Functionalized Silica Nanoparticles Mitigate Salt Stress in Soybean: Comprehensive Insights of Physiological, Metabolomic, and Microbiome Responses

Silica nanoparticles (SiO₂ NPs) have potential for mitigating salt stress in crops; however, the effects of surface modifications in enhancing their effectiveness remain unclear. This study investigated the effects of pristine and functionalized SiO₂ NPs (SiO₂-NH₂ and SiO₂-COOH) on soybean growth, root metabolism, and microbiome dynamics under 200 mM NaCl stress. All SiO₂ NPs treatments significantly reduced Na⁺/K⁺, with SiO₂-COOH NPs showing the greatest efficacy, reducing by 46.6%. Enhanced salt tolerance correlated with altered root metabolism, including increased l-tyrosine, uridine, and indole-3-acetamide levels and enrichment of stress-response pathways. Furthermore, SiO₂-COOH NPs enhanced microbial diversity, increasing the abundance of beneficial genera <i>Variovorax</i> and <i>Pseudomonas</i> in the endosphere, and <i>Haliangium</i> and <i>Arthrobacter</i> in the rhizosphere. Microbe-metabolite correlations suggest that altered root exudation under functionalized SiO₂ NPs treatments selectively recruits beneficial bacteria, enhancing salt tolerance. These findings highlight the potential of functionalized SiO₂ NPs, particularly SiO₂-COOH, as nanoenabled biostimulants for sustainable agriculture.