Adaptive Trajectories of Bacteriophages: Evolutionary Dynamics Across Contrasting Environments

Bacteriophages are among the fastest-evolving biological entities, yet the early dynamics and constraints of their adaptive trajectories remain incompletely understood. This PhD project investigates the evolutionary potential of bacteriophages through controlled experimental evolution across contrasting environmental conditions. Using a model system consisting of Pseudomonas fluorescens and its associated phage, populations are serially passaged using automated liquid handling systems to ensure consistent propagation, while genomic changes are tracked through sequencing of selected phage populations at defined time points. The project aims to identify which genes and genomic regions are targeted during early adaptation, determine which mutations rise to dominance, and understand how individual mutations combine into broader evolutionary pathways. Particular emphasis is placed on how environmental context shapes these trajectories. Three experimental regimes are employed: - variation in infection dynamics (fast versus slow burst phages), where rapid infection cycles may favor enhanced codon adaptation and drive host-range shifts through mutations in tail fiber and baseplate proteins - spatially structured growth in biofilm-like environments, which better reflect natural and clinical settings where phages encounter surface-associated bacteria, and where extracellular matrix barriers and spatial heterogeneity impose selection for improved host access and dispersal, potentially favoring adaptations in structural and enzymatic host-interaction components such as tail fibers and depolymerases - high-salt conditions that impose physiological stress, potentially altering both the rate and molecular spectrum of adaptive mutations and revealing stress-specific evolutionary signatures. By comparing these conditions, the project examines whether distinct environments lead to convergent or divergent adaptive routes, with a focus on mutations in host-interaction genes, codon usage bias, and replication-associated functions. The work further explores how trade-offs between infection dynamics, host range expansion, and environmental resilience influence long-term genomic evolution. Overall, this study provides a systematic framework for tracing phage evolutionary routes from early mutations to complex adaptive outcomes, offering insights into viral adaptability, host- phage coevolution, and the predictability of evolutionary processes.

PhD start: 04/01/2026