Experimental community genomics
PhD project of Johannes Cairns
My PhD project (co-supervised by Teppo Hiltunen from the neighboring experimental evolution group and Marko Virta from MEB) complements studies of environmental samples performed by other members in the MEB groups with laboratory experiments using model organisms and communities. I focus on the effects of low antibiotic concentrations on bacteria embedded in microbial communities, manipulating biotic and abiotic environmental complexity. These effects include but are not limited to antibiotic resistance mutations and horizontal transfer of antibiotic resistance genes. I am also interested in the emergent effects of antibiotic stress on key ecological and evolutionary factors in microbial communities, such as evolutionary patterns under multivariate selection, trophic interactions, and the stability, diversity, resistance and resilience of microbial communities. To understand these effects, I combine a variety of experimental and molecular techniques to track relevant parameters over time―e.g. community dynamics and composition, phenotypes of interest, whole-population genomics, and horizontal gene transfer networks―as well as developing novel methods and model systems.