Understanding Zea mays genetic influence on the structure and function of the rhizosphere microbiome

Favela, Alonso

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Description

Title

Understanding Zea mays genetic influence on the structure and function of the rhizosphere microbiome

Author(s)

Favela, Alonso

Issue Date

2021-04-22

Director of Research (if dissertation) or Advisor (if thesis)

Kent, Angela D.

Doctoral Committee Chair(s)

Kent, Angela D.

Committee Member(s)

• Bohn, Martin O.
• Yannarell, Anthony C.
• Heath , Katy D.
• Leakey, Andrew D.B.

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

Keyword(s)

• Microbiome
• Rhizosphere
• Nitrogen Cycle
• Sustainability
• Maize
• Heritability
• Genetics
• Ecosystems
• BNI

Abstract

Assembly of the plant rhizosphere microbiome is driven by plant genetic and evolutionary history. Plant microbiomes play a major role in altering plant resilience, fitness, nutrition, and productivity. Plant hosts selectively filter microorganisms that colonize their rhizosphere. This selective process is heritable across plant cultivars, yet the implication of heritability on rhizosphere microbiome function has been relatively unexplored. This dissertation attempts to characterize the N-cycling functions associated with heritable recruitment to the rhizosphere microbiome. The following dissertation aims to address these specific objectives: examine whether the contemporary agricultural practices that maize has experienced over the past 50 years of breeding has altered the rhizosphere N-cycling microbiome assembly, determine how domestication altered modern maize rhizosphere microbiome assembly from its ancestral progenitor teosinte, assess whether these genotype driven microbiome assembly processes persist in the field setting and influence N-cycling ecosystem function and finally attempt to determine the underlying genetic regions and mechanisms contributing to differential microbial community assembly and function in the rhizosphere. The findings of these specific objectives suggest that the maize microbiome has been unintentionally altered through the process of contemporary breeding and domestication, resulting in the microbiome interaction to be less agriculturally sustainable. These anthropogenic driven changes to the maize microbiome can be characterized by changes in nitrifying and denitrifying microbiome recruitment that consequently alter the rates of nitrification and denitrification of a soil. Furthermore, wild genetic diversity appears to house more sustainable N-cycling microbiome interactions compared to modern maize. The dissertation closes by showing how “rewilding” the plant microbiome interaction could be a potential solution to improve our agricultural system. Modern agricultural practices have resulted in the unprecedented degradation of our global nitrogen cycle. This N-cycle disruption by agriculture has been primarily driven by the over-application of synthetic N fertilizers. On average only about half of this applied synthetic N is taken up by our focal crop, while the remainder is lost through microbiome activities such as nitrification and denitrification. Broadly, the work in this dissertation shows that genotype-driven rhizosphere microbiome assembly can have a considerable effect on N-cycling functional groups that carry out nitrification and denitrification. Additionally, this dissertation suggests that at least in maize, a global staple crop, it appears that breeding has disrupted N-cycling functional group control in the rhizosphere especially when compared to its wild progenitor teosinte. Finally, we show that modern maize can regain the ability to influence N-cycling microbes in the rhizosphere with genetic introgressions from teosinte. Overall, this dissertation uses a combination of microbial ecology and plant genetics to provide some explanations for why our contemporary agricultural system is so unsustainable (via N-pollution) and provides some potential solutions to improve it (via rewilding).

Graduation Semester

2021-05

Type of Resource

Thesis

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Copyright and License Information

Copyright 2021 Alonso Favela

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