{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/115523"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/115523","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Microbial-biogeochemical interactions in tropical lacustrine environments","abstract":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-05-01","abstract_html":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-05-01","abstract_has_math":false,"creators":["Chen, Mingfei"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Geology","degree_department":null,"school":null,"contributors":["Conroy, Jessica L.","Sanford, Robert A.","Fouke, Bruce W.","Johnson, Thomas M."],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-05","date_published":"2022-05","updated_at":"2026-07-22T22:24:54Z","subjects":["Kiritimati","microbes","geochemistry","carbonate","stable isotope","metagenomics","geochemical modeling","sequence analysis"],"languages":["en","eng"],"rights":["Copyright 2022 Mingfei Chen"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/115523","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Conroy, Jessica L.","Sanford, Robert A.","Fouke, Bruce W.","Johnson, Thomas M."]},{"key":"dc:creator","label":"Author","values":["Chen, Mingfei"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2022-05","2022-04-06"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Geology"]},{"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":["Kiritimati","microbes","geochemistry","carbonate","stable isotope","metagenomics","geochemical modeling","sequence analysis"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2022 Mingfei Chen"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/115523"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-05-01","The student, Mingfei Chen, accepted the attached license on 2022-04-04 at 09:30.","The student, Mingfei Chen, submitted this Dissertation for approval on 2022-04-04 at 09:39.","This Dissertation was approved for publication on 2022-04-06 at 08:18.","DSpace SAF Submission Ingestion Package generated from Vireo submission #17576 on 2022-11-11 at 11:55:55","Microbes (single-cell or colony of cells of microorganisms) in aquatic environments play important roles in shaping regional and global biogeochemical cycles. Sedimentary records of past microbial activity also provide a means of understanding past geological and biological events and related paleoenvironmental conditions. In addition, understanding the modern response of microbes to environmental stressors can provide insight into potential future changes due to anthropogenic forcing. Sedimentary microbial activities that occur in tropical aquatic environments represent an essential component of the global biogeochemical cycle, and can be resolved at a relatively high temporal resolution (e.g., decadal), relative to marine sediments. Here I apply genomic techniques and geochemical modeling to explore how microbes can impact and respond to physio-chemical variables in lakes on the coral atoll island of Kiritimati, in the central tropical Pacific (1.9°N, 157.4°W). First, I assess paired stable nitrogen isotope (δ15N) values of sediment organic matter with metagenomics data from a hypersaline lake sediment record to reveal molecular-level evidence of the microbial activities that drive δ15N variability. Both taxonomy and functional gene results from metagenomes indicate that the relative abundances of microbes related to the nitrogen cycle fluctuate considerably across the sediment core, and that specific microbial activities such as denitrification, nitrogen fixation, and ammonification can affect the primary δ15N signatures in the lake sediment core. Therefore, molecular-level evidence can provide important insights into the interpretation of traditional sedimentary geochemical data in paleolimnology. Next, I present an assessment of the abiotic and biotic factors that control the δ13C values of carbonate spherules and syndepositional carbonate mud in the same hypersaline lacustrine sediment record. Relatively higher δ13C values of the carbonate spherules cannot be explained by abiotic, mineralogic fractionation factors or external perturbations, suggesting an important role for local biological activities. Combining traditional petrography, mineralogy, and carbonate isotope data with metagenomic and geochemical modeling results, I show that the spatial and temporal changes of photosynthesis in the microbial mat influence carbonate δ13C values, supporting the hypothesis that spherules preferentially form in the surface layer of the mat at times of peak photosynthesis. The δ13C offset between spherules and matrix is also highly correlated with primary productivity indicators (total organic carbon and total nitrogen), which can indicate primary productivity from sedimentary and rock records. Finally, I evaluate changes in microbial communities of Kiritimati lake sediments before and after an extreme El Niño event to understand how microbes adapt to sudden environmental changes. Between from 2014 and 2019, the microbial communities of the sampled lakes change significantly and these changes are strongly correlated with salinity, with more halophilic taxa found in 2014 samples and more mesosaline or salinity-sensitive taxa found in 2019. For functional groups, more aerobic chemoheterotrophs are found in 2014 samples, and more photoautotrophs are found in 2019 samples. Furthermore, functional genes such as nifH and nrfA genes show that the diversity and dominant taxa within the functional groups shift dramatically with salinity. This study provides an understanding of how microbes respond to abrupt salinity changes caused by environmental stressors. Additionally, the analysis can shed light on future microbial responses to salinity influenced by climatic and anthropogenic change."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Microbial-biogeochemical interactions in tropical lacustrine environments"]}]}],"canonical_facts":{"dc:contributor":["Conroy, Jessica L.","Sanford, Robert A.","Fouke, Bruce W.","Johnson, Thomas M."],"dc:creator":["Chen, Mingfei"],"dc:date":["2022-05","2022-04-06"],"dc:description":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-05-01","The student, Mingfei Chen, accepted the attached license on 2022-04-04 at 09:30.","The student, Mingfei Chen, submitted this Dissertation for approval on 2022-04-04 at 09:39.","This Dissertation was approved for publication on 2022-04-06 at 08:18.","DSpace SAF Submission Ingestion Package generated from Vireo submission #17576 on 2022-11-11 at 11:55:55","Microbes (single-cell or colony of cells of microorganisms) in aquatic environments play important roles in shaping regional and global biogeochemical cycles. Sedimentary records of past microbial activity also provide a means of understanding past geological and biological events and related paleoenvironmental conditions. In addition, understanding the modern response of microbes to environmental stressors can provide insight into potential future changes due to anthropogenic forcing. Sedimentary microbial activities that occur in tropical aquatic environments represent an essential component of the global biogeochemical cycle, and can be resolved at a relatively high temporal resolution (e.g., decadal), relative to marine sediments. Here I apply genomic techniques and geochemical modeling to explore how microbes can impact and respond to physio-chemical variables in lakes on the coral atoll island of Kiritimati, in the central tropical Pacific (1.9°N, 157.4°W). First, I assess paired stable nitrogen isotope (δ15N) values of sediment organic matter with metagenomics data from a hypersaline lake sediment record to reveal molecular-level evidence of the microbial activities that drive δ15N variability. Both taxonomy and functional gene results from metagenomes indicate that the relative abundances of microbes related to the nitrogen cycle fluctuate considerably across the sediment core, and that specific microbial activities such as denitrification, nitrogen fixation, and ammonification can affect the primary δ15N signatures in the lake sediment core. Therefore, molecular-level evidence can provide important insights into the interpretation of traditional sedimentary geochemical data in paleolimnology. Next, I present an assessment of the abiotic and biotic factors that control the δ13C values of carbonate spherules and syndepositional carbonate mud in the same hypersaline lacustrine sediment record. Relatively higher δ13C values of the carbonate spherules cannot be explained by abiotic, mineralogic fractionation factors or external perturbations, suggesting an important role for local biological activities. Combining traditional petrography, mineralogy, and carbonate isotope data with metagenomic and geochemical modeling results, I show that the spatial and temporal changes of photosynthesis in the microbial mat influence carbonate δ13C values, supporting the hypothesis that spherules preferentially form in the surface layer of the mat at times of peak photosynthesis. The δ13C offset between spherules and matrix is also highly correlated with primary productivity indicators (total organic carbon and total nitrogen), which can indicate primary productivity from sedimentary and rock records. Finally, I evaluate changes in microbial communities of Kiritimati lake sediments before and after an extreme El Niño event to understand how microbes adapt to sudden environmental changes. Between from 2014 and 2019, the microbial communities of the sampled lakes change significantly and these changes are strongly correlated with salinity, with more halophilic taxa found in 2014 samples and more mesosaline or salinity-sensitive taxa found in 2019. For functional groups, more aerobic chemoheterotrophs are found in 2014 samples, and more photoautotrophs are found in 2019 samples. Furthermore, functional genes such as nifH and nrfA genes show that the diversity and dominant taxa within the functional groups shift dramatically with salinity. This study provides an understanding of how microbes respond to abrupt salinity changes caused by environmental stressors. Additionally, the analysis can shed light on future microbial responses to salinity influenced by climatic and anthropogenic change."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/115523"],"dc:language":["en","eng"],"dc:rights":["Copyright 2022 Mingfei Chen"],"dc:subject":["Kiritimati","microbes","geochemistry","carbonate","stable isotope","metagenomics","geochemical modeling","sequence analysis"],"dc:title":["Microbial-biogeochemical interactions in tropical lacustrine environments"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Geology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:54Z"}