CMOP Seminar: Metagenomic Analyses of Coastal Oregon and Southern California Current Ecosystem Bacterioplankton Populations

Lisa ZeiglerSPEAKER
Lisa Zeigler, J. Craig Venter Institute

WEBCAST
Watch Video of Seminar

ABSTRACT
Metagenomics has emerged as a powerful tool enabling the discovery of vast genetic diversity relating to microbial communities; primarily the uncultivable populations. In collaboration with the California Cooperative Oceanic Fisheries Investigations (CalCOFI), which samples transects along the California current each season, and the Center for Coastal Margin Observation and Prediction (CMOP), which is focused on estuarine and nearshore waters of the Oregon Coast, we collected a unique subset of samples that are being integrated into the JCVI Global Ocean Sampling (GOS) expedition.

Exploiting the immense hydrographic metadata acquired by CalCOFI and CMOP, we have a rare opportunity to use metagenomic analyses to describe the genetic diversity and metabolic profiles (e.g. metabolic footprint) associated with the waters typical of these environments, i.e., nutrient-rich up-welled waters, hypoxic zones, and chlorophyll maxima. In addition to total genomic analyses, we have extended our efforts to search for site-specific correlations among nutrients, taxa, and metabolism.

Our findings, following initial sequencing, have shown these environments to be taxonomically rich with many examples of particular ribotypes associated with specific hydrographic data. Using APIS (Automated Phylogenetic Inference System) for the phylogenomic taxonomic assignment of ORFs (predicted proteins) from reads, we identify sites elevated in particular marine microbial taxa that correlate to distinct nutrient profiles.

For example, there is a increase in Bacteriodetes spp. associated with the samples collected from the southern region of the California current. Also of significance, is a dramatic spike in the abundance of Planctomyces genes perhaps in association with a phytoplankton bloom, and Nitrosopumilus in the hypoxic sample, preliminary analysis of viral data from upwelling sites in the CCE indicate a sharp increase in genes encoding for various genes in the bacterial nitrate assimilation pathway.

Ongoing analyses are focused on relating functional gene repertoire to microbial diversity profiles in an effort to link the metabolic potential of particular microbes to specific habitat types

SPEAKER BIO
Dr. Zeigler obtained a B.S. in biological sciences with a focus on microbial genetics from Washington State University. It was during this time that she became interested in marine sciences, so she ventured down to San Diego, California, and joined William Fenical’s group at Scripps Institution of Oceanography (SIO). She is currently finishing her Ph.D. at SIO while working as a member of the Environmental Genomics group at the J. Craig Venter Institute.

VIDEOCONFERENCING
CMOP has the ability to videoconference and webcast this seminar. You must email a request to the center's videoconferencing coordinator to receive the videoconference/webcast.

Send your videoconferencing/webcast request to Jim Mohan for details.