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dc.contributor.authorRich, Virginia Isabel  Concept link
dc.coverage.spatialMonterey Bay, CA
dc.date.accessioned2008-12-24T15:32:37Z
dc.date.available2008-12-24T15:32:37Z
dc.date.issued2008-09
dc.identifier.urihttps://hdl.handle.net/1912/2605
dc.descriptionSubmitted 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 2008en
dc.description.abstractThis 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.en
dc.description.sponsorshipThis work was supported by a National Science Foundation (NSF) Microbial Observatories Award (MCB-0348001, to E.F.D.), a grant from the Gordon and Betty Moore Foundation (to E.F.D.), a grant from the David and Lucille Packard Foundation (to E.F.D.), and NSF Science and Technology Center Award EF0424599 (to E.F.D.).en
dc.format.mimetypeapplication/pdf
dc.language.isoen_USen
dc.publisherMassachusetts Institute of Technology and Woods Hole Oceanographic Institutionen
dc.relation.ispartofseriesWHOI Thesesen
dc.subjectMicrobial genomesen_US
dc.subjectMarine microbial ecologyen_US
dc.titleDevelopment of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, Californiaen
dc.typeThesisen
dc.identifier.doi10.1575/1912/2605


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