Bacteria-Phage-Antibiotic interactions in variable environments: a community ecology perspective
There is increasing awareness that diversity in microbial communities likely plays a critical role in multiple biological processes, from regulating human health to sustaining ecosystem services. Along with advances in molecular technologies, this realisation has seen a rapid growth in efforts to catalogue microbial life, and yet we still have a surprisingly poor understanding of the mechanisms maintaining microbial diversity. With up to 1,000 different species in the human gut alone, classical ecological explanations for diversity maintenance appear unlikely to hold. A resolution to this coexistence paradox may lie in the dynamic nature of microbial environments. The goal of this project is to investigate whether recent theoretical advances in understanding coexistence in non-equilibrium systems can provide insights into microbial diversity in the presence of viral parasites and antimicrobial agents that naturally vary in concentration in space and time. To this end, I will conduct a series of innovative experiments on multi-strain communities of pathogenic and non-pathogenic Escherichia coli under spatial and temporal variability in nutrient resources, phages and antibiotics. The project is unique in community ecology in leveraging high-throughput methods in a model microbial system of significant human interest; and in its focus on the interaction between non-linear growth functions and environmental variability as a critical determinant of community dynamics. The results will i) enhance our understanding of the role of viral parasitism in regulating diversity; ii) provide insight into emerging theory on the operation of coexistence mechanisms at different spatial and temporal scales; and iii) inform evolutionary and epidemiological research into the combined effect of antibiotics and phages on bacterial performance.