Author ORCID Identifier

Date of Award


Document Type

Thesis (Ph.D.)

Department or Program

Biological Sciences

First Advisor

Carey Nadell, PhD

Second Advisor

George O’Toole, PhD

Third Advisor

Kimberly Kline, PhD


Despite the critical nature which microbial communities play in the natural world and human civilization, the breadth of understanding remains shallow. Challenged by scale, high variability between environments, and extensive diversity, microbial ecologists strive to understand connections between a community’s structure and function, as well as the ecological and evolutionary mechanisms underlying observed natural patterning of communities. Biofilms are the predominate mode of growth for microbial communities—characterized by cellular attachment to a surface via a self-produced matrix and heterogeneous structure, often resulting in a primary growth front along the biofilm surface due to differential access to bulk nutrients (cite). This growth style reciprocally influences and is influenced by ecological and social interactions such as mutualism and competition (cite). These aspects of ecology have been explored extensively in experimental and theoretical context for macroscale systems, yet many questions remain as microbes have been observed to follow some macroscale ecological trends while opposing other fundamental hypotheses (cite). Among these is the process of community assembly. Biofilms exhibit vast diversity in both structure and composition, yet the mechanisms by which these mixed communities are constructed remain vague. Microbial community ecologists have long sought to determine the degree of influence of deterministic and stochastic processes such as selection and social interactions, and genetic drift, respectively. In this document, we explore two primary model systems to study community assembly dynamics. The first examines an E. coli monospecies community comprising of two distinct ecological populations and how the community composition and structure is altered by bacteriophage pressure. The second examines the colonization and community assembly dynamics of a dual culture E. coli and E. faecalis on a medically relevant titanium surface. We observed phage pressure applied to a young E. coli biofilm selected for coexistence of E. coli phage susceptible and phage resistant populations due in part to the cost of resistance and spatial patterning of the community. We also observed mature E. coli biofilms with surface sequestered phages can repel invading E. coli cells in a time dependent manner. This effect required sufficient expression and cell coverage with a matrix protein, curli fibers. Finally, in the dual culture model system, we observed how differing movement and colonization strategies resulted in a spatial competition, ultimately influencing the stable climax communities observed. Competition outcomes could be manipulated by altering physical and temporal variables of the system. Collectively, we utilized unique microfluidic approaches to address outstanding questions in the field of microbial community assembly.

Original Citation

Simmons EL, Bond MC, Koskella B, Drescher K, Bucci V, Nadell CD. Biofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible Bacteria. mSystems. 2020 Jun 23;5(3):e00877-19. doi: 10.1128/mSystems.00877-19. PMID: 32576653; PMCID: PMC7311319.

Bond MC, Vidakovic L, Singh PK, Drescher K, Nadell CD. Matrix-trapped viruses can prevent invasion of bacterial biofilms by colonizing cells. Elife. 2021 Jul 9;10:e65355. doi: 10.7554/eLife.65355. PMID: 34240700; PMCID: PMC8346279.