The origins of bacterial species and pangenomes in the wild

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Bacteria and other microbes account for over half the active biomass on Earth, control essential nutrient fluxes, and encode enormous genetic diversity. Despite an abundance of genomic and metagenomic sequencing from the environment, the basics of bacterial population genetics remain poorly defined: what is a bacterial species, and is it even worth defining? What are the rates of mutation, recombination, and natural selection in the wild and how do these forces interact to structure bacterial populations? Here I propose a combination of sampling bacterial isolates and metagenomes from natural environments and semi-natural mesocosm experiments to improve the empirical grounding of bacterial population genetics, providing a link between theory, laboratory evolution experiments, and the natural world. The proposal aims to answer three major sets of questions: Q1: What are the basic units of bacterial evolution? Under what conditions are individual genes versus species (ensembles of genes) the basic units? Q2: How do the early stages of bacterial speciation (ecological differentiation) proceed in nature, across different environments and regimes of natural selection? Q3: What controls rates of bacterial speciation (or diversification more broadly) in nature? My team (including 18 HQP to be trained through the proposed projects) will address these questions using a combination of (i) publicly available sequence data (e.g. from the Earth Microbiome Project to test competing diversification models across biomes, and the FijiCOMP set of ~40,000 mobile genes from the human gut to test whether variation in population genetic parameters is driven mainly by the mobile gene family or by the bacterial host genome), (ii) time series population genomes being sequenced in my lab (e.g. bloom-forming cyanobacteria in Lake Champlain and Methylobacterium across different tree species in Quebec) to track ecological differentiation in nature, and (iii) a controlled semi-natural mesocosm system: the Large Experimental Array of Ponds (LEAP) at the McGill University Gault Nature Reserve, where selective sweeps can be tracked with metagenomics under known selective pressures (e.g. pesticides). Impact. Species are generally considered the basic units of evolution, yet bacteria and other microbes are difficult to group into species. Under certain conditions and time scales, genes rather than species might be the most relevant level of selection, with implications for how best to study and engineer microbiomes. By studying bacterial evolution in real time and in natural setting, this proposal will improve our understanding of bacterial speciation, its underlying mechanisms, and the ecological factors that promote it. On a more applied level, our results will inform predictive models of how the microbial foundations of important ecosystems (e.g. freshwaters, forests, the human gut) will respond to environmental change (e.g. acidification, pesticide pollution, antibiotics).