Leucocalocybe mongolica Fungus Enhances Rice Growth by Reshaping Root Metabolism, and Hormone-Associated Pathways

The fungal species Leucocalocybe mongolica has garnered attention due to its plant growth-promoting capabilities without fertilizers and emerged as a significant subject of research offering promising applications in sustainable agricultural practices. This study investigated the effects of LY9-transformed soil on rice growth and development through physiochemical, phenotypic, transcriptomic, and metabolomic analyses. Soil treated with varying concentrations of LY9 (10%, 30%, and 50%) exhibited significant improvements in nutrient availability compared to untreated controls. Rice plants grown in LY9-transformed soil enhanced phenotypic characteristics, including increased tillering (up to 20.29 tillers vs. 9 in control), greater root length (52.5 cm vs. 42 cm), and elevated chlorophyll content (1.21 mg/g vs. 0.38 mg/g). Transcriptomic analysis revealed significant alterations in genes related to primary and secondary metabolism, with 2,612 upregulated and 3,419 downregulated genes. KEGG pathway analysis highlighted modifications in nitrogen metabolism (24 genes), photosynthesis (41 genes), hormone signaling and tillering (222 genes), and cell wall and amino acids biosynthesis (365 genes). LC-MS/MS metabolomic profiling identified substantial increases in key amino acids, alkaloids, and phytohormones in LY9-treated rice roots. Notably, tryptophan and its derivatives showed more than 2-fold increases, suggesting enhanced auxin biosynthesis potential. The study revealed intricate molecular mechanisms underlying LY9-mediated growth promotion, particularly through modulation of nitrogen metabolism and hormone signaling pathways. These findings demonstrate the potential of LY9 as a sustainable soil amendment for improving rice productivity and provide valuable insights into the molecular basis of plant-fungal interactions in agricultural systems.