Date of Award

Winter 2014

Project Type


Program or Major


Degree Name

Doctor of Philosophy

First Advisor

Vaughn S Cooper

Second Advisor

Elise R Sullivan

Third Advisor

Jessica A Bolker


Currently, we do not understand how much biodiversity may be maintained in any environment, especially not in the structured environments of biofilms, which constitute the dominant mode of microbial life. Although maintenance is associated with the complex spatial structure of biofilm architecture and resulting ecological opportunities, how both the abiotic and biotic environment defines available niches remains poorly understood. Here, we experimentally evolved three replicate populations founded by Pseudomonas aeruginosa strain PA14 for 540 generations under conditions favoring a regular cycle of biofilm formation and dispersal. Utilizing a variety of laboratory and genomic sequencing approaches, we characterize the population genetic structure of these hypermutator populations and identify key genotypic innovations that allowed for the evolution of rare biofilm specialists creating strong interdependency between isolates, the maintenance of distinct ecological units driven by trade-offs associated with anaerobic growth, the repeated evolution of hypermutation and modification of the 'stick-or-swim' decision cascade via polyphosphate production and the sensing of free phosphate. Overall, this body of work illustrates the vast diversity harbored in biofilms and establishes methods to identify novel targets of adaptation to structured environments amidst a very high noise to signal ratio.