (Bacillariophyceae) from iron-limited waters in the northeast subarctic Pacific. J. Phycol. 44 (3) 650-661.
Hood Canal in February, 2008
Ph.D., Biological Oceanography. University of Washington (2013).
M.Sc., Oceanography. University of Washington (2009).
B.A. summa cum laude, Biological Sciences. Rutgers University (2005).
My research is motivated by the overarching question, How does nitrogen availability affect diatom physiology and in turn, how does diatom physiology impact the marine environment through the drawdown of nitrogen?
During my graduate school tenure, I have worked in the laboratory on individual diatom species, as well as embarked on several research cruises off of central California, Oregon, Washington and Vancouver Island to interrogate diatom nitrogen metabolism in diverse nitrogen regimes. My goal has been to identify and quantify transcript abundances for molecular markers of diatom N metabolism, including responses to different nitrogen sources and responses to different degrees of nitrogen availability. Ultimately, these molecular markers will be used as part of larger metatranscriptomic datasets to monitor changes in diatom N uptake and N assimilation in the field.
Project 1: The role of the urea cycle in the model marine diatom Thalassiosira pseudonana
This work improves our understanding of diatom intracellular processes by incorporating the urea cycle into the bigger picture of N metabolism in a model diatom and by examining the effect of nitrogen sources on these metabolic pathways.
(Shown left: Simplified schematic of diatom nitrogen metabolism. Protist 2012)
Project 2: Comparative diatom transcriptomics in response to the onset of nitrate starvation.
This project is motivated by the need to better understand diatom-shared traits of N metabolism during growth on low nitrogen, and to determine whether assumptions about a "uniform diatom response" to changes in nitrogen availability, are relevant given the diversity of the diatom group.
Project 3: Using in situ markers of diatom metabolism coupled to metatranscriptomes to determine the nitrogen response of diatom field communities to changing nitrogen regimes.
Several research cruises steaming from the coast to the open ocean have allowed us to conduct onboard, deck incubations of the ambient phytoplankton community, as well as to collect large-scale filtrations for metatranscriptomic sequencing. This includes a recent collaboration between our lab group and GEOTRACES to couple 'omics sampling to trace ocean elements. Analyses of all of this work will provide a snapshot of diatom metabolism in the field, told from the cell's perspective.
Durkin, C.A., Bender, S.J., Chan, K.Y.K., Gaessner, K., Grunbaum, D., and Armbrust, E.V. (2013). Silicic acid supplied to coastal diatom communities influences cellular silicification and the potential export of carbon. Limnology and Oceanography. 58(5):1707-1726.
Bender, S.J., Parker, M.S. and Armbrust, E.V. (2012). The coupled effects of light and nitrogen source on the urea cycle and nitrogen metabolism over a diel cycle in the marine diatom Thalassiosira pseudonana. Protist. 163: 232-51.
Durkin, C.A., Marchetti, A., Bender, S.J., Truong, T., Morales, R., Mock, T. and Armbrust, E.V. (2012). Frustule-related gene transcription and the influence of diatom community composition on silica precipitation in an iron-limited environment. Limnology and Oceanography. 57(6): 1619-1633.
Bidle, K.D. and Bender, S.J. (2008). Iron starvation and culture age activate metacaspases and programmed cell death in the marine diatom, Thalassiosira pseudonana. Eukaryotic Cell. 223-46.
As a research technician in Ginger Armbrust's lab I am fortunate to be involved in a range of diverse projects. I help graduate students and post-docs investigate questions on marine phytoplankton dynamics and participate in cruises to collect samples that are used for many projects in the lab.
I began working in the Armbrust lab as a sophomore undergraduate student at UW and am still working on research that began as my senior project on the molecular analysis of Pseudo-nitzschia species. The project is part of an ongoing collaboration with the Woods Hole Oceanographic Institute to examine the diversity and distribution of Pseudo-nitzschia species along the East Coast of the United States. Pseudo-nitzschia is a potentially harmful diatom species that has the ability to produce the biotoxin domoic acid during harmful algae bloom events. The overall objective of this project is to better understand the occurrence of domoic acid. Because species of Pseudo-nitzschia are difficult to identfy by microscopy and morphology, we used a DNA fingerprinting technique (ARISA) developed by Kate Hubbard (a former graduate student in our lab) to distinguish between species and strains. By examining Pseudo-nitzschia communities in samples collected from Georges Bank and the Gulf of Maine during May, June, and July of 2008 we are hoping to provide further insight to different water parameters necessary for Pseudo-nitzschia species distributions and the processes that are likely important in the occurrence of domoic acid and harmful algae blooms.
One of my current projects includes testing culture samples for the presence of domoic acid by using surface plasmon resonance (SPR). This innovative approach analyzes binding of domoic acid to antibodies immobilized on sensor chips coated with gold surfaces. The Soelberg lab has developed a compact portable SPR machine that allows us to test samples in the lab and at sea on research cruises.
I will be continuing my investigative research experience by attending graduate school at UW in the fall. The outstanding mentoring and guidance I received while working in the Armbrust lab contributed to my interest in research, and my training and experiences will contribute to my success as a graduate student.
I am a research scientist in the School of Oceanography at the University of Washington. I combine molecular tools and bioinformatics with physiology experiments for the study of marine diatoms. Diatoms are some of the most dominant and important organisms for global carbon cycling in the world’s oceans. They are responsible for about 40% of marine primary production and play a critical role in global climate. Through photosynthesis, diatoms capture the greenhouse gas carbon dioxide and produce oxygen. Annually, diatoms generate one fifth of the oxygen we breathe.
I am specifically interested in the diatom genus Pseudo-nitzschia because many of these species can produce a potent neurotoxin called domoic acid (DA). DA can accumulate in filter feeders such as clams, mussels and oysters. When humans consume shellfish contaminated with DA, they can become very sick. The condition is known as amnesic shellfish poisoning because symptoms include memory loss. DA is also associated with illness and mortality in marine mammals and other vertebrates such as sea birds. I am using comparative transcriptomics (gene expression) to understand the genes that are differentially expressed in Pseudo-nitzschia species when the cells are producing the toxin. The goal is to uncover genes involved in toxin production and develop these as markers for assessing toxin production in field samples. In collaboration with the Joint Genome Institute, we have a draft genome of Pseudo-nitzschia multiseries, in addition to several RNASeq libraries which we are currently analyzing.
I have several other projects that I collaborate on with current and former members in our lab at the Center for Environmental Genomics. These include: the discovery of an iron storage protein called ferritin in Pseudo-nitzschia, which may help explain their success in open ocean iron-poor environments, as well as a metatranscriptome of an iron-addition experiment at Ocean Station Papa (see Adrian Marchetti's website for more information on these projects). Currently, I am also using comparative genomics to investigate strain level diversity within the species Thalassiosira pseudonana (with a lot of help from Chris, Dave and Rhonda in our lab). We have used a SOLiD Analyzer to re-sequence six additional strains (for a total of 7 genomes) and have run light treatment experiments with two of these strains for a whole transcriptome level comparison. I am also collaborating with one of our graduate students, Sara Bender, to investigate the role of the urea cycle in diatoms (see Sara's page for more information).
For my Ph.D. thesis research, I investigated the expression of genes involved in the cycling of carbon and nitrogen within a diatom cell during photorespiration.
* maiden name = Schnitzler
rkodner at u.washington.edu
UW Center for Environmental Genomics
UW Friday Harbor Labs
Beam Reach Marine Science and Sustainability School
Harvard University PhD, Biology, 2007
Department of Organismic and Evolutionary Biology
Thesis Advisor: Dr. Andrew Knoll
University of Wisconsin-Madison Bachelors of Science, 2000
Majors: Paleobiology with honors and History
Academic Advisor: Dr. Linda E. Graham
I have my training as a geobiologist and have experience working with molecular biology, organic geochemistry and fossils. I integrate methods from a variety of fields to best address the questions that most interst me . My past work has focused on recognizing and interpreting evidence of life in the geologic record and using it to understand the past contribution of marine organism to global carbon sinks. I used modern organisms as a platform for exploring the past recorded in microfossils and organic geochemical signatures. Thus, my thesis work combined comparative biochemistry, phylogenetics, genomics, micropaleonotolgy, SEM/TEM and microchemical techniques.
My current research is focusing on modern marine phytoplankton and using targeted metagenomics to study phytoplankton communities response to environmental change. I am investigating the sources and sinks of organic carbon from marine phytoplankton communities by studying environmental genomes and transcriptomes. I am working on a number of datasets in collaboration with the Armbrust lab, including one from my field site is the San Juan Islands (WA) where I am a resident scientist at the Friday Harbor Labs (http://depts.washington.edu/fhl/) and Faculty for the Beam Reach Marine Science and Sustainabitly School (http://www.beamreach.org/). This work will contribute to the growing effort to understand the biological feedback in the global carbon cycle.
Overview of Research Interests
I'm interested in phytoplankton communitiy dynamics and their role in biogeochemistry at multiple scales - from seasonal, to geologic time scales. I use metagenomics, metatrancriptomics, and comparative genomics to study these microbial eukaryotic communities. The foundations of my work bring together ideas from evolutionary biology, geology, and biological oceanography to study the co-evolution of the biosphere and the geosphere. My focus is the evolutionary history and functional ecology of photosynthetic eukaryotes in past and present environments. In particular I am interested in the role of phytoplankton in the global carbon cycle and linking genomic data with geological and environmental data. Though eukaryotic phytoplankton are quantitatively highly influential in the global carbon cycle, they have generally been understudied in the field of genomics and have only recently become the subjects of metagenomic and metatrancriptomic studies. In my work I seek to increase our knowledge of microbial eukaryotic genomics and ecology in the context of the changing Earth system.
My current research focus is developing in three areas: (1) developing bioinformatic tools and pipelines for gene identification in metagenomes and metatranscriptomes using phylogenetic methods (2) analyzing a variety of metagenomic and metatrancriptomic projects (3) synthesizing environmental, biochemical, and genomic data, with specific emphasis on the carbon cycle. In addition, I have begun to apply these research directions to two applied projects: investigating harmful algal blooms and algae-based biofuel.
(1) I have been collaborating with Frederick Matsen, a mathematical and computational biologist at University of California – Berkeley on a new, phylogenetics based gene identification program called pplacer (Matsen, Kodner, and Armbrust, in prep). Identification of sequences via phylogenetic analysis is preferable to similarity searches like BLAST, because it provides evolutionary information about each sequence and allows for identification of yet unidentified groups. Look for info on pplacer here http://matsen.fhcrc.org/pplacer/.
(2) I am currently working on one metagenome project in collaboration with Alex Worden's group at MBARI. This project is looking at eukaryotic phytoplankton functional diversity thought a transect from the coast of Montery Bay, CA to to the off shore waters. I am also collaborating on two metatranscriptome projects, one in collaboration with other folks in the Armbrust lab, looking at sample from Station P in the subarctic North Pacific and the other in collaboration with Jon Zehr's group at UC Santa Cruz, looking at a transect through the Amazon River plume.
(3) I am working on sequencing samples from Eastsound, WA, where I sampled thorough a toxic diatom bloom in June, 2009, 2010 and 2011. I've also been advising work on mixed community cultures for algal biofuel for Bodega Algae in Cambrige, MA.
I'm also interested in experiential education and community based science education, outreach, and citizen science. I'm working on developing a citizen science phytoplankon monitoring program in the San Juans to help build a base-line for understanding changes in phytoplankton communitiies on various time scales. I'm currently teaching field-based courses out of the Friday Harbor labs and working with many boat-based partners in the San Juans who are out and about collecting planton for me. Stay tuned or more info!
I worked on a number of projects during my PhD work at Harvard University in Andy Knoll's lab (http://www.fas.harvard.edu/%7Eknollgrp/index.htm), and with Roger Summons (MIT, Department of Earth, Atmospheric, and Planetary Sciences) and Ann Pearson (Department of Earth and Planetary Sciences, Harvard University).
One of the pioneering areas of my research is using genomic data to identify genes for biomarker biosynthesis, in order to investigate taxonomic specificity and evolution of these molecules. I defined the biosynthetic potential of an organism to produce sterol biomarkers using genes from a complete genome sequence. I use this approach in a study with choanoflagellates, marine microorganisms with a sequenced genome and that hold an important phylogenetic position with respect to the origin of metazoans. The origin of metazoans is putatively marked in the geologic record by a sterol-derived biomarker, believe to be specific to demosponges. I investigated the potential of choanoflagellates to make this biomarker using genomic information. The genomic approached allowed a new way to determine the potential of biomarker production and to investigate the evolution of the biosynthetic pathway of a biomarker using phylogenomics (Kodner, et. al, PNAS, July 22, 2008).
I created a database of sterol lipids, the progenitor of one of the most common classes of lipid biomarkers, from algal groups in the kingdom Plantae. These lipids (characterized with GC-MS) were again placed within a phylogenetic framework to describe the distribution and evolutionary history of these molecules within a diverse monophyletic lineage. This analysis aids in interpreting the Paleozoic sterane record, and is currently used as evidence that green algae were dominant primary producers in ancient oceans (Kodner, et al., in press, Geobiology, August 2008).
I characterized a biopolymer thought to be a green algal biomarker (algaenan) from a diverse group of algae using pyrolysis GC-MS and put it in a phylogenetic context. This work helped to establish that algaenan, found in great abundance in the geologic record, actually has a very limited distribution among modern green algae and is not likely to be the source of the common geopolymer (Kodner, et al. in prep).
I study a unique marine green algal phytoplankton from the genus Halosphaera, which is a phycomate prasinophyte. The phycoma, a green algal reproductive structure presented as the best modern analog for the most ancient eukaryotic organic microfossils. The phycoma has long been thought to have substantial preservation potential and superficially resembles many ancient spheroidal microfossils. By this association, much of the organic walled microfossil record has been described as remains of phytoplankton. This project involved locating and field sampling this elusive structure, which remains unculturable. My SEM, TEM, and chemical analyses show limited support for the relation of spheroidal microfossils and phycoma, and support some new fossil ultrastructure data that suggest a greater diversity of organisms produce spheroidal microfossils than previously thought (Cohen, Kodner, and Knoll, in prep). This work has also called into question long standing ideas about microfossil preservation. In addition, I am describing the species I work on in Washington as a new species Halosphaera.
Kodner, R. B., Matsen, F.A., Hoffman, N., Berthiaume, C., Armbrust, E. V., A fast, phylogenetic based pipeline for shotgun environmental sequences analysis. In prep
Marchetti, A, Schruth D., Durkin C., Berthiaume C. ,Morales, R., Parker M.S., Kodner, R.B. Armbrust, E.V. Taxonomic and metabolic shifts in an iron-stimulated eukaryotic marine plankton community from the NE Pacific Ocean revealed through comparative metatranscriptomics. submitted
Matsen, F.A., Kodner, R. B, and Armbrust, E. V., pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of metagenomic sequences on a reference tree. 2010. BMC Bioinformatics, 11:538 (30 October 2010)
Phoebe A. Cohen, Knoll, A.H., and Kodner, R.B. Large spinose microfossils in Ediacaran rocks as resting stages of early animals. Proceedings of the National Academy of Sciences. 2009.: Issue 106:6519-6524
Kodner, R. B., Summons, R.E., Knoll, A. H. Phylogenetic Investigation of the Aliphatic, Non-hydrolyzable Biopolymer Algaenan, with a Focus on the Green Algae. Organic Geochemistry, 2009
Kodner, R. B., Summons, R.E., Pearson, A., King, N., and Knoll A. H. Sterols in a unicellular relative to the metazoans. 2008. Proceedings of the National Academy of Sciences, 105: 9897-9902
Kodner, R. B., Summons, R.E. Pearson, A., and Knoll, A. H. A quantitative investigation of sterols in the red and green algae from a phylogenetic perspective: Relevance for the interpretation of geologic steranes. 2008. Geobiology, 6(4):411-20
Graham, L. E., R. B. Kodner, M. M. Fisher, J. M. Graham, L. W. Wilcox, J. M. Hackney, J. Obst, P. C. Bilkey, D. T. Hanson, M. E. Cook. 2003. Early land plant adaptations to stress: a focus on phenolics. In The Evolution of Plant Physiology, A. R. Hemsley and I. Poole [eds.], Academic Press, London. pp. 155–170.
Redecker D, R. Kodner, L.E. Graham. 2002. Palaeoglomus grayi from the Ordovician. Mycotaxon 84: 33-37
Kodner R. B. and L.E. Graham. 2001. High-temperature, acid-hydrolyzed remains of Polytrichum (Musci, Polytrichaceae) resemble enigmatic Silurian-Devonian tubular microfossils. American Journal of Botany 88 (3): 462-466
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Science 289: 1920-1921
Two characteristics of diatoms that influence biogeochemical cycles are their high productivity and their unique silica cell walls. As a result, diatoms control the silicon cycle in the ocean and couple the carbon and silicon cycles. The largest particle export in the ocean is associated with sinking diatoms, which sequesters carbon into the deep ocean. My research is motivated by the complicated factors that influence whether diatoms bloom, how much silica they incorporate into their cells, and their tendency to sink. I am identifying which genes are involved in cell wall formation and how they respond to different nutrient conditions. This involves comparing gene content among diatom genomes, measuring gene expression in controlled lab experiments, and correlating changes in gene expression with changes in cell wall physiology. I am also applying what we learn about these genes in lab experiments to understanding natural populations. My goal is to use these genes to directly measure how diatoms in the ocean are responding in a particular environment. This will help us to identify which diatoms are responding, how they are changing their physiology, and under what conditions. Ultimately, this type of information will help us understand the conditions, timing, and community composition that most influence biogeochemical cycles.
Durkin, C.A., T. Mock, E.V. Armbrust. 2009. Chitin in diatoms and its association with the cell wall. Eukaryotic Cell 8:1038-1050
1. Identifying shared genes among diverse diatoms that are likely associated with the cell wall, and measuring gene expression in different nutrient limiting conditions. Genes found among diverse lab diatoms will be easier to find in diverse field populations.
Franzika Lutz and Tiffany Truong and two undergrads helping with this project.
2. Measuring diatom cell wall changes along the Line P transect in the subarctic North Pacific using both a silica stain (PDMPO) and gene expression.
Adrian Marchetti and Rhonda Morales collecting water from the CTD on the JP Tully in June 2008
3. Measuring community responses to different silicic acid concentrations along the Washington and Oregon Coasts with the CMOP program.
Sara Bender and Jarred Swalwell deploying a CTD in rough seas aboard the RV New Horizon in May 2009.
I am a technician in the lab of Dr. Ginger Armbrust. My research revolves around the many various projects Dr. Armbrust and the post-docs in the lab are currently working on. I also deal with many of the collaborative projects that come through including our current collaborations with the Joint Genome Institute to sequence the genomes of Pseudonitzschia multiseries and Fragilariopsis under the direction of Dr. Micaela Parker and Dr. Thomas Mock respectively. I am also involved with the development of several EST libraries with the Joint Genome Institute at the level of RNA extraction. I have in the past been involved with generating several subtraction libraries for the organism Pseudonitzschia australis to analyze what genes are turned on when it starts to produce the chemical domoic acid, a marine toxin. Domoic acid is a dangerous toxin that can contaminate the shellfish population and eventually work it's way up the food chain where it can cause permanent short term memory loss in humans, and in the worst cases it can be fatal. It is our hope that we can better understand on a molecular level some of the chemical pathways and triggers for why these diatoms go toxic. I also participate with Dr. Micaela Parker and Dr. Adrian Marchetti in the study of iron and the genes used to regulate it. My studies revolve around trying to pull the gene ferritin, a gene discovered in the previously mentioned subtraction libraries, out of different types of phytoplankton using specially designed code-hop primers. I am also currently the Megabace technician for our facility. I am involved in running and maintaining our Megabace 1000 sequence analyzer whom we have affectionately named “Sofia”. The sequencing facility supports the sequencing efforts of faculty, students, and researchers from various labs in the larger University of Washington's scientific community as well as our own smaller marine molecular community.
Email: irinao at uw.edu
As a research scientist in the Armbrust lab, I am responsible for maintaining our extensive culture collection and am the lab's diatom culturing guru. I also assist the graduate students and postdoctoral fellows in implementing their experiments and enjoy working in such a collaborative environment.
Adrian has moved to the University of North Carolina at Chapel Hill. Visit his website here.
Thomas is currently a faculty member at the University of East Anglia (UEA) in Norwich.
Before I came to the University of Washington, I obtained my Dr. rerum naturalis from the University of Bremen (Germany) at the Alfred Wegener Institute for Polar and Marine Research (AWI) in 2003 after graduating (Diploma) from the Kiel University (Germany) with a degree in Biological Oceanography in 1998. I have subsequently done postdoctoral work for 2 years at the AWI. My research topics are acclimation and adaptation of marine and particularly polar sea ice diatoms to their extreme environmental conditions (link). My postdoctoral work here at the Department of Oceanography in the group of Ginger Armbrust is related to genome wide expression analysis with the marine diatom Thalassiosira pseudonana. We are intent to construct the first Microarrays for this diatom in order to identify transcription units, which are related to important environmental conditions such as excess light intensity, carbon dioxide limitation or iron limitation. Publications
Tatiana Rynearson is currently a faculty member at the Graduate School of Oceanography, University of Rhode Island.