Elucidating microbial-induced cold tolerance gene expression pathways in Arabidopsis thaliana by SA-producing bacterium Sphingomonas paucimobilis.

Low temperature severely limits crop productivity, yet the molecular mechanisms by which beneficial microbes enhance plant cold tolerance remain insufficiently defined, particularly regarding the role of microbial-derived salicylic acid (SA) in host signaling. This study investigated whether bacterial SA contributes to cold adaptation and how it modulates plant regulatory networks. Arabidopsis thaliana wild-type (Col-0), the SA-signaling mutant npr1-1, and the SA-degrading line nahG were inoculated with the SA-producing bacterium Sphingomonas paucimobilis ZJSH1 or its SA-deficient mutant (ΔpchB), followed by exposure to 4 ℃ for 14 days. Endogenous SA was quantified by UPLC-MS, physiological parameters were measured, and transcriptomic changes were analyzed using RNA sequencing. S. paucimobilis strain ZJSH1 inoculation significantly increased endogenous SA levels (2.40-3.37 µg g⁻1 protein), chlorophyll content (11.65-13.12 µg g⁻1 protein), and proline accumulation (up to 7.33 µg g⁻1 protein), enhanced antioxidant enzyme activities (SOD up to 346.24 U mg⁻1 protein; POD up to 5402.22 U g⁻1 protein, and CAT up to 1051.11 U mg⁻1 protein), and reduced lipid peroxidation compared with ΔpchB and non-inoculated controls. RNA-seq identified 8,307, 5,341, and 6,953 differentially expressed genes in Col-0, npr1-1, and nahG, respectively, enriched in photosystem stabilization, ICE-CBF-COR signaling, MAPK pathways, and redox homeostasis. Growth-related hormone pathways (auxin, cytokinin, gibberellin) were activated, whereas abscisic acid (ABA)-associated responses were repressed. Comparative genotype analysis revealed that photosynthetic protection and antioxidant activation were largely SA-driven and independent of NPR1, while NPR1 mediated transcriptional fine-tuning and proteostasis regulation. These findings define a dual SA regulatory mechanism underlying microbe-induced cold tolerance and provide mechanistic support for the use of S. paucimobilis strain ZJSH1 as a microbial strategy to enhance plant resilience under low-temperature stress.