Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California
Rich, Virginia Isabel
MetadataShow full item record
LocationMonterey Bay, CA
This thesis describes the development and application of a new tool for profiling marine microbial communities. Chapter 1 places the tool in the context of the range of methods used currently. Chapter 2 describes the development and validation of the “genome proxy” microarray, which targeted marine microbial genomes and genome fragments using sets of 70-mer oligonucleotide probes. In a natural community background, array signal was highly linearly correlated to target cell abundance (R2 of 1.0), with a dynamic range from 102-106 cells/ml. Genotypes with ≥~80% average nucleotide identity to those targeted cross-hybridized to target probesets but produced distinct, diagnostic patterns of hybridization. Chapter 3 describes the development an expanded array, targeting 268 microbial genotypes, and its use in profiling 57 samples from Monterey Bay. Comparison of array and pyrosequence data for three samples showed a strong linear correlation between target abundance using the two methods (R2=0.85- 0.91). Array profiles clustered into shallow versus deep, and the majority of targets showed depth-specific distributions consistent with previous observations. Although no correlation was observed to oceanographic season, bloom signatures were evident. Array-based insights into population structure suggested the existence of ecotypes among uncultured clades. Chapter 4 summarizes the work and discusses future directions.
Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2008
Showing items related by title, author, creator and subject.
Jennings, Robert M. (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2005-09)The overarching goal of this thesis was to investigate marine benthic invertebrate phylogenetics and population genetics, focused on the phylum Annelida. Recent expansions of molecular methods and the increasing diversity ...
Marine particle dynamics : sinking velocities, size distributions, fluxes, and microbial degradation rates McDonnell, Andrew M. P. (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2011-02)The sinking flux of particulate matter into the ocean interior is an oceanographic phenomenon that fuels much of the metabolic demand of the subsurface ocean and affects the distribution of carbon and other elements ...
Identity and dynamics of the microbial community responsible for carbon monoxide oxidation in marine environments Tolli, John D. (Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2003-09)As colored dissolved organic matter in seawater absorbs UV solar radiation, a variety of simple chemical species are produced, including carbon monoxide (CO). The ocean surface water is saturated with respect to CO, and ...