From genome to lifestyle: adaptive strategies of <i>Pseudomonas</i> sp. AU10 and its Antarctic lineage

Antarctica harbors diverse <i>Pseudomonas</i> lineages, yet their evolutionary histories and ecological strategies remain poorly understood. Growing genomic resources now enable comparative analyses that link genome information to lifestyles. Here, we report the complete genome of <i>Pseudomonas</i> sp. AU10, an Antarctic freshwater isolate, and use it as a model to investigate polar adaptation through phylogenomics, pangenomics, metabolic reconstruction, and phenotypic assays. Incorporating the 40 most closely related genomes from public databases, we identified that all 11 strains from permanently cold environments clustered into two well-defined monophyletic clades with contrasting biogeographic patterns: a geographically restricted "Antarctic clade," to which AU10 belongs, and a "cold clade" distributed worldwide from the Himalayas to the Arctic and Antarctica. The two lineages lacked a shared conserved gene set for adaptation to permanently frozen habitats; instead, clade-specific genomic signatures suggested independent adaptive strategies. The Antarctic clade resolved into two species, both sharing distinctive features related to ionic/osmotic homeostasis, respiratory flexibility, and virulence factors, including insecticidal toxins. Within this clade, AU10's species showed expanded virulence factors and iron acquisition systems. Genomic evidence pointed to a potential pathogenic lifestyle involving freshwater arthropods, supported by AU10's metabolism oriented toward protein, lipid, and chitin hydrolysis and the overrepresentation of transport systems for amino and organic acids. Intraspecific variability involved the replacement of O-antigen gene clusters and a mobilome comprising a natural plasmid and several prophages carrying UV-resistance and outer-envelope modification genes. Overall, these findings place AU10 within a long-evolving Antarctic lineage with distinct adaptations, offering insights into bacterial evolution in extreme environments.IMPORTANCEAntarctica is one of the most extreme environments on Earth, yet it sustains diverse microbial life. How these microorganisms adapt to permanent cold conditions and the lifestyles they adopt remain difficult to elucidate. The growing wealth of genomic data offers opportunities to reconstruct these evolutionary histories. Still, in versatile genera such as <i>Pseudomonas</i>, extracting consistent biological meaning from comparative genomics remains challenging. Here, we focused on a restricted set of genomes closely related to the Antarctic strain <i>Pseudomonas</i> sp. AU10 and integrated genomic analyses with phenotypic assays and metabolic reconstruction. This strategy uncovered two cold-adapted lineages with contrasting biogeographic patterns, highlighted lineage-specific genomic features associated with adaptation to the extreme Antarctic environment, and provided insights into their ecological strategies. Ultimately, this approach underscores the value of linking genomic, phenotypic, and ecological information to illuminate bacterial evolution in extreme environments.