(1) Objective: The biosynthesis of medicinal secondary metabolites in Dendrobium nobile Lindl. is regulated by complex environmental, hormonal, and microbial interactions. However, the mechanisms by which subtle variations in plant elevation shape metabolite accumulation through plant–microbe–hormone networks remain largely unexplored. (2) Methods: We conducted a multi-omics investigation of D. nobile cultivated under simulated wild conditions at four elevation gradients (347–730 m) in Chishui, China. High-throughput transcriptome sequencing and ITS-based fungal community profiling were combined with hormone quantification and functional prediction (FUNGuild), enabling integrated analysis of hormone pathway activation, microbial structure–function dynamics, and dendrobine levels. (3) Reults: This study systematically investigated D. nobile cultivated under simulated wild conditions across four elevation gradients (347–730 m) in the Danxia region of Chishui, China. We identified a dual regulatory mechanism underlying the elevation-dependent accumulation of dendrobine alkaloids, involving both plant hormone signaling and endophytic fungal communities. Transcriptomic analyses revealed coordinated upregulation of key hormone pathway genes, including DELLA, PYR/PYL, SnRK2, COI1-JAZ-MYC2, and NPR1-TGA, particularly in CY01Y samples at 670 m elevation from ChiYan base in Chishui city, which corresponded to the highest dendrobine content. Concurrently, functional prediction of the ITS-based fungal sequencing data revealed that CY01Y harbored a stable, functionally enriched fungal community dominated by saprotrophs, fungal parasites, and plant pathogens. (4) Conclusions: Through integrative hormone profiling, gene expression, and microbial function analysis, we propose that elevation-induced environmental cues reshape hormone pathways both directly and indirectly via microbial feedback. Specific microbial taxa were identified as potential modulators of hormone signaling and secondary metabolism. The coordinated interaction between plant hormones and endophytic fungi supports a hormone–microbiome–metabolite network that dynamically regulates dendrobine biosynthesis in response to micro-elevation variation.

Objective: To explore the mechanism by which Schizophyllum commune elevates dendrobine accumulation in Dendrobium nobile, and verify whether cellulase derived from this fungus triggers jasmonate biosynthesis to mediate the regulation of alkaloid production. Methods: Endophytic fungi were isolated from D. nobile stems via tissue block isolation and identified by ITS sequencing. A plant–fungus symbiotic system was established with axenic plantlets. Dual RNA seq transcriptomic analysis, RT qPCR, pharmacological interventions with methyl jasmonate (MeJA) and the JA biosynthesis inhibitor salicylhydroxamic acid (SHAM) and Extracellular cellulase activities assays was performed. Results: In this study, none of 29 endophytic fungal strains from D. nobile stems produced dendrobine independently. Symbiotic screening subsequently identified Schizophyllum commune CY01 1H (SC) as the best strain that significantly increased dendrobine accumulation in D. nobile plantlets. Dual RNA seq revealed that SC colonization substantially activated jasmonic acid (JA) biosynthesis, accompanied by marked upregulation of the key biosynthetic gene DnLOX2. In contrast, downstream JA-signaling components exhibited an atypical transcriptional pattern, DnJAR was downregulated, whereas DnJAZ was upregulated. These results suggest that SC colonization induces a reconfiguration of JA signaling that may contribute to the maintenance of symbiotic homeostasis. In the fungus, cellulase-encoding genes were significantly induced. Experimental verification that MeJA promoted dendrobine accumulation, whereas SHAM suppressed it, and SC symbiosis partially mitigated this suppression. Stem section assays showed dynamic increases in extracellular cellulase activities (endoglucanase, cellobiohydrolase, β glucosidase), peaking at day 19, with endoglucanase being the highest. Conclusions: These findings support a cross-regulatory model in which S. commune CY01-1H induces cellulolytic enzyme production during colonization, coinciding with host JA-biosynthetic activation and JA-signaling reprogramming, ultimately enhancing dendrobine accumulation. This study provides integrated evidence from fungal and host transcriptomes and enzymatic assays, expanding our understanding of endophyte-mediated regulation of medicinal plant metabolism. S. commune CY01 1H represents a promising biostimulant for sustainable improvement of dendrobine yield in cultivated D. nobile.