Microbial population and community dynamics in natural and managed freshwater systems: From methodology development to mechanistic insights

Natural and managed freshwater ecosystems are hotspots of biodiversity, biogeochemical cycling, and provide numerous societal services (e.g., drinking water production, wastewater treatment). The microbial communities that inhabit these systems form complex assemblages of interacting microbial taxa, for which the community structure and function are not yet fully understood. This research presents new insights into the microbial community ecology of both natural and managed freshwater systems by developing and validating new technologies to study them and by investigating the genomic adaptations to their freshwater habitat. A first line of hypotheses focused on the development and application of novel flow cytometry tools to monitor the structure of aquatic microbial communities in a fast and non-invasive manner. These tools were then applied to both natural (Lake Michigan) and managed (cooling and drinking water) freshwater ecosystems. In parallel, a second line of hypotheses delved into the genomic properties that some of the abundant populations in these communities have evolved to their freshwater environment.