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

Ahlawat, Ashish LU orcid (2026)
Abstract
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... (More)
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.
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Abstract (Swedish)
Cellulosa är den vanligaste biopolymeren på jorden och en viktig reservoar av organiskt kol i terrestra ekosystem. I skogar kommer mycket av denna cellulosa från trä och bryts ner av saprotrofa basidiomyceter. Dessa svampar klassificeras traditionellt som vitröta eller brunröta baserat på deras sönderfallsmekanismer i lignocellulosasubstrat. Huruvida dessa funktionella kategorier förblir distinkta när lignin saknas är fortfarande oklart. I denna avhandling integreras transkriptomiska och Ramanspektroskopiska data från svampar odlade på kristallin cellulosa för att utvärdera differentiering av sönderfallstyper under enbart cellulosaförhållanden, med betoning på kvävetillgänglighet och tidsmässig dynamik. Jämförande transkriptomiska analyser... (More)
Cellulosa är den vanligaste biopolymeren på jorden och en viktig reservoar av organiskt kol i terrestra ekosystem. I skogar kommer mycket av denna cellulosa från trä och bryts ner av saprotrofa basidiomyceter. Dessa svampar klassificeras traditionellt som vitröta eller brunröta baserat på deras sönderfallsmekanismer i lignocellulosasubstrat. Huruvida dessa funktionella kategorier förblir distinkta när lignin saknas är fortfarande oklart. I denna avhandling integreras transkriptomiska och Ramanspektroskopiska data från svampar odlade på kristallin cellulosa för att utvärdera differentiering av sönderfallstyper under enbart cellulosaförhållanden, med betoning på kvävetillgänglighet och tidsmässig dynamik. Jämförande transkriptomiska analyser visar att cellulosansönderfallsstrategier bildar ett kontinuum snarare än diskreta vitröta- och brunrötagrupper. En konserverad uppsättning gener uttrycks konsekvent över svampar under cellulosaförhållanden, vilket indikerar ett gemensamt transkriptionsprogram för cellulosautnyttjande. Detta konserverade svar domineras av oxidativa mekanismer, med utbredd uppreglering av lytiska polysackaridmonooxygenaser över alla taxa. Brunrötesvampar uppvisar däremot en distinkt och reproducerbar transkriptionssignatur som kännetecknas av uppreglering av specifika oxidoreduktaser, transportörer och monooxygenaser som saknar cellulosabindande domäner. Detta mönster indikerar att brunrötesvampar, trots flera evolutionära ursprung, konvergerande har förvärvat liknande gennätverk specialiserade för oxidationsdriven störning av kristallin cellulosa.
Vitrötesvampar uppvisade större transkriptionsplasticitet, med cellulolytiska svar starkt påverkade av kvävetillgänglighet. En jämförbar kväveeffekt observerades också i Coniophora puteana, vilket tyder på att denna art inte överensstämmer med en kanonisk brunrötesstrategi och behåller funktionella egenskaper som vanligtvis förknippas med vitrötesvampar, inklusive uttrycket av cellobiohydrolaser. Strönedbrytare, mjukrötesvampar och svampar med olösta nedbrytningsstrategier uppvisade blandade transkriptionsprofiler som kombinerar konserverade cellulosaresponsgener med härstamningsspecifik reglering, vilket ytterligare utmanar strikta klassificeringar av nedbrytningstyper. Ramanspektroskopi gav en substratcentrerad bild av cellulosamodifiering och fångade biokemiska förändringar som inte enbart återspeglas i genuttryck. Ramanegenskaper associerade med cellulosaoxidation och kristallinitet var informativa, där det högfrekventa spektralområdet starkt bidrog till differentieringen mellan sönderfallstrajektorier. Ramansignaturer återspeglade konsekvent kvävetillgänglighet och tid.
Maskininlärning tillämpad på integrerade transkriptomiska och Raman-dataset förbättrade urskiljningen av sönderfallsstrategier och identifierade viktiga molekylära och spektrala egenskaper som ligger till grund för funktionell divergens. Tillsammans visar dessa resultat att vitröta- och brunrötastrategier fortfarande delvis kan särskiljas på kristallin cellulosa, men att deras gränser är dynamiska och kontextberoende. (Less)
Please use this url to cite or link to this publication:
author
supervisor
opponent
  • Docent Lundell, Taina Kristina, Faculty of Agriculture and Forestry, University of Helsinki, Finland
organization
alternative title
Nedbrytning av svampcellulosa : 83 Insikter i nedbrytningsstrategier med hjälp av spektroskopiska och molekylära metoder
publishing date
type
Thesis
publication status
published
subject
keywords
white rot fungi, brown rot fungi, Raman spectroscopy, transcriptomics
pages
78 pages
publisher
Lund University
defense location
Blue Hall, Department of Biology
defense date
2026-03-13 09:00:00
ISBN
978-91-8104-790-5
978-91-8104-789-9
language
English
LU publication?
yes
id
cbdd4f78-72a4-484d-bb01-970b2ca18e7a
date added to LUP
2026-02-05 10:50:19
date last changed
2026-02-18 10:41:24
@phdthesis{cbdd4f78-72a4-484d-bb01-970b2ca18e7a,
  abstract     = {{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.<br/>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.<br/>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.<br/>}},
  author       = {{Ahlawat, Ashish}},
  isbn         = {{978-91-8104-790-5}},
  keywords     = {{white rot fungi; brown rot fungi; Raman spectroscopy; transcriptomics}},
  language     = {{eng}},
  month        = {{03}},
  publisher    = {{Lund University}},
  school       = {{Lund University}},
  title        = {{Fungal cellulose decomposition : Insights into decomposition strategies using spectroscopic and molecular approaches}},
  url          = {{https://lup.lub.lu.se/search/files/241479196/Thesis_Ashish_Ahlawat_LUCRIS.pdf}},
  year         = {{2026}},
}