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    Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California

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    Rich_thesis.pdf (30.97Mb)
    Date
    2008-09
    Author
    Rich, Virginia Isabel  Concept link
    Metadata
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    Citable URI
    https://hdl.handle.net/1912/2605
    Location
    Monterey Bay, CA
    DOI
    10.1575/1912/2605
    Keyword
     Microbial genomes; Marine microbial ecology 
    Abstract
    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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    • WHOI Theses
    • Biology
    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/1912/2605
     

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