Our ongoing research subjects include lignocellulose and waste biomass bioconversions, biofuel production, forest fungal interactions, metabolites and wood decay mechanisms, and fungal lifestyle omics on wood and lignocelluloses.
Tuulia Mali's PhD defence


Tuulia Mali defended her Doctoral Dissertation on October 21st, 2021, on the topic 

"Interactions of Basidiomycota brown rot and white rot fungi: temporal and spatial effects in decay metabolism and wood degradation


Electronic version of the thesis book is available at

Polyporales fungal interactions

Aim of the Academy project Fungcolife is to reveal the biochemical and genetic responses initiated when diverse species of wood-decay fungi are interacting. The project integrates omics data with interaction experiments on natural substrates (wood and other plant materials).


Mali T, Kuuskeri J, Shah F, Lundell TK (2017) Interactions affect hyphal growth and enzyme profiles in combinations of coniferous wood-decaying fungi of Agaricomycetes. PLoS One 27;12(9):e0185171.


Waste lignocellulose bioconversions

Research project focuses on bioconversion of lignocellulos waste materials by Polyporales fungi. Main efforts have been put in designing a single-step single species ethanol bioconversion method. This research aims to better understand the simultaneous saccharification and fermentation by studying the gene expression and regulation of wood degradation and core metabolism together with metabolite profiles. One of the aims is also to design bioreactors suited for solid state cultivations.


Mäkinen MA, Risulainen N, Mattila H, Lundell TK (2018) Transcription of lignocellulose-decomposition associated genes, enzyme activities and production of ethanol upon bioconversion of waste substrate by Phlebia radiata. Appl Microbiol Biotechnol 102(13):5657-5672. 

Mattila H, Kuuskeri J, Lundell T (2017) Single-step, single-organism bioethanol production and bioconversion of lignocellulose waste materials by phlebioid fungal species. Bioresour Technol 225:254-261.

Genomics, transcriptomics and proteomics

We have sequenced the nuclear and mitochondrial genomes of the white rot fungus Phlebia radiata in collaboration with the DNA Sequencing and Genomics laboratory (Institute of Biotechnology, University of Helsinki). The nuclear genome has been functionally annotated and especially genes involved with plant cell wall degradation have been manually curated. Comparative genomic analyses between P. radiata and other closely related phlebioid species are ongoing. The transcriptome and proteome of P. radiata growing on solid spruce wood has been analyzed confirming that the fungus expresses and produces all the hydrolytic and oxidative enzymes necessary for a white rot type of decay.


Kuuskeri J, Häkkinen M, Laine P, Smolander O-P, Tamene F, Miettinen S, Nousiainen P, Kemell M, Auvinen P, Lundell T (2016) Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata: growth on spruce wood and decay effect on lignocellulose. Biotech Biofuels 9:192.

Salavirta H, Oksanen I, Kuuskeri J, Mäkelä M, Laine P, Paulin L, Lundell T (2014) Mitochondrial genome of Phlebia radiata is the second largest (156 kbp) among fungi and features signs of genome flexibility and recent recombination events. PLoS One 13;9(5):e97141.