Genomic signatures of radiation stress adaptations in Kocuria rhizophila: insights from strain 301 of the Jáchymov radon springs.

Several strains of Kocuria rhizophila have been reported to tolerate ionizing radiation and other environmental stresses; however, this phenotype is unevenly distributed across the species. Here, we characterize K. rhizophila strain 301, isolated from chronically radioactive radon springs in Jáchymov (Czech Republic). Strain 301 displayed exceptional stress resilience, retaining approximately 10% viability after exposure to 1.0 kGy of γ-irradiation, and maintaining ~20% survival following 30 days of desiccation. These responses sharply contrasted with the pronounced sensitivity of the type strain K. rhizophila TA68. Complete genome sequencing produced a single circular chromosome of 2.77 Mbp. Comparative genomic analyses revealed extensive duplication of genes involved in DNA repair, antioxidant defense, and metal ion homeostasis, including multiple paralogs of uvrA, uvrD, sodA, and Mn/Fe transport systems. In contrast to the paradigm established by Deinococcus radiodurans, strain 301 lacks radiation-specific or lineage-exclusive genes, instead suggesting that resilience may be associated with quantitative reinforcement of conserved cellular pathways. Pan-genome analysis further demonstrated a closed K. rhizophila pangenome, with strain 301 forming a distinct phylogenetic lineage. Together, these findings position K. rhizophila 301 as a model system of adaptation to chronic radiation exposure and illustrate how sustained environmental pressure may promote modifications and adaptations based on core functions rather than novel innovative genetic traits.