A ‘reverse ecology’ approach for environmental microbes

We are in the process of generalizing to other groups of microbes our previous insights into the evolution of population structure gained in our Vibrio model. We hypothesized that although genes in genomes have no consistent signal of common evolutionary descent due to a history of extensive horizontal gene transfer, recent gene flow should on average be higher within than between populations due to genetic and ecological similarity of individuals within populations. Using a novel measure to identify the most recent HGT events among genomes, we constructed gene flow networks for closely related genomes, and found that clusters in these networks match previously defined ecologically cohesive populations in diverse bacteria and archaea. Defining populations based on gene flow also provides a powerful 'reverse ecology’ framework where genomes of closely related, co-occurring microbes from environmental samples can be assayed for genetic cohesion as a rapid means to hypothesize population structure and hence ecological differentiation. Identifying and understanding such fine-scale structure among coexisting bacteria and archaea has implications for a broad species definition and will allow more facile linking genomic to ecological features in both environmental and health applications. In fact, we have recently applied the method to bacterial pathogens and discovered unrecognized population structure and speciation events.


Selected references:

Arevalo, P. VanInsberghe, D., Elsherbini, J., Gore, J., Polz, M.F. (2019) A reverse ecology approach based on a biological definition of microbial populations. Cell 178(4):820-834.e14

VanInsberghe, D., Arevalo, P., Chien, D., Polz, M.F. (2020) How can microbial population genomics inform community ecology? Phil. Trans. R. Soc. B 375:20190253