Genomic Features of E. ruysiae Associated with the Ecological Origin: Implications for the Environmental Hypothesis

Escherichia cryptic clades represent a relatively unexplored taxonomic cluster believed to exhibit characteristics associated with a free-living lifestyle, which is known as the environmental hypothesis. This hypothesis suggests that certain Escherichia strains harbour traits that favour their environmental persistence, thus expanding the ecological commensal niche of the genus. While surveying Escherichia diversity in an urban South American stream we isolated the first environmental cryptic clade IV strain in South America (339_SF). Here we report the genomic characterization of 339_SF strain in the context of existing genomic information for E. ruysiae (cryptic clades III and IV). A comparative analysis of genomes within the same species stemming from diverse ecological sources and geographical locations reveals close phylogenetic proximity between our isolate and strains of environmental origin. Based on genetic content, we observed two clusters associated with the environmental source within E. ruysiae. In addition, we identified genes relatively more represented in the environmental strains: genes associated with carbohydrate metabolism (ydjG), stress response and DNA damage repair (such as umuD, higA and yddM). On the other hand, the gene rrrQ, associated with defense against other microorganisms, was significatively enriched in genomes of commensal origin. Our findings suggest that genomic features within E. ruysiae favoring its persistence in open environments may have arisen more than once, with these events being associated with the use of alternative energy sources and the resistance to various stressors specific to these environments.