{"id":{"repo_id":"woods-hole","oai_identifier":"oai:darchive.mblwhoilibrary.org:1912/2605"},"canonical_url":"https://search.dev.ndltd.org/etd/woods-hole/oai:darchive.mblwhoilibrary.org:1912/2605","repository":{"repo_id":"woods-hole","name":"Woods Hole Oceanographic Institute","base_url":"https://darchive.mblwhoilibrary.org/server/oai/request"},"display":{"title":"Development of a \"genome-proxy\" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California","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.","abstract_html":"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.","abstract_has_math":false,"creators":["Rich, Virginia I."],"institution":"Massachusetts Institute of Technology and Woods Hole Oceanographic Institution","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2008,"date_issued":"2008-09","date_published":"2008-09","updated_at":"2026-07-27T22:05:06Z","subjects":["Microbial genomes","Marine microbial ecology"],"languages":["en_US"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier.doi","label":"DOI","values":["10.1575/1912/2605"],"render_values":[{"text":"10.1575/1912/2605","href":"https://doi.org/10.1575/1912/2605","code":true}]}]},"links":{"outbound_url":"https://hdl.handle.net/1912/2605","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:creator","label":"Author","values":["Rich, Virginia I."]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2008-12-24T15:32:37Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2008-12-24T15:32:37Z"]},{"key":"dc:date.issued","label":"Date","values":["2008-09"]},{"key":"dc:publisher","label":"Institution","values":["Massachusetts Institute of Technology and Woods Hole Oceanographic Institution"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Microbial genomes","Marine microbial ecology"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["en_US"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.doi","label":"DOI","values":["10.1575/1912/2605"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/1912/2605"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["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"]},{"key":"dc:description.abstract","label":"Abstract","values":["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."]},{"key":"dc:format.mimetype","label":"Dc Format Mimetype","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Development of a \"genome-proxy\" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California"]}]}],"canonical_facts":{"dc:creator":["Rich, Virginia I."],"dc:date.accessioned":["2008-12-24T15:32:37Z"],"dc:date.available":["2008-12-24T15:32:37Z"],"dc:date.issued":["2008-09"],"dc: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"],"dc:description.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."],"dc:format.mimetype":["application/pdf"],"dc:identifier.doi":["10.1575/1912/2605"],"dc:identifier.uri":["https://hdl.handle.net/1912/2605"],"dc:language.iso":["en_US"],"dc:publisher":["Massachusetts Institute of Technology and Woods Hole Oceanographic Institution"],"dc:subject":["Microbial genomes","Marine microbial ecology"],"dc:title":["Development of a \"genome-proxy\" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California"],"dc:type":["Thesis"]},"updated_at":"2026-07-27T22:05:06Z"}