Seed bio-priming with a cold-adapted rhizobacterium from the Himalayan phytobiome enhances cold resilience and biocontrol potential in fenugreek (Trigonella foenum-graceum): 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.