Fungal cellulose decomposition : Insights into decomposition strategies using spectroscopic and molecular approaches

Cellulose is the most abundant biopolymer on Earth and a major reservoir of organic carbon in terrestrial ecosystems. In forests, much of this cellulose originates from wood and is decomposed by saprotrophic basidiomycetes. These fungi are traditionally classified as white rot or brown rot species based on their decay mechanisms in lignocellulosic substrates. Whether these functional categories remain distinct when lignin is absent remains unresolved. In this thesis, transcriptomic and Raman spectroscopic data from fungi cultivated on crystalline cellulose are integrated to evaluate decay type differentiation under cellulose only conditions, with emphasis on nitrogen availability and temporal dynamics. Comparative transcriptomic analyses show that cellulose decay strategies form a continuum rather than discrete white rot and brown rot groups. A conserved set of genes is consistently expressed across fungi under cellulose conditions, indicating a shared transcriptional program for cellulose utilization. This conserved response is dominated by oxidative mechanisms, with widespread upregulation of lytic polysaccharide monooxygenases across all taxa. In contrast, brown rot fungi display a distinct and reproducible transcriptional signature characterized by upregulation of specific oxidoreductases, transporters, and monooxygenases lacking cellulose binding domains. This pattern indicates that, despite multiple evolutionary origins, brown rot fungi have convergently acquired similar gene networks specialized for oxidation driven disruption of crystalline cellulose.White rot fungi exhibited greater transcriptional plasticity, with cellulolytic responses strongly influenced by nitrogen availability. A comparable nitrogen effect was also observed in Coniophora puteana, suggesting that this species does not conform to a canonical brown rot strategy and retains functional features typically associated with white rot fungi, including the expression of cellobiohydrolases. Litter decomposers, soft rot fungi, and fungi with unresolved decay strategies showed mixed transcriptional profiles that combine conserved cellulose response genes with lineage specific regulation, further challenging strict decay type classifications. Raman spectroscopy provided a substrate centered view of cellulose modification and captured biochemical changes not reflected in gene expression alone. Raman features associated with cellulose oxidation and crystallinity were informative, with the high frequency spectral region contributing strongly to differentiation among decay trajectories. Raman signatures consistently reflected nitrogen availability and time.Machine learning applied to integrated transcriptomic and Raman datasets improved discrimination of decay strategies and identified key molecular and spectral features underlying functional divergence. Together, these results show that white rot and brown rot strategies remain partially distinguishable on crystalline cellulose, but that their boundaries are dynamic and context dependent.