INVESTIGATING THE IMPACTS OF ANTIBIOTICS AND ALTERNATIVES ON THE SUSTAINABLE MANAGEMENT, DISTRIBUTION, AND SPREAD OF FIRE BLIGHT A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Anna Elizabeth Wallis December 2020 © 2020 Anna Elizabeth Wallis INVESTIGATING THE IMPACTS OF ANTIBIOTICS AND ALTERNATIVES ON THE SUSTAINABLE MANAGEMENT, DISTRIBUTION, AND SPREAD OF FIRE BLIGHT Anna Elizabeth Wallis, Ph.D. Cornell University 2020 Fire blight, caused by the bacteria Erwinia amylovora, is one of the most important diseases of apples. Despite over 200 years of intense investigation, it continues to cause devastating losses to growers worldwide. The most effective management tool in the Eastern US is the antibiotic streptomycin. However, antibiotic use in agriculture has come under scrutiny and there is a need to better understand the sustainability of streptomycin and alternative management solutions. The first goal of this research was to investigate impacts of streptomycin and alternatives on fire blight disease management and orchard health. Application of the plant growth regulator prohexadione-calcium pre-bloom was investigated as a novel alternative to antibiotics. Results indicated significant reduction in disease incidence to levels comparable with streptomycin, without compromising tree growth. Separate work investigated effects of streptomycin on endophytic bacterial communities in the canopy, communities potentially implicated in orchard health and antibiotic resistance. Minimal effects were detected on abundance and structure of communities, indicating the sustainability of current streptomycin programs. The second goal of this work was to describe distribution and spread of fire blight at multiple scales, with consideration for streptomycin resistance. First, we investigated risk of fire blight development and spread using mechanical thinning and pruning. Field trials indicated both practices could be used safely, and any risk mitigated by applying streptomycin after mechanical treatment. Next, distribution within orchard blocks was described for two fields over two years using spatial analyses. These case studies illustrated different mechanisms of introduction and spread. Finally, we investigated geographic distribution of E. amylovora strains and streptomycin resistance in apple production regions in the Northeastern US. Over 150 isolates were described in terms of streptomycin resistance phenotype and CRISPR profile. Several CRISPR profiles were widely distributed, while many others were only identified in one location. In a streptomycin resistant E. amylovora outbreak in Wayne County, all isolates exhibited CRISPR profiles matching the original SmR isolates discovered in NY, indicating the outbreak likely resulted from imperfect eradication. The work presented herein will inform recommendations for sustainable fire blight management, with immediate impacts to commercial production in NY State and beyond. BIOGRAPHICAL SKETCH Anna Wallis was raised in Harford County, Maryland and attended Fallston High School, where she began her academic pursuit of biology and music. She attended University of Maryland where she received a BS in Biology and a BA in Music, with a specialization in vocal performance. As an undergraduate she began working as a teaching assistant for the introduction to horticulture course in the Plant Science Department, where she fell in love with plant science and apple production. During this time and the year following her undergraduate work, she gained experience in plant science, entomology, and community agriculture, working in labs at the University of Maryland in College Park and the USDA in Beltsville, at the Green Farmacy Garden, and at Eco City Farms. She then returned to school to pursue a Master’s Degree in Plant Science with Dr. Chris Walsh, Professor of Horticulture, where she focused on lettuce and apple production in the Mid-Atlantic. After earning her degree, she worked for Cornell Cooperative Extension as the Apple Specialist in the Champlain Valley of Eastern NY for three years, providing support to growers in through educational programming and applied research. She returned to school in 2017 to pursue a Ph.D. in Plant Pathology at Cornell University under the direction of Dr. Kerik Cox, where her work has focused on fire blight, a bacterial disease of apples caused by Erwinia amylovora. iii Dedicated to Colvin, my most loyal and patient companion, relentless mischief-maker, and welcome distraction. iv ACKNOWLEDGEMENTS I cannot thank my advisor Dr. Kerik Cox enough for how he has helped and inspired me. Throughout my graduate work, he provided guidance, encouragement, and opportunity that has enabled my research and successful development as a professional in the fields of tree fruit production and plant pathology. I am continuously amazed by Kerik’s visionary research and teaching, and his tireless commitment to his work, students, and community. I have learned from his example what it takes to accomplish excellent research and cultivate an exciting, supportive lab environment, while maintaining a broad perspective and an all-important sense of humor. I would also like to thank my committee members, Drs. Susan Brown, Lance Cadle- Davidson, Andrea Ottesen, who have provided me with invaluable advice and compassionate support, in both professional and personal capacities. Their accomplishments, passion, and dedication are endless sources of inspiration on which I will model my future career. My work would not be possible without the help of collaborators from the tree fruit community as well as the USDA and FDA, who facilitated this research by contributing their time, resources, and insights to these projects. In particular, Dr. Terry Bradshaw, who allowed me to conduct trials in his orchards at the University of Vermont Horticultural Research Station, the members of the commercial apple industry, Scott Palmer, Tom DeMarree, Kevin Bowman, Chris Carballiera, Pete Ten Eyck, Kevin Bittner, and Bobby Brown, who allowed me to work in their orchards, and the Cornell Cooperative Extension Specialists and private consultants Dan Donahue, Mike Basedow, Jim Eve, and Janet van Zoeren who collected numerous samples. Thank you also to Padmini Ramachandran and Ganyu Gu who invited me into their labs and patiently taught me NGS and bioinformatics skills. v I would like to thank my family and friends for their love and support. I am incredibly fortunate to have so many people invested in celebrating my successes and sympathizing with my failures, no matter how great or small. Thanks Mom, for being my biggest fan and listening to countless practice presentations; thanks Dad, for always reminding me not to lose sight of my goals and who I am; and thanks Maggie, for reminding me to be kind, silly, and happy at a time when it has become easy to take everything too seriously. My labmates, Mei-Wah Choi, Katrin Ayer, David Strickland, and Isabella Yannuzzi, have been incredibly supportive and helpful, and I am so indebted to them for their help with my work, and general encouragement and positivity (Type IV Fun, More Money, and many more inside jokes…); I hope I have been half as much of a positive influence on your work as you have been on mine. Finally, thank you to the groups that supported this work financially, including the Northeast Sustainable Agriculture Research and Education (NESARE) grant LNE19-385R, the New York Farm Viability Institute (NYFVI) grant FVI 19 002, the Department of Agriculture & Markets Apple Research & Development Program (ARDP) grants FY 2018-19 & 2017-18, agrichemical companies of Northeastern United States, and the Arthur Boller Research Fund grant 2019 and 2020. vi TABLE OF CONTENTS Page Front Matter Title Page ....................................................................................................................... i Biographical Sketch ..................................................................................................... iii Dedication .................................................................................................................... iv Acknowledgements ........................................................................................................v Table of Contents ........................................................................................................ vii List of Figures .............................................................................................................. ix List of Tables ............................................................................................................... xi Chapter 1: Introduction ......................................................................................................1 Literature Cited ..............................................................................................................8 Part I: Impacts of Antibiotics and Alternatives on Disease Management and Orchard Health ................................................................................................................11 Chapter 2: Management of Fire Blight Using Pre-bloom Applications of Prohexadione- calcium ...............................................................................................................................12 Abstract ........................................................................................................................12