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

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.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Ecol, Evol, Conservation Biol

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2022

Author dc:creator

• Egenriether, Sada Margaret

Contributors dc:contributor

• Yang, Wendy
• Kent, Angela
• Yannarell, Anthony
• Sanford, Robert
• Zilles, Julie

• Microbial ecology
• biogeochemistry
• nitrogen cycling
• bioinformatics

Statement dc:rights

• Copyright 2021 Sada Egenriether

Language dc:language

en

Handle dc:identifier

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

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/113110