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Monitoring of Fungal Growth and Degradation of Wood Monitoring of Fungal Growth and Degradation of Wood OUTI NIEMENMAA Division of Microbiology Department of Applied Chemistry and Microbiology Viikki Biocenter, University of Helsinki Finland Academic Dissertation in Microbiology To be presented, with the permission of the Faculty of Agriculture and Forestry of the University of Helsinki, for public criticism in the Auditorium 1041 at Viikki Biocenter (Viikinkaari 5, Helsinki) on April 25th at 12 o’clock noon Helsinki 2008 Supervisor Professor Annele Hatakka Department of Applied Chemistry and Microbiology University of Helsinki, Finland Reviewers Professor Leif Jönsson Biochemistry, Department of Chemistry and Biochemical Sciences Karlstad University, Karlstad, Sweden Professor Anne-Christine Ritschkoff VTT Espoo, Finland Opponent Docent Kristiina Kruus VTT Espoo, Finland Printed Yliopistopaino, 2008, Helsinki, Finland Layout Otso Koski ISSN 1795-7079 ISBN 978-952-10-4649-0 paperback ISBN 978-952-10-4650-6 pdf version, http://ethesis.helsinki.fi e-mail outi.niemenmaa@helsinki.fi Cover photo: Brown-rotted timber from an old wooden cabin in Polvijärvi 2 Contents List of original publications ..................................................................................................5 The author’s contribution ......................................................................................................5 Abbreviations ........................................................................................................................6 Abstract .................................................................................................................................7 Tiivistelmä (Abstract in Finnish) ..........................................................................................8 1 INTRODUCTION ...........................................................................................................10 1.1 Wood, lignocelluloses and lignin ..............................................................................10 1.1.1 Lignocellulosic biomass .....................................................................................10 1.1.2 Cellulose .............................................................................................................10 1.1.3 Hemicellulose .....................................................................................................10 1.1.4 Lignin ................................................................................................................. 11 1.1.5 Synthetic lignin DHP (dehydrogenative polymerizate) .....................................13 1.2 Degradation of wood by fungi ..................................................................................14 1.2.1 Types of wood decay ..........................................................................................14 1.2.2 White-rot fungi ...................................................................................................15 1.2.3 Extracellular lignin-degrading enzymes .............................................................16 1.2.4 Brown-rot fungi ..................................................................................................19 1.3 Low-molecular weight compounds and radicals in the degradation of wood ..........21 1.4 Analysis of fungal growth and activity .....................................................................23 1.4.1 Enzyme production ............................................................................................24 1.4.2 Radiorespirometric methods based on 14C-labelled compounds .......................25 1.4.3 Biomass quantification by ergosterol analysis ...................................................26 2 OBJECTIVES OF THE PRESENT STUDY ...................................................................33 3 MATERIALS AND METHODS .....................................................................................34 3.1 Methods used in publications I-IV ............................................................................34 3.2 Other methods ...........................................................................................................34 3.2.1 Liquid flask cultures ...........................................................................................34 3.2.2 Separation of enzyme proteins ...........................................................................34 3.3 Statistical analysis .....................................................................................................36 4 RESULTS AND DISCUSSION .......................................................................................38 4.1 Production of lignin-modifying enzymes of Phlebia radiata and Phlebia tremellosa .38 4.1.1 Culture conditions for the production of lignin-modifying enzymes ................38 4.1.2 Production of enzymes by P. radiata ................................................................38 4.1.3 Production of enzymes by P. tremellosa ...........................................................38 4.1.4 Separation of enzymes from P. radiata .............................................................39 4.1.5 Separation of enzymes from P. tremellosa ........................................................42 4.1.6 Characterization of enzymes ..............................................................................42 4.2 Degradation of 14C-(ring)-labelled DHP by Phlebia spp. (I) ....................................44 4.3 Demethoxylation of lignin model compounds (II, III) ...........................................45 4.3.1 White-rot fungi P. radiata and P. chrysosporium (II) .........................................46 4.3.2 Brown-rot fungi G. trabeum and P. placenta (III).............................................46 4.4 Ergosterol as a measure of fungal growth (II, III, IV) ..............................................48 3 4.4.1 Ergosterol as an indicator of fungal biomass .....................................................48 4.4.2 Correlation of dry weight and ergosterol content of fungal liquid cultures (IV) 48 4.4.3 Ergosterol as a measure of growth (II, III, IV) ...................................................51 4.4.4 Conversion factor in measurements of biomass .................................................52 4.4.5 Use of conversion factors in wood block and agar cultures ...............................54 4.4.6 Phlebia radiata monitored by different methods ..............................................55 5 SUMMARY .....................................................................................................................56 6 CONCLUSIONS .............................................................................................................57 7 ACKNOWLEDGEMENTS .............................................................................................58 8 REFERENCES ................................................................................................................60 4 List of original publications This thesis is based on the following original publications, referred to in the text by their Roman numerals (I-IV). In addition, unpublished data are also presented. I Vares, T., Niemenmaa, O. and Hatakka, A. 1994. Secretion of ligninolytic enzymes and mineralization of 14C-ring-labelled synthetic lignin by three Phlebia tremellosa strains. Applied and Environmental Microbiology 60:569-575 II Niemenmaa, O., Uusi-Rauva, A. and Hatakka, A. 2006. Wood stimulates the 14 demethoxylation of [O CH3]-labelled lignin model compounds by the white-rot fungi Phanerochaete chrysosporium and Phlebia radiata. Archives of Microbiology 185:307-315 III Niemenmaa, O., Uusi-Rauva, A. and Hatakka, A. 2008. Demethoxylation of 14 [O CH3]-labelled lignin model compounds by the brown-rot fungi Gloeophyllum trabeum and Poria (Postia) placenta. Biodegradation DOI: 10.1007/s10532-007- 9161-3. IV Niemenmaa, O., Galkin, S., Hatakka, A. 2008. Ergosterol contents of some wood- rotting basidiomycete fungi grown in liquid and solid culture conditions. International Biodeterioration & Biodegradation doi:10.1016/j.ibiod.2007.12.009 The original publications are reprinted with the permission of the copyright holders. The author’s contribution I Outi Niemenmaa planned the experiments together with Tamara Vares, and did the laboratory work together with her: culturing of fungi, the enzyme assays from the fungal liquid cultures, enzyme purification with anion-exchange chromatography and characterization of the enzyme with SDS-PAGE and IEF. Outi Niemenmaa conducted the mineralization experiments of 14C-(ring)-labelled synthetic lignin (DHP). Outi Niemenmaa interpreted the results with Tamara Vares. II-IV Outi Niemenmaa planned the experiments and did the laboratory work, except the ergosterol analysis by HPLC, interpreted the results, analysed the data and wrote the articles. 5 Abbreviations AAO aryl alcohol oxidase (EC 1.1.3.7) ABTS 2,2’-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) ADMS asparagine ammonium nitrate dimethylsuccinate medium ATP adenosine triphosphate CBQ cellobiose:quinone oxidoreductase (EC 1.1.5.1) CO2 carbon dioxide DHP dehydrogenation polymerizate, synthetic lignin DMF dimethyl formamide dw dry weight EG endo-1,4-β-glucanase (EC 3.2.1.4) FPLC fast protein liquid chromatography FT-NIR Fourier transform near-infrared (spectroscopic technique) GC-MS gas chromatography - mass spectrometry GLOX glyoxal oxidase (EC 1.2.3.5) HBT 1-hydroxybenzotriazole HC high glucose (1.0%) HN high-nutrient nitrogen medium, containing
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