Cold-tolerant bacteria isolated from alpine plants can promote growth and mitigate cold stress in tomato seedlings by complex transcriptional reprogramming of stress-related genes

Cold stress adversely affects crop growth, and climate change is increasing its severity and frequency in many agricultural regions. Tomato plants are sensitive to low temperatures, although they activate some stress response mechanisms. Beneficial microorganisms can enhance cold-stress acclimation in tomato plants, but the transcriptional regulation underlying this process remains poorly understood. This study aimed to investigate the transcriptional processes activated by cold stress in tomato plants following inoculation with cold-tolerant bacteria isolated from alpine plants to identify genes potentially involved in cold stress acclimation. Among 41 cold-tolerant bacterial isolates tested, Chryseobacterium sp. GRCS301 and Pseudomonas sp. GRCS202 inoculation in sterilized soil promoted tomato growth under controlled non-stress (25 ± 2 °C) and cold-stress (10 ± 2 °C) conditions. Bacterial inoculations lowered H2O2 content and affected the transcriptional regulations activated in tomato shoots after one day and 14 days of incubation under cold-stress conditions. In mock-inoculated plants, cold stress downregulated genes related to energy generation, photosynthesis, and reproductive processes, highlighting its detrimental effects. Conversely, plants inoculated with Chryseobacterium and Pseudomonas upregulated genes involved in DNA replication, galactose metabolism, polysaccharide metabolism, photosynthesis, and protein metabolism in response to cold stress. Bacterial inoculation induced the expression of genes involved in reactive oxygen species homeostasis, cold-stress response, and hormonal signaling, suggesting that cold-tolerant bacteria trigger key transcriptional changes in tomato plants and enhance cold-stress acclimation