Unlocking the Phyllosphere’s Role: Selenium Nanoparticles Reprogram Sulfur Metabolism and Enrich Sphingomonas to Reduce Cadmium in Wheat

Although selenium nanoparticles (SeNPs) can mitigate cadmium (Cd) accumulation in crops, comparative system-level mechanisms among different SeNPs remain unclear, particularly in wheat. Herein, we compare chemically and biologically synthesized SeNPs (CH/BI-SeNPs) to elucidate Cd detoxification via phyllosphere metabolism–microbiome interactions. Results showed that foliar application of both SeNPs significantly reduced Cd accumulation and mitigated cell membrane damage in wheat. CH-SeNPs exhibited the strongest Cd reduction effect, decreasing grain Cd content by 30.9%. Metabolomic profiling revealed a substantial reorganization of sulfur metabolic pathways under CH-SeNPs treatment, characterized by the accumulation of S-adenosylhomocysteine (SAH), decreased homomethionine, and reduced oxidized glutathione (GSSG), indicating a shift in sulfur flux toward enhanced synthesis of reduced thiol compounds. CH-SeNPs activated the glutathione biosynthesis pathway, significantly increasing the activity of γ-glutamylcysteine synthetase and the contents of cysteine and glutathione, thereby promoting Cd chelation, and reducing its translocation to grains. 16S rRNA sequencing further demonstrated that CH-SeNPs significantly enriched Sphingomonas, a genus involved in sulfur cycling, in the phyllosphere, rhizosphere, and rhizosphere soil, suggesting that microbial interactions facilitated sulfur metabolism and contributed to a systemic reduction in Cd bioavailability. Additionally, HPLC-ICP-MS analysis indicated an increased proportion of selenomethionine in grains under CH-SeNPs treatment, enhancing both nutritional value and food safety. This study reveals that SeNPs alleviate Cd stress in wheat via coordinated regulation involving phyllosphere sulfur metabolism and microbial interactions related to sulfur, providing a mechanistic basis for the application of SeNPs in the remediation of heavy metal contamination and nutritional fortification in agriculture.