Integrated transcriptomic and metabolomic analyses reveal coordinated molecular responses associated with nano-enabled arbuscular mycorrhizal symbiosis for salt stress tolerance in rice.

Salinity stress is a major environmental constraint limiting rice growth and yield. Seed nanopriming with calcium oxide nanomaterials (CaO NMs) in combination with arbuscular mycorrhizal fungus (AMF) has recently emerged as an effective strategy to enhance resilience, although the underlying responses remain unexplored. In the present study, rice seeds primed with CaO NMs (80 ppm) and inoculated with the AMF Claroideoglomus claroideum at transplanting were evaluated under 175 mM NaCl stress to assess their effects on plant performance and metabolic responses. The combined treatment significantly enhanced mycorrhizal colonization under non-stress conditions, with arbuscule abundance exceeding 40%, whereas AMF colonization was reduced under salinity stress in the corresponding SMN treatment. Despite this reduction, SMN improved physiological performance under salinity, chlorophyll stability index increased by 71% and also improved several yield-related parameters. Untargeted metabolomic profiling of leaves identified 391 differentially accumulated metabolites (DAMs) in response to the combined treatment under salinity stress, predominantly enriched in pathways associated with amino acid metabolism (glycine-serine-threonine and alanine-aspartate-glutamate), sulfur metabolism (cysteine and methionine), and aromatic amino acid metabolism (phenylalanine and tryptophan). These metabolic changes suggest enhanced osmoprotection, improved redox homeostasis, and activation of secondary metabolite biosynthesis. Transcriptomic analysis further identified the upregulation of genes associated with photosynthetic antenna complexes, peroxidase-mediated redox regulation, and Ca2+ signaling components including two-pore Ca2+ channel 1 (TPC1) and EF-hand proteins, together with reduced expression of lipid peroxidation-associated oxidative stress markers, suggesting coordinated molecular responses associated with salinity tolerance. Collectively, the metabolomic and transcriptomic findings suggest coordinated metabolic and transcriptional adjustments that may contribute to improved photosynthetic performance, redox homeostasis, and grain yield under saline conditions. Overall, this study provides new insights into nano-enabled AMF symbiosis and suggests that CaO NM seed priming combined with AMF inoculation represents a promising strategy for improving rice resilience under saline conditions.