Transcriptome Analysis of Genes and Metabolic Pathways Associated with Caffeine Degradation in Desarmillaria tabescens

Caffeine contamination poses significant risks to both ecosystems and human health. Conventional remediation approaches, including adsorption and extraction, remain costly and lack substrate specificity, emphasizing the relevance of microbial degradation. The fungal species Desarmillaria tabescens demonstrated strong caffeine-degrading capacity under optimized conditions: malt extract medium supplemented with 900 mg/L caffeine at 28 °C and pH 8. HPLC and UPLC-MS/MS analyses revealed critical intermediates such as theobromine and 3-methylxanthine, indicating a branched catabolic route involving N-demethylation and C8 oxidation. Transcriptomic profiling identified stage-specific differential expression, with nine cytochrome P450 genes consistently upregulated. On this basis, a three-phase regulatory framework—“Stress-Degradation-Homeostasis”—was proposed, delineating the coordination of detoxification, energy metabolism, and secondary metabolic pathways. The elucidation of this mechanism not only advances understanding of D. tabescens caffeine metabolism but also provides genetic resources for bioremediation and the development of low-caffeine products.