{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/113110"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/113110","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Management, microbiology, and machine learning: A systems approach to evaluating the nitrogen cycling microbiome in agricultural soils","abstract":"Soil microorganisms are integral to the regulation of Earth’s biogeochemical cycles. Within the nitrogen (N) cycle, the soil microbiome is responsible for a multitude of competing processes, some which lead to ecosystem N retention, and others to loss. Because they determine the fate of nitrogenous fertilizer inputs, these processes and the microbes that catalyze them are of special interest in agricultural settings. This dissertation explores several different aspects of the N cycling soil microbiome, ranging from community-level impacts of conservation agriculture to the effects of phylogenetic diversity on bioinformatics clustering methods. I first demonstrate that the combination of heavy N fertilizer inputs and minimal soil disturbance in no-till agricultural systems generate unique pH dynamics that differentially influence several key N cycling functional groups. Next, I illustrate the risk of introducing Type II statistical errors to our downstream data analysis when we fail to consider the breadth of diversity represented among the functional genes we assess. I then show that dissimilatory nitrate reduction to ammonium (DNRA), a process previously assumed unimportant in terrestrial soils, can occur under both canonical highly reducing conditions as well as oxic conditions within the same soil. I close by synthesizing the body of literature reporting DNRA under oxic conditions together with our understanding of the physiology and ecology of soil N cycling microbes to propose a function for DNRA as a nitrite toxicity mitigation strategy in oxic soils. This work emphasizes the importance of using a systems approach to adequately address the emergent properties within our study systems. I conclude that N cycling microbiome research requires careful consideration of the ecological and phylogenetic context in which a given study system is situated.","abstract_html":"Soil microorganisms are integral to the regulation of Earth’s biogeochemical cycles. Within the nitrogen (N) cycle, the soil microbiome is responsible for a multitude of competing processes, some which lead to ecosystem N retention, and others to loss. Because they determine the fate of nitrogenous fertilizer inputs, these processes and the microbes that catalyze them are of special interest in agricultural settings. This dissertation explores several different aspects of the N cycling soil microbiome, ranging from community-level impacts of conservation agriculture to the effects of phylogenetic diversity on bioinformatics clustering methods. I first demonstrate that the combination of heavy N fertilizer inputs and minimal soil disturbance in no-till agricultural systems generate unique pH dynamics that differentially influence several key N cycling functional groups. Next, I illustrate the risk of introducing Type II statistical errors to our downstream data analysis when we fail to consider the breadth of diversity represented among the functional genes we assess. I then show that dissimilatory nitrate reduction to ammonium (DNRA), a process previously assumed unimportant in terrestrial soils, can occur under both canonical highly reducing conditions as well as oxic conditions within the same soil. I close by synthesizing the body of literature reporting DNRA under oxic conditions together with our understanding of the physiology and ecology of soil N cycling microbes to propose a function for DNRA as a nitrite toxicity mitigation strategy in oxic soils. This work emphasizes the importance of using a systems approach to adequately address the emergent properties within our study systems. I conclude that N cycling microbiome research requires careful consideration of the ecological and phylogenetic context in which a given study system is situated.","abstract_has_math":false,"creators":["Egenriether, Sada Margaret"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Ecol, Evol, Conservation Biol","degree_department":null,"school":null,"contributors":["Yang, Wendy","Kent, Angela","Yannarell, Anthony","Sanford, Robert","Zilles, Julie"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-01-12T22:34:37Z","date_published":"2022-01-12T22:34:37Z","updated_at":"2026-07-22T22:24:53Z","subjects":["Microbial ecology","biogeochemistry","nitrogen cycling","bioinformatics"],"languages":["en"],"rights":["Copyright 2021 Sada Egenriether"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/113110","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Yang, Wendy","Kent, Angela","Yannarell, Anthony","Sanford, Robert","Zilles, Julie"]},{"key":"dc:creator","label":"Author","values":["Egenriether, Sada Margaret"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2022-01-12T22:34:37Z","2024-01-12T22:35:30Z","2021-04-19","2021-08"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Ecol, Evol, Conservation Biol"]},{"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":["Microbial ecology","biogeochemistry","nitrogen cycling","bioinformatics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2021 Sada Egenriether"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/113110"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Soil microorganisms are integral to the regulation of Earth’s biogeochemical cycles. Within the nitrogen (N) cycle, the soil microbiome is responsible for a multitude of competing processes, some which lead to ecosystem N retention, and others to loss. Because they determine the fate of nitrogenous fertilizer inputs, these processes and the microbes that catalyze them are of special interest in agricultural settings. This dissertation explores several different aspects of the N cycling soil microbiome, ranging from community-level impacts of conservation agriculture to the effects of phylogenetic diversity on bioinformatics clustering methods. I first demonstrate that the combination of heavy N fertilizer inputs and minimal soil disturbance in no-till agricultural systems generate unique pH dynamics that differentially influence several key N cycling functional groups. Next, I illustrate the risk of introducing Type II statistical errors to our downstream data analysis when we fail to consider the breadth of diversity represented among the functional genes we assess. I then show that dissimilatory nitrate reduction to ammonium (DNRA), a process previously assumed unimportant in terrestrial soils, can occur under both canonical highly reducing conditions as well as oxic conditions within the same soil. I close by synthesizing the body of literature reporting DNRA under oxic conditions together with our understanding of the physiology and ecology of soil N cycling microbes to propose a function for DNRA as a nitrite toxicity mitigation strategy in oxic soils. This work emphasizes the importance of using a systems approach to adequately address the emergent properties within our study systems. I conclude that N cycling microbiome research requires careful consideration of the ecological and phylogenetic context in which a given study system is situated.","Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2023-08-01","The student, Sada Egenriether, accepted the attached license on 2021-04-19 at 08:46.","The student, Sada Egenriether, submitted this Dissertation for approval on 2021-04-19 at 08:51.","This Dissertation was approved for publication on 2021-04-19 at 12:57.","DSpace SAF Submission Ingestion Package generated from Vireo submission #16400 on 2022-01-12 at 12:51:19","Made available in DSpace on 2022-01-12T22:34:37Z (GMT). No. of bitstreams: 2 EGENRIETHER-DISSERTATION-2021.pdf: 2403361 bytes, checksum: 42da6e866d7e4f6635762dde189712ef (MD5) LICENSE.txt: 4213 bytes, checksum: 6dfa614d34e1a7c0a1c2c7cb854f1e6c (MD5) Previous issue date: 2021-04-19","Embargo set by: Seth Robbins for item 121036 Lift date: 2024-01-12T22:35:30Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","U of I Only"]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Management, microbiology, and machine learning: A systems approach to evaluating the nitrogen cycling microbiome in agricultural soils"]}]}],"canonical_facts":{"dc:contributor":["Yang, Wendy","Kent, Angela","Yannarell, Anthony","Sanford, Robert","Zilles, Julie"],"dc:creator":["Egenriether, Sada Margaret"],"dc:date":["2022-01-12T22:34:37Z","2024-01-12T22:35:30Z","2021-04-19","2021-08"],"dc:description":["Soil microorganisms are integral to the regulation of Earth’s biogeochemical cycles. Within the nitrogen (N) cycle, the soil microbiome is responsible for a multitude of competing processes, some which lead to ecosystem N retention, and others to loss. Because they determine the fate of nitrogenous fertilizer inputs, these processes and the microbes that catalyze them are of special interest in agricultural settings. This dissertation explores several different aspects of the N cycling soil microbiome, ranging from community-level impacts of conservation agriculture to the effects of phylogenetic diversity on bioinformatics clustering methods. I first demonstrate that the combination of heavy N fertilizer inputs and minimal soil disturbance in no-till agricultural systems generate unique pH dynamics that differentially influence several key N cycling functional groups. Next, I illustrate the risk of introducing Type II statistical errors to our downstream data analysis when we fail to consider the breadth of diversity represented among the functional genes we assess. I then show that dissimilatory nitrate reduction to ammonium (DNRA), a process previously assumed unimportant in terrestrial soils, can occur under both canonical highly reducing conditions as well as oxic conditions within the same soil. I close by synthesizing the body of literature reporting DNRA under oxic conditions together with our understanding of the physiology and ecology of soil N cycling microbes to propose a function for DNRA as a nitrite toxicity mitigation strategy in oxic soils. This work emphasizes the importance of using a systems approach to adequately address the emergent properties within our study systems. I conclude that N cycling microbiome research requires careful consideration of the ecological and phylogenetic context in which a given study system is situated.","Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2023-08-01","The student, Sada Egenriether, accepted the attached license on 2021-04-19 at 08:46.","The student, Sada Egenriether, submitted this Dissertation for approval on 2021-04-19 at 08:51.","This Dissertation was approved for publication on 2021-04-19 at 12:57.","DSpace SAF Submission Ingestion Package generated from Vireo submission #16400 on 2022-01-12 at 12:51:19","Made available in DSpace on 2022-01-12T22:34:37Z (GMT). No. of bitstreams: 2 EGENRIETHER-DISSERTATION-2021.pdf: 2403361 bytes, checksum: 42da6e866d7e4f6635762dde189712ef (MD5) LICENSE.txt: 4213 bytes, checksum: 6dfa614d34e1a7c0a1c2c7cb854f1e6c (MD5) Previous issue date: 2021-04-19","Embargo set by: Seth Robbins for item 121036 Lift date: 2024-01-12T22:35:30Z Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD system","U of I Only"],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/2142/113110"],"dc:language":["en"],"dc:rights":["Copyright 2021 Sada Egenriether"],"dc:subject":["Microbial ecology","biogeochemistry","nitrogen cycling","bioinformatics"],"dc:title":["Management, microbiology, and machine learning: A systems approach to evaluating the nitrogen cycling microbiome in agricultural soils"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Ecol, Evol, Conservation Biol"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:53Z"}