Ecotype-specific genomic features within the Escherichia cryptic clade IV

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 cryptic clade IV. A comparative analysis of genomes within the same clade stemming from diverse ecological sources and geographical locations reveals close phylogenetic proximity between our isolate and strains of environmental origin. In the genomes of cryptic clade IV strains that were isolated from environmental niches we observed enrichment of functional genes related to responses to adverse environmental conditions and a low number of genes with clinical relevance among. Our findings highlight substantial intra-group genomic structuring linked to ecological origin and shed light on the genomic mechanisms underlying the naturalization phenomena within the Escherichia genus.