Disentangling the impact of abiotic and biotic environmental factors and dispersal dynamics on bacterial pangenome fluidity

Understanding how bacterial pangenomes originate and evolve is crucial for predicting evolutionary trajectories and uncovering ecological interactions. Bacterial pangenome fluidity has been attributed to adaptive evolution, yet its specific ecological drivers remain to be elucidated. Listeria monocytogenes (Lm), a foodborne pathogen causing fatal listeriosis, serves as an ideal model for studying the ecological mechanisms underlying pangenome fluidity due to its high evolutionary divergence, ecological versatility, and public health relevance. Through pangenome analysis of 177 Lm isolates representing three evolutionary lineages (I, II, and III) that we isolated from soil samples systematically collected across the United States, we found that the substantial genome variation among Lm genomes was strongly associated with climatic factors (e.g. precipitation and temperature), soil properties (e.g. aluminum, pH, and molybdenum), and bacterial community composition, particularly Nitrospirae, Planctomycetes, Acidobacteria, and Cyanobacteria. These factors exerted strong selective pressure across many gene functions, with pronounced effects on genes involved in cell envelope synthesis, defense mechanisms, and replication, recombination, and repair. Among Lm lineages, distinct pangenome properties were observed. Lineage III exhibited a highly fluid pangenome, which was attributed to local adaptation to nutrient-limited conditions and strong dispersal limitation. In contrast, lineage I maintained a conserved pangenome, likely due to frequent homogenizing dispersal. Informed by this dispersal pattern, we identified an increased risk of soil-to-human transmission in lineage I, evidenced by epidemiological links between three soil isolates and 17 clinical isolates. Collectively, these findings highlight the combined roles of environmental selection and dispersal in governing the adaptive evolution of bacterial pangenomes.