University of Illinois Urbana-Champaign

Management, microbiology, and machine learning: A systems approach to evaluating the nitrogen cycling microbiome in agricultural soils

Egenriether, Sada Margaret

Content Files
EGENRIETHER-DISSERTATION-2021.pdf

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https://hdl.handle.net/2142/113110

Description

Title
Management, microbiology, and machine learning: A systems approach to evaluating the nitrogen cycling microbiome in agricultural soils
Author(s)
Egenriether, Sada Margaret
Issue Date
2021-04-19
Director of Research (if dissertation) or Advisor (if thesis)
  • Yang, Wendy
  • Kent, Angela
Doctoral Committee Chair(s)
  • Yang, Wendy
  • Kent, Angela
Committee Member(s)
  • Yannarell, Anthony
  • Sanford, Robert
  • Zilles, Julie
Department of Study
School of Integrative Biology
Discipline
Ecol, Evol, Conservation Biol
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Date of Ingest
2022-01-12T22:34:37Z
Keyword(s)
  • Microbial ecology
  • biogeochemistry
  • nitrogen cycling
  • bioinformatics
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.
Graduation Semester
2021-08
Type of Resource
Thesis
Permalink
http://hdl.handle.net/2142/113110
Copyright and License Information
Copyright 2021 Sada Egenriether

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