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Composition and Richness of Fruiting Body and Molecular Fungal Taxa of Woody Debris in Boreal Forest Sites

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Composition and Richness of Fruiting Body and Molecular Fungal Taxa of Woody Debris in Boreal Forest Sites COMPOSITION AND RICHNESS OF FRUITING BODY AND MOLECULAR FUNGAL TAXA OF WOODY DEBRIS IN BOREAL FOREST SITES A Thesis Presented to The Faculty of Graduate Studies of The University of Guelph by ALISON LOUISE FISCHER In partial fulfilment of requirements for the degree of Master of Science April 2008 © Alison Louise Fischer, 2008 Library and Bibliotheque et 1*1 Archives Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington Ottawa ON K1A0N4 Ottawa ON K1A0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-41818-5 Our file Notre reference ISBN: 918-0-494-41818-b NOTICE: AVIS: The author has granted a non­ L'auteur a accorde une licence non exclusive exclusive license allowing Library permettant a la Bibliotheque et Archives and Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par Plntemet, prefer, telecommunication or on the Internet, distribuer et vendre des theses partout dans loan, distribute and sell theses le monde, a des fins commerciales ou autres, worldwide, for commercial or non­ sur support microforme, papier, electronique commercial purposes, in microform, et/ou autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in et des droits moraux qui protege cette these. this thesis. Neither the thesis Ni la these ni des extraits substantiels de nor substantial extracts from it celle-ci ne doivent etre imprimes ou autrement may be printed or otherwise reproduits sans son autorisation. reproduced without the author's permission. In compliance with the Canadian Conformement a la loi canadienne Privacy Act some supporting sur la protection de la vie privee, forms may have been removed quelques formulaires secondaires from this thesis. ont ete enleves de cette these. While these forms may be included Bien que ces formulaires in the document page count, aient inclus dans la pagination, their removal does not represent il n'y aura aucun contenu manquant. any loss of content from the thesis. Canada ABSTRACT COMPOSITION AND RICHNESS OF FRUITING BODY AND MOLECULAR FUNGAL TAXA OF WOODY DEBRIS IN BOREAL FOREST SITES Alison Louise Fischer Co-advisors: University of Guelph, 2008 Professor J. Klironomos Professor J-M. Moncalvo Woody debris and their associated fungi represent key structural and functional components of forest systems. I used fruiting body surveys and molecular methods to compare composition of fungal taxa across two decay classes of softwood logs among sites differing in management history. I also examined three ways of assessing diversity: observed richness based on fruiting body sampling, observed richness based on operational taxonomic unit sampling and a comparison of phylogenetic composition based on the operational taxonomic unit data. I evaluated whether fungal composition varied across different decay classes of logs and sites differing in management history and whether different analyses showed the same picture. Decay class strongly influenced fruiting body and molecular taxon composition. Each sampling method recovered unique fungal taxa suggesting that careful selection of sampling methods is important. Diversity measures appeared robust in their detection of decay class as the strongest environmental signal. Acknowledgements I would first like to thank my committee for their patience helping me with my writing. In particular I would like to thank Jean-Marc Moncalvo for his insights into all things mycological, Tom Nudds for teaching me to keep me focused on the question and John Klironomos for giving me many insightful comments. I would also like to thank Jay Malcolm for organizing this project and his suggestions throughout the course of my degree. This project would not have been possible without funding from the Sustainable Forest Management Network and the Royal Ontario Museum. I would like to thank Damon Dewsbury and Eric Peterson, who spent long days helping me collect fungi and wood cores; rain or shine, bugs or no bugs. Assistance for sampling and describing collections also came from Kathrin Streit and Dan Werner. The Moncalvo and Klironomos labs were also very helpful with comments and moral support. This includes Leena Rizvi, Jes Skillman, Maryna Diduk, Damon Dewsbury, Terri McLenon-Porter and Simona Margaretiscu and honourary Moncalvo lab member Andre Ngo. Pedro Antunes, Alex Koch, Jeff Powell, Ben Sikes and Ashley Downing in the Klironomos lab. Extra thanks to Simona Margaretiscu and Kristen Choffe for helping me with some of the molecular work and Andre Ngo for helping me with the phylogenetic analyses. Thanks also to Uta Matthes for all her help with Canoco and Ashley Downing for helping me box herbarium samples. Special thanks to Terri McLenon-Porter for passing useful literature on to me and helping me with any mycology questions. Finally I would like to thank Isabelle Meusier and Mehrdad Hajibabaei from the Biodiveristy Institute of Ontario for helping me sequence my fruiting body collection. 1 Table of Contents Acknowledgements i Table of Contents ii List of Figures iv List of Tables vi 1. Introduction 1 2. Methods 4 Site selection 4 Coarse woody debris selection 5 Fruiting body sampling 6 Molecular operational taxonomic unit sampling 7 DNA extraction, cloning and sequencing 8 Variation in composition across decay classes and management histories 9 Observed richness of fruiting bodies, operational taxonomic units and the operational taxonomic unit phylogenetic diversity test 10 3. Results 12 Fruiting bodies sampled 12 Molecular operational taxonomic units sampled 12 Comparison between basidiomycete fruiting bodies and molecular operational taxonomic units 13 Variation across decay classes and sites 14 Richness of fruiting bodies, operational taxonomic units and the operational taxonomic unit phylogenetic diversity test 15 4. Discussion 17 ii 5. References 47 Appendix 54 A.l. Methods 54 Comments on sampling 54 A.2. Results 60 iii List of Figures Figure 1 shows the distribution of fungal morphotypes at a phylum level and in total across decay classes for (a) fruiting bodies (FBs) and (b) operational taxonomic units (OTUs) 27 Figure 2 shows the overlap, based on a 99% sequence similarity, between operational taxonomic unit (OTU) and fruiting body (FB) sequences of basidiomycetes for the six sites in which operational taxonomic unit sampling occurred 28 Figure 3 shows the RDA of the total fruiting body data 29 Figure 4 shows the RDA of the operational taxonomic unit data 30 Figure 5 shows the RDA of fruiting bodies of Polyporale fungi on decay class one logs across sites differing in management history 31 Figure 6 shows the observed richness of fruiting bodies across decay class four (DC4) and decay class one (DC1) logs and across sites 33 Figure shows the observed richness of fruiting bodies among decay class four (DC4) and decay class one (DC1) logs across sites 35 Figure 8 shows the observed richness of operational taxonomic units (OTUs) across decay class four (DC4) and decay class one (DC1) logs and unlogged (UL) and mechanically logged (ML) sites 36 Figure 9 shows the observed richness of operational taxonomic units (OTUs) among decay class four (DC4) and decay class one (DC1) logs across unlogged (UL) and mechanically logged (ML) sites 37 Figure 10 shows the observed richness of fruiting bodies (a) and operational taxonomic units (OTUs) (b) across decay class one (DC1) and decay class four (DC4) logs.... 38 iv Figure 11 shows the observed richness of fruiting bodies (a) across unlogged (UL), horse logged (HL) and mechanically logged (ML) sites. The observed richness of operational taxonomic units (OTUs) across unlogged and mechanically logged sites is shown in (b) 39 Figure 12 shows the observed richness of fungi in the order Polyporale on decay class one (DC1) logs across unlogged (UL), horse logged (HL) and mechanically logged (ML) sites 40 Figure 13 shows the regression analysis of the radius of each decay class one (a) and decay class four (b) log in unlogged (solid circle), mechanically logged (empty circle) and horse logged (solid diamond) sites with number of fruiting bodies on the y axis 41 Figure 14 shows the regression analysis of the radius of each decay class one (a) and decay class four (b) logs in unlogged (solid circle) and mechanically logged (empty circle) sites with number of operational taxonomic units (OTUs) on the y axis 42 v List of Tables Table 1 shows the fourteen fruiting body (FB) morphotypes also recovered as operational taxonomic units (OTU) based on a 99% sequence similarity 43 Table 2 shows the results of the Unifrac phylogenetic diversity test across decay classes among sites 44 Table 3 shows the results of the Unifrac phylogenetic diversity test across decay classes only 45 Table 4 shows the results of the Unifrac lineage-based analysis pinpointing two groups of fungi at the genera level that contributed to the significant difference across decay classes detected by the phylogenetic diversity test for operational taxonomic units (OTUs) 46 Table A.1 shows a list of the fifteen sites used for this study. The UTM coordinates are listed in the second column, followed by the tree species recovered from each site. Wood cores were collected from sites highlighted with a * 57 Table A.2 shows the thermocycler settings used for the mixed template PCR reactions. 58 Table A.3 shows the recipes used for both the mixed PCR reactions and the clone PCR reactions 59 Table A.4 shows the fruiting bodies (FBs) recovered from both decay class one and decay class four logs in fifteen sites 60 Table A.5 shows the operational taxonomic units (OTUs) recovered from both decay class one and decay class four logs in six of the fifteen sites 64 vi 1.
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