Miia Mäkelä

I am Principal Investigator and Academy of Finland Research Fellow in the Fungal Genetics and Biotechnology group that studies plant biomass modifying enzymes from asco- and basidiomycete fungi. The research focuses on various aspects of fungal molecular biology and enzymology. Lignocellulose, particularly lignin, degradation has been the long-term interest at the Department of Microbiology. Our research has provided strong international contribution in the field of fungal and enzymatic degradation of lignin and lignocellulose.

The most recent research addresses the molecular level regulation of the plant biomass degradation process in basidiomycete fungi as well as valorization of lignin-rich industrial waste of second generation biofuel plants to higher value products.

In addition, our research topics include functional genomics of plant biomass degrading fungi from various biotopes with different and complementary points of view:

i) Genome mining and characterization of novel plant biomass modifying activities and fungal carbon metabolism

ii) Elucidating the difference in plant biomass strategies between ascomycetes and basidiomycetes

iii) Heterologous production of novel catalysts for lignin valorisation

Current projects:

1. Exploring the regulatory system that controls plant biomass degradation in basidiomycete white rot fungi (ESCaPADE), Academy of Finland (2017-2022)
2. Fuel and chemicals from lignin through enzymatic and chemical conversion (FALCON) EU-H2020 (2017-2020)
3. Experimental validation of a central carbon metabolic models in Aspergillus niger to enable metabolic engineering of this fungal cell factory, Environmental Molecular Sciences Laboratory (EMSL), USA (2018-2019)
4. Dissecting the central metabolic network of Aspergillus niger during growth on plant biomass, EMSL, USA (2019-2020)
5. Validation of metabolic models, extrapolated from the reference sugar catabolism genetic network of Aspergillus niger by using an orthology-based approach, of evolutionarily diverse fungi, Joint Genome Institute (JGI-DOE)-EMSL, USA (2018-2020)
6. Dissecting intraspecies diversity in fungal wood decay, JGI-DOE-EMSL, USA (2015-2019)
7. Enzymes for selective cleavage of lignin (Ph.D. project of Mila Marinović)

Previous projects:

1. Colony plasticity of filamentous fungi, EMSL, USA (2016-2017)
2. Optimized esterase biocatalysts for cost-effective industrial production (OPTIBIOCAT) EU-FP7, KBBE-.2013.3.3-04, (2013-2017)
3. Sustainable biomass conversions by highly efficient catalytic processes (SuBiCat) EU-FP7, Marie Curie-ITN, (2013-2017)
4. Test centers for green energy solutions - Biorefineries and business needs, Norcid Council of Ministers (2014-2015)
5. Plant biomass degradation in Dichomitus squalens (Ph.D. project of Sara Casado López)
6. Plant biomass modifying enzymes of ascomycete fungi  (Ph.D. project of Sadegh Mansouri)
7. Basidiomycete cellulolytic enzymes and their applications (Ph.D. project of Johanna Rytioja)
8. How mushrooms feed on sugars (Ph.D. project of Aleksandrina Patyshakuliyeva)

International collaboration:

• Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands: Elucidating the difference in plant biomass strategies between ascomycetes and basidiomycetes. Project members: Miia Mäkelä (PI), Kristiina Hildén (PI), Ronald de Vries (PI), Miaomiao Zhou, Ad Wiebenga, Aleksandrina Patyshakuliyeva

• Concordia University, Montreal, Canada: Dissection of strategies for plant biomass degradation by Dichomitus squalens. Project members: Miia Mäkelä (PI), Adrian Tsang (PI), Kristiina Hildén (PI), Ronald de Vries (PI)

• Joint Genome Institute, USA: Comparative analysis of Aspergilli to facilitate novel strategies in fungal biotechnology. www.eufgen.org

• Joint Genome Institute, USA: Comparative analysis of 3 Pycnoporus species: P. sanguineus, P. coccineus and P. cinnabarinus.

• Joint Genome Institute, USA: Genome of the polypore Obba rivulosa. Project members: Otto Miettinen (coordinator), Kristiina Hildén, Miia Mäkelä, David Hibbett (Clark University, USA), Joseph Spatafora (Oregon State University, USA), Igor Grigoriev (USDA Joint Genome Institute, USA), Kerrie Barry (USDA Joint Genome Institute, USA), Annele Hatakka, see also newspaper article: http://www.hs.fi/tiede/Kiintoisan+k%C3%A4%C3%A4v%C3%A4n+perim%C3%A4+on+avattu/a1410841027710

Teaching:

I am involved in the teaching of bachelor, master and doctoral students in lectures and laboratory courses in microbiology, biotechnology and mycology. I also supervise BSc, MSc and doctoral theses.

Organizer of Microbiology seminars (MBDP doctoral programme, MBDP-302 & MMB-120)

Bachelor courses (in Finnish): Basics in microbiology (MOLE212C), Fungal biology (MMB-701, MYKO251), Microbial biotechnology (YBIOT315)

Master courses (in English): Advanced methods in microbiology (MIKRO510), Production of recombinant proteins (YBIOT565), Fungal biotechnology research methods (MYKO540), Forest microbiology and biotechnology (YBIOT570), Advanced laboratory training at research group (BIOT422)

Collaborator in PhD programme "Criticat CDT" which is a comprehensive and state-of-the-art PhD training programme in catalytic science funded by the UK funding agency EPSRC. PhD programme (2014 - 2022) is hosted by the Universities of St. Andrews, Edinburgh and Heriot-Watt.