Author ORCID Identifier

https://orcid.org/0009-0000-2205-290X

Date of Award

Winter 3-12-2026

Document Type

Thesis (Ph.D.)

Department or Program

Biological Sciences

First Advisor

Carey Nadell

Abstract

This thesis explores how biofilm architecture determines the spread and ecological consequences for the bacteria-dependent genetic elements phages and plasmids. Using Escherichia coli and Vibrio cholerae as model microbes, and the genetic elements T7 phages, λ phages, and conjugative plasmid pED208, we investigate how spatial structure influences phage infection dynamics, plasmid transfer, and interbacterial interactions within biofilms. We show that densely packed biofilms can protect sensitive bacteria from phage exposure and modulate competitive outcomes between obligately lytic and temperate phages. We find that entirely different outcomes can coöccur within microns of each other dependent on biofilm structure. We also demonstrate that plasmid transfer is enhanced in loosely packed biofilms and can promote biofilm formation and antibiotic tolerance. These spatially mediated interactions alter interspecies interactions, shifting them from competitive to exploitative under selective pressures such as phage infection. These findings highlight biofilm spatial structure as a key determinant of microbial ecology and their dependent genetic elements.

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