SRA

Microbial communities in groundwater ecosystems are inherently difficult to study due to sampling challenges paired with highly dynamic microenvironments. A number of recent efforts have characterized and mined the vast bacterial diversity within groundwater via amplicon surveys and shotgun metagenomics, but these data sources cannot reveal dynamic or historical changes without high-resolution sampling. Here we aimed to identify recent microbial adaptation within groundwater sites by capturing evolutionary signatures from isolate whole genome sequencing. We recovered 139 Pseudomonas isolates which grouped into 15 strains, and found that each strain contained isolates from multiple sampling sites across a broad geographic region. SNP analysis confirmed that recent mutational changes were impacting strains in individual sampling sites, despite a fast-flowing aquifer, and some SNPs in a two-component system showed evidence of positive selection. We also searched for gene gain and loss within strain isolates, and found evidence of transcriptional gene excision within otherwise clonal isolates at a single location. Since isolate sequencing within environmental strains can reveal recent adaptive changes, it is a powerful tool to understand the impact of groundwater perturbations through the lens of microbial genomes.