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 Variovorax and Pseudomonas in the endosphere, and Haliangium and Arthrobacter 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.