Bamboo Inhabiting Fungi and Their Damage to the Substrate
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Bamboo inhabiting fungi and their damage to the substrate Dissertation zur Erlangung der Würde des Doktors der Naturwissenschaften des Fachbereichs Biologie, der Fakultät für Mathematik, Informatik und Naturwissenschaften der Universität Hamburg vorgelegt von Dongsheng Wei aus China Hamburg 2014 USDA Forest Service Forest Products L a bo r a t o r y Date: January 21, 2014 Subject: English Assessment by a Native Speaker www.fpl.fs.fed.us To: University of Hamburg, Ph.D. Dissertation Committee for Dongsheng Wei As a native speaker of the English language, I have checked and made minor editorial corrections to the Ph.D. dissertation entitled, Bamboo inhabiting fungi and their damage to the substrate, authored by Dongsheng Wei. I find that this dissertation is very well written and fulfills the requirements for an English dissertation. Respectively, Daniel Joseph Yelle, Ph.D. Research Forest Products Technologist 1 GIFFORD PINCHOT DRIVE • MADISON, WISCONSIN • 53726-2398 PHONE 608 231-9200 • FAX 608 231-9592 • TDD 608 231-9544 Acknowledgements I would like first to express my greatest gratitude to my supervisor, Prof. Dr. Olaf Schmidt, for giving me the opportunity to work in his laboratory and for guidance in finishing this research work at the Centre for Wood Science, University of Hamburg. The completion of this work would not be possible without his assistance and patience. Furthermore, I would like to express my sincere gratitude to Prof. em. Dr. Dr. h.c. mult. Walter Liese for his endless supply of information and literature about bamboo. I am confident that our friendship will be never ending. Many thanks are to Dr. Uwe Schmitt, Dr Jürgen Plus, PD Dr. Gerald Koch, Dr. Ron Janzon, Tanja Potsch, Daniela Paul, Karin Brandt, Anne-Marie Wettich, Sergej Kaschuro, Anna Knöpfle and Nicole Erasmy at the Thünen Institute for their technical help in lab. They have offered kind and helpful suggestions throughout the duration of the experimental work. Special thanks are to Dr. Mathias Rehbein and Marie-Therese Lenz not only for helping me with fungal degradation experiment and data analysis but also for many tips beyond research that were useful to lead a happy life. I will not forget them for their immense support during my life in Hamburg. My sincere thanks are due to former and current PhD candidates, Thi Kim Hong Tang, Mohsen Bahmani, Stephanie Helmling, Yongshun Feng for providing their constant support and a stimulating and fun environment in which to learn and grow. I gratefully acknowledge is extended to Prof. Dr. Robert A. Samson who gave me two times chances in 2011 to do fungal taxonomy research at the Fungal Biodiversity Centre(CBS), Institute of the Royal Netherlands Academy of Arts and Science. To Dr. Jos Houbraken, Dr. Jan Dijksterhuis, Neriman Yilmaz I am very grateful for their help to carry out experiments as well as for the great working environment. Thanks are also to the Federation of European Microbiological Societies (FEMS) for the grant during my first stay in the Netherlands. I gratefully acknowledge the German Academic Exchange Service (DAAD) for the financial support during my PhD studies. Last but not least, I would like to thank my parents and my three sisters for their continuous moral support, encouragement and love which has helped me enormously. I Table of contents Acknowledgements ............................................................................................................... I Table of contents ................................................................................................................. II Abstract/Zusammenfassung ............................................................................................... V List of abbreviations .......................................................................................................... IX 1 Introduction ....................................................................................................................... 1 1.1 Fungi ............................................................................................................................ 1 1.1.1 Characterization ..................................................................................................... 1 1.1.2 Classification ......................................................................................................... 2 1.1.3 Identification.......................................................................................................... 4 1.1.4 Important genera of bamboo inhabiting fungi ......................................................... 6 1.2 Bamboo ........................................................................................................................ 9 1.2.1 Biology ................................................................................................................ 10 1.2.2 Significance ......................................................................................................... 14 1.2.3 Uses ..................................................................................................................... 15 1.2.4 Damage by fungi and insects ................................................................................ 19 1.3 Factors affecting fungal degradation tests.................................................................... 21 1.4 Modern techniques to study the morphology of degraded bamboo .............................. 22 1.4.1 Scanning electron microscopy (SEM) .................................................................. 23 1.4.2 Confocal laser scanning microscopy (CLSM) ...................................................... 23 1.4.3 Transmission electron microscopy (TEM) ............................................................ 24 1.4.4 Ultraviolet microspectrophotometry (UMSP) ....................................................... 24 1.4.5 Fourier transform infrared (FTIR) spectroscopy ................................................... 25 1.4.6 X-ray photoelectron spectroscopy (XPS) .............................................................. 26 1.5 Aim of the study ......................................................................................................... 27 2 Material and Methods ..................................................................................................... 28 2.1 Molecular identification of bamboo inhabiting fungi ................................................... 28 2.1.1 Collection of infected bamboo samples ................................................................ 28 2.1.2 Isolation and purification of fungi ........................................................................ 28 2.1.3 DNA extraction and amplification by polymerase chain reaction (PCR) ............... 29 2.1.4 PCR products examination and purification ......................................................... 29 2.1.5 Sequencing and sequence analysis ....................................................................... 29 II 2.2 Identification of Penicillium and Aspergillus isolates from bamboo ............................ 30 2.2.1 Morphological identification of Penicillium and Aspergillus isolates .................... 31 2.2.2 Molecular identification of Penicillium and Aspergillus isolates ........................... 31 2.3 Blue-stain test ............................................................................................................. 32 2.3.1 Used blue-stain fungi ........................................................................................... 32 2.3.2 Investigated bamboo ............................................................................................ 32 2.3.3 Blue-stain test set-up ............................................................................................ 33 2.3.4 Assessment of hyphal growth and chlamydospores in bamboo ............................. 33 2.4 Degradation tests ........................................................................................................ 34 2.4.1 Preserving jar test................................................................................................. 34 2.4.1 Fungus cellar test ................................................................................................. 36 2.4.3 Kolle flask test ..................................................................................................... 37 2.4.4 Vermiculite test .................................................................................................... 40 2.4.5 Field test .............................................................................................................. 42 2.5 Chemical analysis of bamboo after degradation .......................................................... 43 2.5.1 Degraded bamboo samples ................................................................................... 43 2.5.2 Acetone and ethanol extraction ............................................................................ 43 2.5.3 Hydrolysis ........................................................................................................... 44 2.5.4 HPAEC-borate analysis ....................................................................................... 45 2.6 Transmission electron microscopy (TEM) studies of degraded bamboo ...................... 46 2.7 Ultraviolet microspectrophotometry (UMSP) studies of degraded bamboo.................. 46 2.7.1 Light microscopic analysis ..................................................................................