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Ericaceae Root Associated Fungi Revealed by Culturing and Culture – Independent Molecular Methods

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Ericaceae Root Associated Fungi Revealed by Culturing and Culture – Independent Molecular Methods a Ericaceae root associated fungi revealed by culturing and culture – independent molecular methods. by Damian S. Bougoure BSc (Hons) Thesis submitted in accordance with the requirements for the degree of Doctor of Philosophy Centre for Horticulture and Plant Sciences University of Western Sydney February 2006 2 ACKNOWLEDGEMENTS Although I am credited with writing this thesis there is a multitude of people that have contributed to its completion in ways other than hitting the letters on a keyboard and I would like to thank them here. Firstly I’d like to thank my supervisor, Professor John Cairney, whose knowledge and guidance was invaluable in steering me along the PhD path. The timing of John’s ‘motivational chats’ was uncanny and his patience particularly, during the writing stage, seemed limitless at times. I’d also like to thank the Australian government for granting me an Australian Postgraduate Award (APA) scholarship, Paul Worden from Macquarie University and the staff from the Millennium Institute at Westmead Hospital for performing DNA sequencing and the National Parks and Wildlife Service of New South Wales and Environmental Protection agency of Queensland for permission to collect the Ericaceae plants. Thankyou to Mary Gandini from James Cook University for showing me the path to a Rhododendron lochiae population through the thick North Queenland rainforest. Without her help and I’d still be pointing the GPS at the sky. Thankyou to the other people in the lab studying mycorrhizas including Catherine Hitchcock, Susan Chambers, Adrienne Williams and particularly Brigitte Bastias with whom I shared an office. Everyone mentioned was generally just as willing as I was to talk about matters other than mycorrhizas. I’d also like to thank David Midgley and Nicole Sawyer, both former members of the research group who remained good friends after they’d moved on. Thanks particularly to Dave who I faced off against many times 3 on the squash court. This was useful in offsetting the fruits of our homebrew enterprise (A science background has more than one use). Thanks also to my friends, George and Peta, who, to my relief at times, knew absolutely nothing of the world of mycorrhizas. They helped me become a resident expert on the clubs of Western Sydney and we enjoyed multiple concerts at such venues as well as the ritual band nights at Hyland Road. I’d also like to thank everyone at the Macaulay Institute in Aberdeen who made an Aussie feel most welcome. Thankyou particularly to Ian Anderson who gave me the opportunity to work in his group and Pamela Parkin who ensured my work there went like clockwork. Thanks also to Ian Alexander from The University of Aberdeen for help with statistical analyses and whose enthusiasm for science was always refreshing. I also thank him for choosing the sunniest day of the year in Scotland to sample in the field. Thankyou to all my family which has recently extended to include a set of in-laws. Dad and Mum have always supported my endeavours, including this PhD, and continue to offer unconditional help whenever they’re called upon, for that I am eternally grateful. Bones and Mizz, thankyou for being model siblings that have always made life outside the lab interesting and worthwhile. Special thanks to my wife, Bec. Without her this thesis would not have been completed. Her love, support, friendship, understanding and patience have helped me every day, particularly the hard ones when doing a PhD in Science seemed like a bad idea. Going 4 home to Bec at Myrtle street after a day in the lab was always something to look forward to when pouring agar plates became too much. Funnily enough, for someone with no biology background, Bec has developed (by no choice of her own) a substantial understanding of ericoid mycorrhizas. Finally, I’d like to dedicate this thesis to my Nana who passed away during my PhD. She once gave me a second chance when I probably didn’t deserve one. Without that chance there’d be no thesis to dedicate to her. Damian Bougoure March 2006 5 I hereby certify that this thesis is my own work and contains no material that has been submitted for the award of any other degree or diploma in any university or any other tertiary institution and, to the best of my knowledge and belief, contains no material previously published or written by another person, except where due reference has been made in the text. Signature:…………………… Date:……………….. Damian Bougoure i TABLE OF CONTENTS Table of Contents ........................................................................................................................... i Abbreviations ............................................................................................................................... vi Abstract......................................................................................................................................... ix CHAPTER 1: General Introduction ........................................................................................... 1 1.1. The plant family Ericaceae............................................................................................... 1 1.2. Fungal endophytes ............................................................................................................ 3 1.3. Ericoid mycorrhizas in Ericaceae.................................................................................... 4 1.4. Other fungal root endophytes of Ericaceae .................................................................... 7 1.5. Community biology of Ericaceae endophytes .............................................................. 12 1.6. Analysis of Ericaceae fungal root endophytes using directly extracted DNA ........... 15 1.7. Research Aims ................................................................................................................. 17 CHAPTER 2: Assemblages of ericoid mycorrhizal and other root-associated fungi from Epacris pulchella (Ericaceae) as determined by culturing and direct DNA extraction from roots .................................................................................................................. 18 2.1. Introduction..................................................................................................................... 18 2.1.1 Diversity of ericoid mycorrhizal fungi ....................................................................... 18 2.1.2 Identification of cultured endophytes ......................................................................... 21 2.1.3 Synthesis of ericoid mycorrhizas in gnotobiotic culture ............................................ 23 2.1.4 Are unculturable ericoid mycorrhizal fungal endophytes present in Ericaceae ii roots?................................................................................................................................... 26 2.1.5 Identification of fungal root endophytes using DNA extracted directly from environmental samples........................................................................................................ 27 2.2. Experimental Procedures ............................................................................................... 34 2.2.1. Collection of plants and isolation of fungal cultures ................................................ 34 2.2.2. Testing for ericoid mycorrhiza formation ................................................................. 35 2.2.3. DNA extraction.......................................................................................................... 36 2.2.4. ITS amplification, cloning, RFLP analysis and sequence analysis........................... 36 2.2.5. ITS amplification for DGGE analysis ....................................................................... 39 2.2.6. DGGE analysis.......................................................................................................... 40 2.3. Results .............................................................................................................................. 41 2.3.1. ITS-RFLP analysis of cultured fungal assemblages and clones from directly extracted DNA ..................................................................................................................... 41 2.3.2. Sequence analysis of ITS RFLP-types ....................................................................... 49 2.3.3. Ericoid mycorrhiza formation ................................................................................... 50 2.3.4. Phylogenetic analysis of RFLP-types........................................................................ 53 2.3.5. DGGE analysis.......................................................................................................... 57 2.4. Discussion......................................................................................................................... 59 CHAPTER 3: Chitinolytic activities of ericoid mycorrhizal and other root- associated fungi from Epacris pulchella ................................................................................... 68 3.1. Introduction..................................................................................................................... 68 iii 3.1.1 Edaphic stresses in habitats of Ericaceae and their associated ericoid mycorrhizal fungi................................................................................................................. 68 3.1.2 Abilities of ericoid mycorrhizal fungi to utilise organic nitrogen sources................
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