{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/49750"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/49750","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Identifying ecological differentiation in microbial communities across taxonomic scales","abstract":"Microbial diversity, both genetic and phenotypic, is a product of evolutionary and ecological processes interacting at multiple levels of biological organization. High-throughput sequencing is providing a means to resolve the vast amount of genetic diversity in microbial assemblages. However, a current fundamental challenge is associating genetic diversity, whether at the community or population scale, to phenotypic variation that defines ecological roles and dictates how microbial community diversity and ecosystem functioning respond to environmental change. In this body of work, I have used sequencing-based techniques to identify ecological differentiation at taxonomic scales ranging from a whole bacterial community to a single population of methanogenic archaea. At the broadest taxonomic scale, I used a whole-ecosystem disturbance along with 16S rRNA 454-pyrosequencing to identify ecologically relevant distinctions among taxonomic groups defined at various taxonomic scales. The findings showed that bacterial lineages require different taxonomic definitions to capture ecological patterns. At a more refined taxonomic breadth, I used a culture-independent approach to elucidate how methanogen community diversity was distributed within and between a set of freshwater lakes and also identified the ecological processes dictating this spatial distribution of diversity. Finally, at the highest resolution, I employed a comparative genomics approach to identify genomic signals of adaptive evolution in a Methanosarcina mazei population in order to link genetic variation to the ecological processes that define spatial and temporal distributions of methanogen populations. Together, this work has helped to resolve the interdependencies between genetic diversity and ecological processes, which concomitantly act to create and maintain microbial diversity across time and space.","abstract_html":"Microbial diversity, both genetic and phenotypic, is a product of evolutionary and ecological processes interacting at multiple levels of biological organization. High-throughput sequencing is providing a means to resolve the vast amount of genetic diversity in microbial assemblages. However, a current fundamental challenge is associating genetic diversity, whether at the community or population scale, to phenotypic variation that defines ecological roles and dictates how microbial community diversity and ecosystem functioning respond to environmental change. In this body of work, I have used sequencing-based techniques to identify ecological differentiation at taxonomic scales ranging from a whole bacterial community to a single population of methanogenic archaea. At the broadest taxonomic scale, I used a whole-ecosystem disturbance along with 16S rRNA 454-pyrosequencing to identify ecologically relevant distinctions among taxonomic groups defined at various taxonomic scales. The findings showed that bacterial lineages require different taxonomic definitions to capture ecological patterns. At a more refined taxonomic breadth, I used a culture-independent approach to elucidate how methanogen community diversity was distributed within and between a set of freshwater lakes and also identified the ecological processes dictating this spatial distribution of diversity. Finally, at the highest resolution, I employed a comparative genomics approach to identify genomic signals of adaptive evolution in a Methanosarcina mazei population in order to link genetic variation to the ecological processes that define spatial and temporal distributions of methanogen populations. Together, this work has helped to resolve the interdependencies between genetic diversity and ecological processes, which concomitantly act to create and maintain microbial diversity across time and space.","abstract_has_math":false,"creators":["Youngblut, Nicholas"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Microbiology","degree_department":null,"school":null,"contributors":["Whitaker, Rachel J.","Metcalf, William W.","Olsen, Gary J.","Slauch, James M."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2014,"date_issued":"2014-05-30T17:07:50Z","date_published":"2014-05-30T17:07:50Z","updated_at":"2026-07-22T22:25:40Z","subjects":["Methanosarcina","humic lakes","methanogen","microbial community","taxonomic scale","population genomics"],"languages":["en"],"rights":["Copyright 2014 Nicholas Youngblut"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/49750","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Whitaker, Rachel J.","Metcalf, William W.","Olsen, Gary J.","Slauch, James M."]},{"key":"dc:creator","label":"Author","values":["Youngblut, Nicholas"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2014-05-30T17:07:50Z","2016-09-22T20:59:25Z","2014-05"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Microbiology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Methanosarcina","humic lakes","methanogen","microbial community","taxonomic scale","population genomics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2014 Nicholas Youngblut"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/49750"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Microbial diversity, both genetic and phenotypic, is a product of evolutionary and ecological processes interacting at multiple levels of biological organization. High-throughput sequencing is providing a means to resolve the vast amount of genetic diversity in microbial assemblages. However, a current fundamental challenge is associating genetic diversity, whether at the community or population scale, to phenotypic variation that defines ecological roles and dictates how microbial community diversity and ecosystem functioning respond to environmental change. In this body of work, I have used sequencing-based techniques to identify ecological differentiation at taxonomic scales ranging from a whole bacterial community to a single population of methanogenic archaea. At the broadest taxonomic scale, I used a whole-ecosystem disturbance along with 16S rRNA 454-pyrosequencing to identify ecologically relevant distinctions among taxonomic groups defined at various taxonomic scales. The findings showed that bacterial lineages require different taxonomic definitions to capture ecological patterns. At a more refined taxonomic breadth, I used a culture-independent approach to elucidate how methanogen community diversity was distributed within and between a set of freshwater lakes and also identified the ecological processes dictating this spatial distribution of diversity. Finally, at the highest resolution, I employed a comparative genomics approach to identify genomic signals of adaptive evolution in a Methanosarcina mazei population in order to link genetic variation to the ecological processes that define spatial and temporal distributions of methanogen populations. Together, this work has helped to resolve the interdependencies between genetic diversity and ecological processes, which concomitantly act to create and maintain microbial diversity across time and space.","Item withdrawn by Laura Spradlin (lspradl2@illinois.edu) on 2014-01-03T14:30:26Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 2 Youngblut_Nicholas.docx: 16351841 bytes, checksum: a476dc03cd1d4fc0592dee17ed2716e3 (MD5) Youngblut_Nicholas.pdf: 10863054 bytes, checksum: 634658680a2f7783bdcef5e98352d1e6 (MD5)","Made available in DSpace on 2014-05-30T17:07:50Z (GMT). No. of bitstreams: 3 Nicholas_Youngblut.pdf: 10862446 bytes, checksum: 87e31ba1ce792ffd4b4dd20c01e13977 (MD5) Nicholas_Youngblut.docx: 16354205 bytes, checksum: 6554f72709fa0c0c1e898d28fff4d68a (MD5) license.txt: 4068 bytes, checksum: b005bd44ee560973c60ae354a776c44b (MD5)","Restriction data tranferred 2014-07-01T11:39:30-05:00 Original Data Group with Access UIUC Users [automated] Release Date: 2016-05-30 12:09:03 UTC Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Item marked as restricted to the 'UIUC Users [automated]' Group (id=2) by Seth Robbins (robbins.sd@gmail.com) on 2014-05-30T17:09:59Z Item is restricted until 2016-05-30T17:09:03Z","U of I Only Restriction Lifted for Item 49801 on 2016-09-22T20:59:25Z."]},{"key":"dc:title","label":"Title","values":["Identifying ecological differentiation in microbial communities across taxonomic scales"]}]}],"canonical_facts":{"dc:contributor":["Whitaker, Rachel J.","Metcalf, William W.","Olsen, Gary J.","Slauch, James M."],"dc:creator":["Youngblut, Nicholas"],"dc:date":["2014-05-30T17:07:50Z","2016-09-22T20:59:25Z","2014-05"],"dc:description":["Microbial diversity, both genetic and phenotypic, is a product of evolutionary and ecological processes interacting at multiple levels of biological organization. High-throughput sequencing is providing a means to resolve the vast amount of genetic diversity in microbial assemblages. However, a current fundamental challenge is associating genetic diversity, whether at the community or population scale, to phenotypic variation that defines ecological roles and dictates how microbial community diversity and ecosystem functioning respond to environmental change. In this body of work, I have used sequencing-based techniques to identify ecological differentiation at taxonomic scales ranging from a whole bacterial community to a single population of methanogenic archaea. At the broadest taxonomic scale, I used a whole-ecosystem disturbance along with 16S rRNA 454-pyrosequencing to identify ecologically relevant distinctions among taxonomic groups defined at various taxonomic scales. The findings showed that bacterial lineages require different taxonomic definitions to capture ecological patterns. At a more refined taxonomic breadth, I used a culture-independent approach to elucidate how methanogen community diversity was distributed within and between a set of freshwater lakes and also identified the ecological processes dictating this spatial distribution of diversity. Finally, at the highest resolution, I employed a comparative genomics approach to identify genomic signals of adaptive evolution in a Methanosarcina mazei population in order to link genetic variation to the ecological processes that define spatial and temporal distributions of methanogen populations. Together, this work has helped to resolve the interdependencies between genetic diversity and ecological processes, which concomitantly act to create and maintain microbial diversity across time and space.","Item withdrawn by Laura Spradlin (lspradl2@illinois.edu) on 2014-01-03T14:30:26Z Item was in collections: University of Illinois Theses & Dissertations (ID: 1) No. of bitstreams: 2 Youngblut_Nicholas.docx: 16351841 bytes, checksum: a476dc03cd1d4fc0592dee17ed2716e3 (MD5) Youngblut_Nicholas.pdf: 10863054 bytes, checksum: 634658680a2f7783bdcef5e98352d1e6 (MD5)","Made available in DSpace on 2014-05-30T17:07:50Z (GMT). No. of bitstreams: 3 Nicholas_Youngblut.pdf: 10862446 bytes, checksum: 87e31ba1ce792ffd4b4dd20c01e13977 (MD5) Nicholas_Youngblut.docx: 16354205 bytes, checksum: 6554f72709fa0c0c1e898d28fff4d68a (MD5) license.txt: 4068 bytes, checksum: b005bd44ee560973c60ae354a776c44b (MD5)","Restriction data tranferred 2014-07-01T11:39:30-05:00 Original Data Group with Access UIUC Users [automated] Release Date: 2016-05-30 12:09:03 UTC Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Item marked as restricted to the 'UIUC Users [automated]' Group (id=2) by Seth Robbins (robbins.sd@gmail.com) on 2014-05-30T17:09:59Z Item is restricted until 2016-05-30T17:09:03Z","U of I Only Restriction Lifted for Item 49801 on 2016-09-22T20:59:25Z."],"dc:identifier":["http://hdl.handle.net/2142/49750"],"dc:language":["en"],"dc:rights":["Copyright 2014 Nicholas Youngblut"],"dc:subject":["Methanosarcina","humic lakes","methanogen","microbial community","taxonomic scale","population genomics"],"dc:title":["Identifying ecological differentiation in microbial communities across taxonomic scales"],"dc:type":["text"],"thesis:degree_discipline":["Microbiology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:40Z"}