Schaal, K. A.; Wang, Y.-J.; Nauta, J.; Pilosof, S. A.; De Domenico, M.; Hall, J. P.

Microbial communities are shaped by complex forces, including interspecies interactions and the effects of mobile genetic elements such as plasmids. How these forces interact to affect community responses to environmental perturbations remains unclear, particularly considering the qualitatively different natures of competitive and plasmid transfer interactions. We investigated the role of bacterial and plasmid interaction networks in community responses to single and multiple environmental perturbations, using a model community of three bacteria and two plasmids grown in rich media over five 2-day transfers. Bacterial interactions were the primary driver of community response, to the extent that plasmids were not always retained in the community even when they carried relevant resistance genes. Overall, our results indicate that while bacterial and plasmid interactions both shape community responses to environmental perturbations, bacterial interactions may be the primary drivers of community dynamics.