Our ongoing research subjects comprise forest fungal interactions, metabolites and wood decay mechanisms, and fungal omics on wood and lignocelluloses.
Polyporales fungal interactions

The aim of the ongoing research project ForMic (2022-2026, funded by the Research Council of Finland) is to investigate fungal interactions in co-cultures and in forest microbiomes, by means of genomics, transcriptomics and bioactivity measurements. This research is tightly linked to the earlier project Fungcolife (2015-2019, Research Council of Finland) which looked into the biochemical and genetic responses initiated when diverse species of wood-decay fungi are interacting. These projects integrate omics data with interaction experiments on natural substrates (wood and other plant materials).


Mali T, Laine K, Hamberg L, Lundell T (2023) Metabolic activities and ultrastructure imaging at late-stage of wood decomposition in interactive brown rot - white rot fungal combinations. Fungal Ecology 61, 101199. https://doi:10.1016/j.funeco.2022.101199

Mali T (2021) Interactions of Basidiomycota brown rot and white rot fungi: temporal and spatial effects in decay metabolism and wood degradation. University of Helsinki.

Mäki M, Mali T, Hellén H, Heinonsalo J, Lundell T, Bäck J (2021) Deadwood substrate and species-species interactions determine the release of volatile organic compounds by wood-decaying fungi. Fungal Ecology 54, 101106. https://doi:10.1016/j.funeco.2021.101106

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

Previous research projects studied bioconversion of lignocellulos waste materials by Polyporales fungi. Main efforts were put into designing a single-step single species ethanol bioconversion method. This research aimed at better understanding the simultaneous saccharification and fermentation by studying the gene expression and regulation of wood degradation and core metabolism together with metabolite profiles.


Mattila HK (2020) Phlebia radiata as an ethanol producing fungus: conversion of lignocelluloses and metabolic regulation under hypoxia. University of Helsinki.

Mattila HK, Mäkinen M, Lundell T (2020) Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus. Biotechnology for Biofuels 13, 26. https://doi:10.1186/s13068-020-01677-0

Mattila H, Kačar D, Mali T, Lundell T (2018) Lignocellulose bioconversion to ethanol by a fungal single-step consolidated method tested with waste substrates and co-culture experiments. AIMS Energy 6, 866–879. https://doi:10.3934/energy.2018.5.866

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  and the brown rot fungus Fomitopsis pinicola in collaboration with the DNA Sequencing and Genomics laboratory (Institute of Biotechnology, University of Helsinki). The genome sequence of F. pinicola is still under processing. 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. In addition, studies of gene expression under varying conditions are being conducted.


Österman-Udd J, Lundell TK (2023) Complete mitochondrial genome sequence of the Agaricomycetes brown rot fungus Fomitopsis pinicola isolate FBCC1181. Microbiology Resource Announcements 12, e00503-23. https://doi:10.1128/MRA.00503-23

Mäkinen M, Kuuskeri J, Laine P, Smolander O-P, Kovalchuk A, Zeng Z, Asiegbu FO, Paulin L, Auvinen P, Lundell T (2019) Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi. BMC Genomics 20, 430. https://doi:10.1186/s12864-019-5817-8

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.