Current Projects


Our lab’s primary focus is on understanding microalgae community diversity and evolution over time, in both marine and alpine environments.  We ultimately hope to understand how these communities functionally adapt to changing environments, especially as our marine and alpine environments in the pacific northwest are changing rapidly.  We use high-throughput sequencing of DNA or RNA to characterize the taxonomic diversity (large-scale tag sequencing projects) and functional diversity (metagenomics)

Diversity and Dynamics of Snow Algae Communities 


Pink snow, commonly referred to as watermelon snow, represents a community of organisms that include microalgae and bacteria.  Though the algae in these communities have been known a long time from microscope studies, ours is the first large-scale biogeographic DNA survey of the whole community using the newest technology in high-throughput DNA sequencing.  See News.

Diversity and Dynamics of Marine Microeukaryotes 

We are working on characterizing the whole phytoplankton community over space and time through periodic summer hypoxic conditions in Bellingham Bay.  We use high-throughput surveys of 18S SSU ribosomal genes (V4 region).

Phylogenetic-based metagenome analysis pipelines

We are working on analyzing metagenomic data from existing and new project and improving our existing phylogenetics-based analysis pipeline.  This utilizes the pplacer software package that Dr. Kodner helped develop with Erick Matsen at the Fred Hutchenson Cancer Research Center.  Since its publication in 2010, we have been working on a pipeline to run pplacer across thousands of genes in any large sequence dataset.

Phycomate Prasinophyte Diversity in the Salish Sea

In 2006, while in graduate school, Dr. Kodner came to Washington for the first time to collect Halosphaera, a genus of phycomate prasinophyte that cannot be cultured and is difficult to find.  It is our best modern analog for the most ancient eukaryotic fossils and thus, an important evolutionary lineage.  We have collected samples in 2013 and 2014 to begin to characterize this population using more advanced microscopy techniques and genomics.

Halosphaera dubeii phycoma collected from the Salish Sea. Phycoma roughly 400 µm. Image: R. Kodner.

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