Integrative transcriptome-metabolome analysis reveals the mechanism of salinity stress mitigation by trehalose-coated silica nanoparticles in lentil

The use of silica nanoparticles (SiNPs) has been reported to confer significant tolerance to salinity stress in plants. Moreover, their surface functionalization with bioactive molecules has been observed to further improve the potential of bare nanoparticles. However, this research builds on our earlier study highlighting the synergistic effects of trehalose and silica nanoparticles (SiNPs), aiming to clarify the molecular mechanisms underlying the potential of trehalose-functionalized SiNPs (TSiNPs, 5 g/L) to mitigate NaCl stress (300 mM) in Lens culinaris seedlings. In this connection, physiological and biochemical indicators of plant health, transcriptome (RNA-seq), and metabolome (untargeted LC-MS/MS) analyses have been conducted to decipher the mechanism by which TSiNPs ameliorate salinity stress. Results indicated that the TSiNPs alleviated the effects of salinity stress in lentil seedlings by improving water balance, chlorophyll content, ionic balance, membrane integrity, and ROS scavenging. The whole-transcriptome analysis revealed enhanced expression of ion transporters, phytohormones, redox enzymes, and photosynthetic genes in TSiNPs-treated seedlings. Joint pathway analysis further confirmed these results, showing higher expression of the glycolysis, MAP kinase, and ABA signaling pathways in TSiNPs-treated seedlings. Finally, the better accumulation of stress-responsive metabolites in TSiNPs-applied seedlings also demonstrated the stress-alleviation potential of TSiNPs. The integrative omics analysis revealed that the regulation of alanine, aspartate, and glutamate metabolism, fatty acid biosynthesis, and galactose metabolism contributed to stress alleviation. Overall, this study provides an in-depth analysis of the genes and metabolites involved in mitigating salinity stress by TSiNPs. • Trehalose-coated silica nanoparticles (TSiNPs) mitigated NaCl-induced stress. • TSiNPs improved water balance, chlorophyll levels, and membrane stability. • RNA-seq showed upregulation of ion transporters, phytohormones, and photosynthetic genes. • Omics analysis revealed activation of glycolysis, MAPK, and ABA signaling pathways. • Stress-related metabolites increased, confirming TSiNP-mediated salinity tolerance.