Oxford Nanopore Technologies Sequencing and Targeted Amino Acid Metabolomics Reveal Spatially Segregated Microbial Hijacking and Metabolic Collapse During <i>Trichoderma</i> Infection of Golden Ear Mushroom

This study combines Oxford Nanopore (ONT) third-generation sequencing with targeted amino acid metabolomics to elucidate the mechanisms underlying the structural and metabolic responses of the microbial community in Golden Ear Mushroom (<i>Naematelia sinensis</i>) during <i>Trichoderma</i> infection. By comparing healthy tissue (MOCK), adjacent healthy areas (HAF) and the core lesion area (DiR), the results indicate that pathogen infection significantly reduces bacterial community diversity, with a progressive decline observed across these regions. In the DiR region, the fungal community underwent significant restructuring, with the abundance of the <i>Trichoderma</i> genus (<i>T. lixii</i> and <i>T. afroharzianum</i>) rising to over 45%, whilst that of host symbiotic fungi (<i>Stereum</i> and <i>Tremella</i>) decreased by 50-60%. Metabolomic analysis indicated that levels of various amino acids and antioxidant-related metabolites were significantly reduced in the host tissue of the DiR region, suggesting that amino acid metabolism was inhibited. Concurrently, changes were observed in certain metabolites associated with nitrogen metabolism (e.g., L-glutamine). KEGG analysis further revealed that amino acid biosynthesis and D-amino acid metabolic pathways were inhibited, whilst ABC transporters and arginine/proline metabolic pathways were activated. All metabolic changes originated from the host fungal tissue itself, rather than from commensal microorganisms. In summary, <i>Trichoderma</i> may promote the infection process by disrupting the host microbial community and metabolic networks, providing a theoretical basis for understanding the mechanisms of fungal diseases and their control.