Interested Members of the University Community are invited to attend the Final Oral Examination for the Degree of Doctor of Philosophy of Michelle E. H. Thompson Of the Department of Plant Agriculture 

DATE: Thursday, December 14th, 2023
TIME: 9:00 am
LOCATION: In Room 307, Crop Science Building
ZOOM LINK: https://zoom.us/j/96319465314?pwd=YjkreVBaa2NaY0tYUGZOLzhQd1krdz09
MEETING ID: 963 1946 5314
PASSCODE: 476406 

Thesis Title: DISCOVERY AND TESTING OF POLLINATED MAIZE SILK-ASSOCIATED MICROBES INCLUDING MICROBIOME ASSISTED SELECTION OF BIOCONTROL AGENTS AGAINST FUSARIUM GRAMINEARUM 

Advisory Committee 
Dr. Manish Raizada, Advisor
Dr. Rebecca Shapiro
Dr. Art Schaafsma
Dr. Jeffrey Farber
Dr. Joseph Colasanti

Examination Committee
Dr. Francois Tardif, Chair
Dr. Christine Abreu de Oliveira Paiva, External Examiner
Dr. Manish Raizada
Dr. Rebecca Shapiro
Dr. Jennifer Geddes-McAlister                                   

ABSTRACT 

The style tissue in maize, the silks, are female reproductive channels in flowering plants that receive pollen and transmit sperm nuclei to ovules, enabling fertilization/reproduction. Style/silks are susceptible to abiotic stresses. Furthermore, during maize fertilization, fungal pathogens including Fusarium graminearum (Fg), the causative agent of Gibberella ear rot (GER), enter ovules through silks, depositing mycotoxins dangerous to humans/livestock. I hypothesized silk-associated bacteria have adapted to silk stresses to promote host fertilization/health, ensuring their own transmission to future generations. From cob portions protected from the environment by husk leaves, I cultured >1000 fertilization-stage silk bacteria from 14 field-grown maize genotypes spanning North American heterotic breeding group diversity. Half of the plants were infected with Fg. Using a subset of tissues reported in a parallel Raizada Lab bioinformatic-limited microbiome study that employed short-read 16S-V4-MiSeq sequencing, I taxonomically classified isolates using longer-read 16S-rRNA sequencing, then matched them to this microbiome study. Improved taxonomic resolution demonstrated that previously-defined important taxa [core microbiome and induced by Fg (“Fg-indicators”)] are more diverse than previously reported. With improved resolution, I evaluated the shift in the culturable microbiome community composition after Fg-infection at two distances from Fg inoculation. Taxonomic-matching was used to test whether bioinformatic microbiome data could predict which isolates have anti-Fg activity within my large culture collection to reduce workload in future biocontrol pipelines. I analyzed microbes for possible functions using gene mining, in vitro testing, light/confocal fluorescence microscopy, and greenhouse testing. Novel methods were designed to facilitate confocal microscopy-based studies of microbe interactions on living silks, and discovered isolates colonizing silk trichomes, Fg-hyphae, forming biofilms, and entering silks via wounds. Using healthy silk isolates, I also asked fundamental questions about the fertilization-stage style microbiome. Gene mining and in vitro testing were used to demonstrate that fertilization-stage silk bacteria encode adaptations to silk/pollen abiotic stresses, and signaling compounds that may promote host fertilization. Novel methods were devised to evaluate the origin of silk-inhabiting microbes (environment or maternal parent). This thesis represents the first systematic investigation of the style microbiome in any plant species including genetic and phenotypic analyses, and reveals novel traits with potential for crop improvement.