- Shady A. Amin
- E. Virginia Armbrust
- Sara J. Bender
- Chris Berthiaume
- Tony Chiang
- Gwenn M. Miller Hennon
- Vaughn Iverson
- Rhonda Morales
- Micaela S. Parker
- Rita Peterson
- Francois Ribalet
- Jarred Swalwell
- Helena van Tol
- Jeffrey W. Turner
- Former Lab Members
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
Redecker D, R. Kodner, L.E. Graham. 2000. Glomalean fungi from the Ordovician.
Science 289: 1920-1921