Comparative genomic analysis of Rahnella sp. PAMC25617 isolated from cryoconite reveals a glutathione-dependent formaldehyde detoxification pathway.

Rahnella species are environmentally versatile bacteria widely distributed in terrestrial and aquatic ecosystems; however, the genomic basis of formaldehyde detoxification and stress adaptation in cryoconite-associated Rahnella remains poorly understood. In this study, we performed phylogenomic, comparative genomic, pan-genomic, stress-response, and functional analyses of Rahnella sp. PAMC25617 isolated from polar cryoconite to investigate glutathione (GSH)-dependent formaldehyde detoxification and its evolutionary conservation. Genome-based phylogeny, average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) analyses demonstrated that PAMC25617 represents a distinct genomic lineage within the genus Rahnella. The draft genome comprised 5.33 Mb with a GC content of 52% and encoded multiple genes associated with formaldehyde detoxification and one-carbon metabolism, including frmA, yeiG, yeiP, yeiR, and a putative formate dehydrogenase gene cluster. Comparative genomic analyses further showed that these detoxification genes were consistently associated with GSH transport (gsiA-D), redox-associated (frdA-D), and regulatory (fnr) genes, suggesting coordinated roles in detoxification and redox homeostasis. Comparative stress-response gene profiling across 121 Rahnella genomes further revealed widespread conservation of oxidative stress defense systems, including oxidoreductases, aldehyde dehydrogenases, GSH-associated enzymes, thioredoxin, catalase, and molecular chaperones. Notably, PAMC25617 possessed an enriched repertoire of oxidative stress and detoxification-related genes, indicating enhanced stress adaptation potential in cold and chemically challenging environments. Pan-genome analysis indicated a highly diverse and open pan-genome structure with a low Heap's law exponent (γ = 0.336), reflecting ongoing genome diversification and ecological adaptation. Multiple sequence alignment (MSA) further demonstrated strong conservation of catalytic motifs and active-site residues in FrmA and YeiG among phylogenetically diverse bacteria. Physiological assays showed that PAMC25617 exhibited tolerance to formaldehyde stress under liquid culture conditions. These findings suggest that R. sp. PAMC25617 employs an integrated GSH-dependent detoxification and oxidative stress response system that may facilitate survival and adaptation in extreme polar environments.