The diversity of fungi in four Irish forest types By Richard O’Hanlon B.Sc. (Ed) A thesis submitted for the degree of Doctor of Philosophy, At the Faculty of Science and Engineering, University of Limerick, Ireland. Supervisor: Dr Thomas Harrington, Department of Life Sciences, University of Limerick. Submitted to the University of Limerick: May 2011 i ii “The task of an ecologist” There is an old story about a man who, returning home one night found his neighbour searching the ground beneath a street lamp. “Can I help you find something?” he asked. “I lost my key” replied the neighbour. “Do you know about where you dropped it?”, “Yes” replied the neighbour “over there” pointing to a dark corner of the street. “If you dropped it over there then why are you looking here” asked the man. “Because this is where the light is” replied the neighbour. The task of the ecologist is not to bring the search to where the light is, but to bring the light to where the search is. Perry et al. (2008) iii iv Abstract Sampling of the macrofungal sporocarps, ectomycorrhizal morphotypes and vascular plants was carried out in 28 plots from four forest types (ash, oak, Scot’s pine, Sitka spruce) between the years 2007 and 2009. A total of 409 macrofungal species, 51 ectomycorrhizal morphotypes and 68 vascular plant species were recorded over the three years. It was found that at equal sampling intensities, there were no significant differences in total macrofungal species or ectomycorrhizal morphotype richness between the oak, Scot’s pine and Sitka spruce forest types. Species richness estimation revealed that between 45 and 77% of the above- ground macrofungal species richness and between 57 and 100% of the below- ground ectomycorrhizal morphotype richness were recorded. Cortinarius, Mycena, Russula, Lactarius and Inocybe were the most species-rich genera recorded. Forty-eight macrofungal species are new records to Ireland and five of the species recorded are on the British Red-Data List. Based on sporocarp frequency over the three year’s sampling, distinctive macrofungal communities were distinguished using nonmetric multi-dimension scaling, which corresponded to the dominant tree type of the forest. Ash forests lacked the ectomycorrhizal species component, oak forests had many wood- and litter-decay species present, Scot’s pine forests had some specific Lactarius species present (e.g. L. rufus, L. hepaticus ) and Sitka spruce forests had a large diversity of Mycena species. The below-ground ectomycorrhizal communities were surveyed in soil cores taken from four plots from each of three of the forest types. The ectomycorrhizal communities of the forest types (oak, Scot’s pine and Sitka spruce) were distinctly different according to the dominant tree species of the plot. The use of mantle descriptions, RFLP and sequencing methods allowed for the identification of 36 ectomycorrhizal species. The morphology and anatomy of remaining 15 morphotypes is described. The ability of plantation forests to provide a supplementary habitat for native fungal species richness and diversity is discussed. v vi Declaration I hereby declare that I am the sole author of this thesis and that it has not been submitted for any other academic award. References and acknowledgements have been made, where necessary, to the work of others. Date: . Richard O’Hanlon Department of Life Sciences University of Limerick Ireland vii viii Acknowledgements I wish to thank my supervisor Dr Tom Harrington for all his help and guidance throughout the work involved in this thesis. I am very grateful for the many hours spent in the lab passing on his taxonomic knowledge of fungi and also for the help he gave me to develop this thesis and also my writing skills. I would like to thank all the staff of the Department of Life Sciences for their help, support and friendship during my years as both an undergraduate and post- graduate. Prof. John Breen, University of Limerick and Dr Gareth Griffith, Aberystwyth University, provided valuable comments and corrections to an earlier draft of this thesis. I am very grateful to the Council for Forest Research and Development (COFORD) for funding this PhD through the FUNCTIONALBIO project. I would like to express my gratitude to Prof. Tom Bolger, School of Biology and Environmental Science, UCD, for his organisation and management of the FUNCTIONALBIO project. I would like to thank my sponsors whom accepted me as a Visiting Scholar during this research. Dr Sue Grayston, Department of Forest Sciences, University of British Columbia, for all her help in organising my trip to Canada. Dr Dan Luoma and Dr Joyce Eberhart for their kindness, support and explanation of the methods for describing ectomycorrhizal communities during my Visiting Scholar trip to Oregon. Both Visiting Scholar exchanges greatly broadened my views on ecology and mycology. COFORD is gratefully acknowledged for funding both Visiting Scholar exchanges. I am grateful to my family for their support and encouragement during my time at University. I would also like to thank all of my friends and fellow postgrads for talking about topics other than my research with me. I would like to thank Dr Chris Quine, Forest Research, and Dr Jonathan Humphrey for allowing access to the “Biodiversity in Britain’s planted forests” data. ix x List of Abbreviations Abbreviation Full term ACE Abundance-based Coverage Estimator ANOVA Analysis of Variance CHAO2 Chao 2 richness estimator CWD Coarse Woody Debris DBH Diameter at Breast Height DNA Deoxyribonucleic Acid ECM Ectomycorrhizal FAO Food and Agriculture Organisation FSC Forest Stewardship Council ICE Incidence-based Coverage Estimator ITS Internal Transcribed Spacer IV Indicator Value JI Jaccard Index MRPP Multi-Response Permutation Procedure NMS Nonmetric Multi-dimensional Scaling PAR Photosynthetic Active Radiation PCR Polymerase Chain Reaction PRS Plant Root Simulator RFLP Restriction Fragment Length Polymorphism SD Standard Deviation SFM Sustainable Forest Management SP Scot’s pine SS Sitka spruce U.K. United Kingdom xi xii Usage of Terms Shown below is a word cloud created from the most frequently used words in the main body of the thesis. The size of the word relates to the frequency of its use. The usage frequencies range from 60 to 1700 uses, depending on font size. Species Soil Ireland Coniferous Plot Vegetation Sitka spruce Lactarius Scot’s pine Variables Forest Diversity Function Ash Rarefaction Fungi CWD Tree Russula Ectomycorrhizal Native Cortinarius Indicator Richness Significant Estimation Genus Plantation Analysis Biodiversity Habitat Community Oak Irish xiii xiv Contents Abstract…………………………………………….…….…………...……...…..iii Declaration…………………………………………….………...……………….iv Acknowledgements………………………………….……………………………v Listof Abbreviations………………………………...……………………………xi Usage of terms………………..…………………………………………………xiii Chapter 1: Introduction 1.1 The changing face of Irish forests ........................................................................... 3 1.2 Biodiversity and Irish forests .................................................................................. 4 1.3 The Functionalbio project ....................................................................................... 6 1.4 Macrofungi in forest ecosystems ............................................................................ 7 1.5 Layout of the thesis ................................................................................................. 8 Chapter 2: Literature review 2.1 Sustainable forest management and certification .................................................. 13 2.2 COFORD and recent forest research in Ireland .................................................... 14 2.3 Studies of fungi in forest ecosystems. ................................................................... 16 2.4 Forest management practices and their effects on forest fungi ............................. 17 2.5 Functional groupings for fungi ............................................................................. 21 2.6 Below-ground ectomycorrhizal diversity in forests .............................................. 26 2.7 Soil and site variables and their relationship with fungal diversity ...................... 27 Chapter 3: The sites: vegetation and site variables measured 3.1 Introduction ........................................................................................................... 41 3.1.1 Forests of Ireland: Extent and current trends ..................................................... 41 3.1.2 Classification of Irish forest habitats ................................................................. 43 3.1.3 Rational for site selection ................................................................................... 44 3.2 Aims of this chapter .............................................................................................. 47 3.3 Materials and methods .......................................................................................... 48 3.3.1 The sites ............................................................................................................. 48 3.3.2 Data collection methods ..................................................................................... 52 3.3.3 Statistical analysis .............................................................................................. 54 3.4 Results ................................................................................................................... 58 3.4.1 Soils