Summary 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 DNA survey of the whole community using the newest technology in high-throughput DNA sequencing. Using these new powerful environmental genomic techniques, we are starting to investigate a number of questions: (1) are there are biogeographic patterns to snow algae communities, (2) how does the algae community diversity change with elevation and latitude, and (3) how may these communities be affected by a reduction of snowpack in the future.
We made a video in 2015 with our friend Eli Loomis on why we study snow algae. You can watch the video here: Studying Snow Algae video
We also run a citizen science/community science/climber and skier science program to engage the public in helping us sample for snow algae. In 2014 Dr. Kodner is working with the North Cascades National Park as a part of their BioBlitz program to utilize citizen scientists to collect snow algae from locations across the park and the region. If you are interested in participating, please contact us and check out this page: The Living Snow Project.
Phytoplankton Community Structure Across Temporal and Spatial Scales in Bellingham Bay
We have been working on characterizing the whole phytoplankton community over space and time through periodic summer hypoxic conditions in Bellingham Bay over the past 4 years. We characterize the various size fractions of phytoplankton via flow cytometry, microscopy, and quantitative cell counts, and will be doing high-throughput surveys of 18S SSU ribosomal genes (V4 region).
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.
Improving phylogenetic-based metagenome analysis pipelines We are working on analyzing metagenomic data from existing and new project and improving on 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 data set.
Halosphaera dubeii phycoma collected from Salish Sea. Phycoma roughly 400 µm. Image: R. Kodner.