Microbial Ecology and Evolution

Ecology and evolution of species interactions in a changing world

Our group is interested in the eco-evolutionary dynamics of species interactions in multi-trophic communities. We are specifically focused on plant rhizosphere and human lung microbiomes and how interactions within these microbial communities affect the fitness and survival of associated host organisms. Elucidating these processes is especially important for understanding bacterial disease dynamics in agricultural and medical contexts and developing new ways to control infections. Moreover, we are interested in how the rapid evolution of species interactions might feedback and change the composition, stability and functioning of microbial ecosystems and host-associated microbiomes.

We use two main study systems in our research. First, we use a tomato rhizosphere microbiome model to study bacteria-phage-plant interactions in soil focusing on Ralstonia solanacearum plant pathogenic bacterium (a causative agent of bacterial wilt disease). Second, we use a model cystic fibrosis lung microbiome to focus on understanding how the evolution of Pseudomonas aeruginosa bacterial pathogen is shaped by sub-inhibitory antibiotic concentrations, other co-occurring bacteria and lytic phages. Our research combines experimental evolution with environmental and clinical sampling, field and greenhouse experiments, genome sequencing and bioinformatic analysis, and work with various microbes including bacteria, phages, and protists.