CARROT ENDOPHYTES: DIVERSITY, ECOLOGY and FUNCTION by Sahar Abdelrazek
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CARROT ENDOPHYTES: DIVERSITY, ECOLOGY AND FUNCTION by Sahar Abdelrazek A Dissertation Submitted to the Faculty of Purdue University In Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy Department of Horticulture West Lafayette, Indiana December 2018 2 THE PURDUE UNIVERSITY GRADUATE SCHOOL STATEMENT OF COMMITTEE APPROVAL Dr. Lori A. Hoagland, Chair Department of Horticulture and Landscape Architecture Dr. Mary C. Aime Department of Botany and Plant Pathology Dr. Tesfaye Mengiste Department of Botany and Plant Pathology Dr. Philipp W. Simon Department of Life Science Communication, College of Agriculture and Life Science, University of Madison, Wisconsin. Approved by: Dr. Hazel Y. Wetzstein Head of the Graduate Program 3 ACKNOWLEDGMENTS Truly I am indebted to many people for their assistance and support in completing my PhD study at Purdue University Firstly, I would like to express my sincere gratitude to my major advisor Dr. Lori Hoagland, for providing me the valuable opportunity to receive my PhD. training and conducting research in her lab. Dr. Hoagland, always been accessible to discuss scientific and personal matters. She always encourages, motivates and supports me during this journey. I would like also to thank the rest of my thesis committee members: Dr. Catherine Aime, Dr. Tesfaye Mengiste and Dr. Philipp Simon for their continuous support and insightful comments. I would like to thank all my former and current lab members for their stimulating discussions, help and all the fun we have had in the last four years. Finally, I would like to acknowledge my parents, my husband (Mohamed), my brother, and sister whose love and support enabled me to keep the focus and drive towards carrying out this work. 4 TABLE OF CONTENTS LIST OF TABLES .......................................................................................................................... 8 LIST OF FIGURES ...................................................................................................................... 10 ABSTRACT .................................................................................................................................. 13 INTRODUCTION .............................................................................................. 15 1.1 Problem Statement ............................................................................................................ 15 1.2 The purpose of the dissertation ......................................................................................... 18 1.3 Outline of this thesis ......................................................................................................... 19 1.4 Review .............................................................................................................................. 20 1.4.1 Definition of endophytes ........................................................................................... 20 1.4.2 Endophyte plant hosts, location within plants, and density ....................................... 21 1.4.3 Factors affecting endophyte composition .................................................................. 22 1.4.3.1 Plant host .............................................................................................................. 22 1.4.3.2 Plant growth stage ................................................................................................ 23 1.4.3.3 Plant organs .......................................................................................................... 23 1.4.3.4 Climate .................................................................................................................. 24 1.4.3.5 Soil characteristics and management practices .................................................... 25 1.4.3.6 Presence of plant pathogens ................................................................................. 26 1.4.4 Managing endophytes to control plant diseases ........................................................ 26 1.4.5 Endophyte mechanisms for controlling plant diseases .............................................. 27 1.4.5.1 Antagonism ........................................................................................................... 27 1.4.5.2 Improving plant growth ........................................................................................ 28 1.4.5.3 Induced host resistance ......................................................................................... 29 1.4.6 Research needs ........................................................................................................... 30 1.5 References ......................................................................................................................... 31 Gossypium hirsutum .............................................................................................................. 39 VERTICAL TRANSMISSION OF CULTURABLE CARROT ENDOPHYTES: COMPOSITION, PLANT GROWTH PROMOTING ABILITIES AND EFFECT OF PLANT GENOTYPE AND DEVELOPMENTAL STAGE ...................................................................... 49 2.1 Introduction ....................................................................................................................... 49 5 2.2 Material and Methods ....................................................................................................... 52 2.2.1 Carrot germplasm ...................................................................................................... 52 2.2.2 Isolation and identification of carrot seed and seedling endophytes ......................... 52 2.2.3 Enumeration of broad bacterial and fungal groups among seed and seedling endophytes: ............................................................................................................................ 54 2.2.4 Indole acetic acid production ..................................................................................... 55 2.2.5 Siderophore production ............................................................................................. 55 2.2.6 Phosphate solubilization ............................................................................................ 56 2.2.7 Nitrogen fixation ability ............................................................................................ 56 2.2.8 Statistical analyses ..................................................................................................... 57 2.3 Results and Discussion ..................................................................................................... 57 2.3.1 Identification of seed and seedling endophytes ......................................................... 57 2.3.2 Enumeration of broad bacterial and fungal groups among seed and seedlings ......... 62 2.3.3 Indole acetic acid production ..................................................................................... 65 2.3.4 Siderophore production ............................................................................................. 67 2.3.5 Phosphate solubilization ............................................................................................ 69 2.3.6 Nitrogen fixation ability ............................................................................................ 70 2.4 References ......................................................................................................................... 73 CARROT ENDOPHYTES: ROLE OF CROP MANAGEMENT SYSTEM AND CARROT GENOTYPE ON COMMUNITY COMPOSITION AND A. DAUCI DYNAMICS 106 3.1 Introduction ..................................................................................................................... 106 3.2 Material and methods ...................................................................................................... 109 3.2.1 Field trial .................................................................................................................. 109 3.2.2 Field soil chemical and biological assays ................................................................ 110 3.2.3 Isolation and enumeration of culturable endophytes in carrot taproots ................... 111 3.2.4 Identification of endophytes .................................................................................... 112 3.2.5 In vitro screening of endophyte isolates for antagonistic activity against Alternaria dauci ................................................................................................................................. 114 3.2.6 Greenhouse trial to quantify potential of selected endophytic isolates to increase carrot growth and enhance tolerance to A. dauci ........................................................................... 114 3.3 Statistical analysis ........................................................................................................... 116 6 3.4 Results and Discussion ................................................................................................... 116 3.4.1 Impact of crop management system on soil chemical and biological properties and carrot yield in the field trial ................................................................................................. 116 3.4.2 Influence of crop management system and carrot genotype on the density of culturable endophytes in carrot taproots ............................................................................................... 117 3.4.3 Identification of endophytic