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Diversity of Yeasts Associated with Wood and the Gut of Wood-Feeding Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2012 Diversity of yeasts associated with wood and the gut of wood-feeding insects Hector Raul Urbina Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Urbina, Hector Raul, "Diversity of yeasts associated with wood and the gut of wood-feeding insects" (2012). LSU Doctoral Dissertations. 1172. https://digitalcommons.lsu.edu/gradschool_dissertations/1172 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. DIVERSITY OF YEASTS ASSOCIATED WITH WOOD AND THE GUT OF WOOD- FEEDING INSECTS A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences by Hector Raul Urbina M.S. Universidad Simón Bolívar, 2005 December 2012 To my lovely family: my mother Lilia, my father Raúl and my brother Federico ii ACKNOWLEDGMENTS I would like to truthfully express my gratitude for the energy, experience, and inspiration of my major professor, Meredith Blackwell. I could not have a better professor to guide me across the years in my development as a researcher. I would also like to thank the professors that composed my advisory committee, Cathie Aime, Prosanta Chakrabarty, James Cronin, Frederick Sheldon, and Ronald Thune for their helpful comments and support. In addition I thank Jeremy Brown for insightful discussions. Many thanks go to Maritza Abril and Stephanie Gross for all of their help with the laboratory routine. At the same time, I would like to thank the undergraduate students Callie Comstock, Elizabeth Cooper, Robert Donner, Robert Frank, Juan Herrera, Matthew Knight, and Simone Mack, for their help during the development of my research. Special thanks to my mates in the Department of Biological Sciences, Anthony Chow, Sandra Galeano, and Metha Klock for several good moments. I also owe a debt of gratitude to Sung-Oui Suh, Nhu Nguyen, and Joseph McHugh and his students at the University of Georgia, who did the early work on the passalid yeast system that served as the basis for my study. I would like to recognize to the National Sciences Foundation (NSF), Mycological Society of America (MSA), Louisiana Experimental Program to Stimulate Competitive Research (LINK-EPSCoR), Boyd Professor fund, the LSU Graduate School, and Biograds (the departmental graduate student organization), for funding my research. I iii would especially like to thank the Louisiana State University Department of Biological Sciences for it support and use of facilities. iv TABLE OF CONTENTS ACKNOWLEDGMENTS .................................................................................................. iii ABSTRACT ..................................................................................................................... vi CHAPTER 1: GENERAL INTRODUCTION ...................................................................... 1 CHAPTER 2: MULTILOCUS PHYLOGENETIC STUDY OF THE SCHEFFERSOMYCES YEAST CLADE AND CHARACTERIZATION OF THE N- TERMINAL REGION OF THE XYLOSE REDUCTASE GENE ........................................ 4 2.1. Introduction ........................................................................................................................ 4 2.2. Materials and methods ....................................................................................................... 6 2.3. Results ............................................................................................................................. 11 2.4. Discussion ........................................................................................................................ 23 CHAPTER 3: SCHEFFERSOMYCES CRYPTOPCERCUS: A NEW XYLOSE- FERMENTING YEAST ASSOCIATED WITH THE GUT OF WOOD ROACHES AND NEW COMBINATIONS IN THE SUGIYAMAELLA YEAST CLADE ...................... 32 3.1. Introduction ...................................................................................................................... 32 3.2. Materials and methods ..................................................................................................... 33 3.3. Results and discussion .................................................................................................... 38 CHAPTER 4: DIVERSITY OF YEASTS ASSOCIATED WITH GUATEMALAN PASSALID BEETLES ..................................................................................................... 48 4.1. Introduction ...................................................................................................................... 48 4.2. Materials and methods ..................................................................................................... 52 4.3. Results and discussion .................................................................................................... 58 4.4. Conclusions ..................................................................................................................... 75 CHAPTER 5: DIVERSITY OF YEASTS ASSOCIATED WITH THAI PASSALID BEETLES ....................................................................................................................... 77 5.1. Introduction ...................................................................................................................... 77 5.2. Materials and methods ..................................................................................................... 80 5.3. Results and discussion .................................................................................................... 81 CHAPTER 6: PURIFYING SELECTION MAINTAINS XYLOSE REDUCTASE ACTIVITY AMONG ASCOMYCETE YEASTS ............................................................... 89 6.1. Introduction ...................................................................................................................... 89 6.2. Materials and methods ..................................................................................................... 92 6.3. Results and discussion .................................................................................................... 95 CHAPTER 7. CONCLUSIONS ..................................................................................... 102 REFERENCES ............................................................................................................. 106 VITA .............................................................................................................................. 129 v ABSTRACT The gut of insects and plant tissues are productive sources for the isolation of undescribed species of yeasts. In particular, the gut of lignicolous insects is colonized by yeasts that can carry out the fermentation of several sugars. The consistent association between xylose-fermenting (X-F) yeasts and the gut of lignicolous insects has been used as evidence of a symbiotic relationship between them. In general passalid beetles (Passalidae) and wood-roaches (Cryptocercidae) feed on rotted wood where they spend most of their lives. Digestion of the substrate depends on the symbiotic microbiota, which include strict and facultative anaerobic microorganisms such as bacteria, parabasalids, and fungi. The objectives of this study were to describe the yeasts associated with hardwoods in Louisiana (Chapter 2), the gut of the wood roach Cryptocercus collected in the Appalachian Mountains (Chapter 3), passalids collected in Guatemala (Chapter 4) and in Thailand (Chapter 5), and to study selection acting on xylose reductase (XR) in yeasts (Chapter 6). This study confirmed the routine presence of ascomycete yeasts from the clades Scheffersomyces, Spathaspora, Lodderomyces, and Sugiyamaella in the guts of wood roaches and passalid beetles, as well as basidiomycete yeasts in the genera Cryptococcus and Trichosporon in passalids exclusively. In this investigation, four new X-F yeasts, Scheffersomyces illinoinensis, Sc. quercinus, Sc. virginianus, and Sc. cryptocercus, were proposed based on multilocus phylogenetic analyses, molecular, and biochemical characterization. The X-F yeasts in the Scheffersomyces clade were the most abundant species in the gut of both wood- roaches and Guatemalan passalids, results that support and expand the previously described relationship between X-F yeasts and lignicolous insects. This finding, vi however, was not observed in Thai passalids, where the most abundant yeasts were closely related to Candida insectamans (Spathaspora clade) that does not ferment xylose. In addition, this study determined that the gut of lignicolous insects is a niche rich in undescribed yeasts classified in several clades. The xylose reductase gene (XYL1) has been shown to be useful as a molecular marker for rapid identification of cryptic yeast species, and the xylose reductase enzyme (XR) has been exposed to purifying selection in ascomycete yeasts. vii CHAPTER 1: GENERAL INTRODUCTION The term “yeast” is used to describe a specific fungal growth form that is unicellular with multiplication by budding at some stage in the life cycle, although
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