Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California
Citable URI
https://hdl.handle.net/1912/2605Location
Monterey Bay, CADOI
10.1575/1912/2605Abstract
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.
Description
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
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Suggested Citation
Thesis: Rich, Virginia Isabel, "Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California", 2008-09, DOI:10.1575/1912/2605, https://hdl.handle.net/1912/2605Related items
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