Seed bio-priming with a cold-adapted rhizobacterium from the Himalayan phytobiome enhances cold resilience and biocontrol potential in fenugreek (): Genomic and physiological evidence

Cold stress in Himalaya is encountered as a major abiotic stress in hilly agri-production along with the fungal invasions as biotic stress. The phytobiome of the Dharamkot Valley in the Western Himalayas was screened for plant growth-promoting (PGP) traits under cold stress conditions. Among 64 isolates, a bacterium identified Pseudomonas bubulae P1 exhibited the most promising attributes, including efficient phosphate solubilization (127.0 ± 0.5 mg/L), siderophore production (75.77 ± 0.9 PSU), and indole-3-acetic acid (IAA) synthesis (28.09 ± 0.7 mg/L) at 10 °C. Pot experiments with the strain P1 treated fenugreek ( Trigonella foenum-graceum ) plants demonstrated enhanced physiological performance, reflected by increased proline (34.01 ± 0.36 mmol kg -1 FW), antioxidant activity (25 ± 0.64 %), and chlorophyll contents (Chl a: 4.15 ± 0.42 mg g -1 FW; Chl b: 3.89 ± 0.59 mg g -1 FW). Seed germination assays and scanning electron microscopy further confirmed its in vitro antifungal activity, showing 59.3 % inhibition of Fusarium oxysporum . Whole-genome analysis of P1 provided genomic evidence associated with PGP functions, biocontrol mechanisms, and cold stress adaptation. The cold-adapted nature of strain P1 was supported by molecular evidence, as qPCR analysis revealed a 15- to 30-fold upregulation of key cold-responsive genes at 4 °C. Furthermore, antiSMASH-based genome mining identified eight biosynthetic gene clusters associated with secondary metabolite production, providing strong genomic evidence of the strain’s biocontrol potential. The findings highlight how plant–microbe associations contribute to the natural resilience of the phytobiome, offering new perspectives for improving crop adaptation and productivity in high-altitude ecosystems. • P. bubulae P1 isolated from the foothills of western Himalayas shows significant PGP attributes under cold stress. • Bio-priming fenugreek seeds with P. bubulae P1 imparts resilience against cold stress as well as F. oxysporum and improves plant physiology. • Genome analysis along with qPCR results reveals the molecular basis of cold stress resilience in P. bubulae P1. • SEM analysis illustrates the colonization of P. bubulae P1 around fungal hyphae of Fusarium oxysporum inhibits its proliferation. • This study illustrates the PGPR mediated regulation of cold and fungal stress for sustainable production of T. foenum-graceum in Himalayan regions.