University of New Hampshire University of New Hampshire Scholars' Repository Master's Theses and Capstones Student Scholarship Winter 2020 NUTRIENT SOLUTION EFFECTS ON PLANT HEALTH AND MICROBIAL COMMUNITY COMPOSITION IN SOILLESS STRAWBERRY CULTURE William Miller Hardesty-Dyck University of New Hampshire, Durham Follow this and additional works at: https://scholars.unh.edu/thesis Recommended Citation Hardesty-Dyck, William Miller, "NUTRIENT SOLUTION EFFECTS ON PLANT HEALTH AND MICROBIAL COMMUNITY COMPOSITION IN SOILLESS STRAWBERRY CULTURE" (2020). Master's Theses and Capstones. 1469. https://scholars.unh.edu/thesis/1469 This Thesis is brought to you for free and open access by the Student Scholarship at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Master's Theses and Capstones by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. NUTRIENT SOLUTION EFFECTS ON PLANT HEALTH AND MICROBIAL COMMUNITY COMPOSITION IN SOILLESS STRAWBERRY CULTURE BY WILLIAM HARDESTY-DYCK Bachelor of Arts, Williams College, 2016 THESIS Submitted to the University of New Hampshire in Partial Fulfillment of the Requirements for the Degree of Master of Science In Agricultural Sciences December, 2020 ii This thesis was examined and approved in partial fulfillment of the requirements for the degree of Master of Science in Agricultural Science by: Thesis Director, Dr. Anissa Poleatewich, Assistant Professor of Plant Pathology Dr. Jessica Ernakovich, Assistant Professor of Microbial Ecology Dr. Todd Guerdat, Civil/Agricultural Engineer, USDA NRCS On December 1 st , 2020 Approval signatures are on file with the University of New Hampshire Graduate School. iii ACKNOWLEDGMENTS This work was supported by the Engineering for Agricultural Production Systems (A1521) grant no. 2018-67022-27844/project accession no. 1015270 from the USDA National Institute of Food and Agriculture. I would like to thank my academic advisor, Dr. Anissa Poleatewich, for her guidance and for her dedication to this research and to my development as a scientist. I extend my gratitude to the members of my thesis committee, Drs. Jessica Ernakovich and Todd Guerdat. I thank Dr. Ernakovich for sharing her knowledge of microbial ecology and bioinformatics. Dr. Guerdat introduced me to the theory and practice of aquaculture and aquaponics and generously allowed me the use of culture water from the recirculating aquaponic systems at Kingman Farm. I would also like to thank my lab mates, Liza DeGenring, Anna DeVitto, Crysta Harris, Madeleine Hassett, Isobel Michaud, Haley Nolen, and Ryan Spelman, for their support, advice, labor, and camaraderie. My gratitude is also with the members of the Guerdat (Sean Fogarty, Ashu Rao, Alex Sitek, and Joe Tetreault) and Ernakovich (Lukas Bernhardt and Stacey Doherty) labs, all of whom contributed to the completion of this thesis. I thank Dr. Tom Davis and the rest of the Davis lab for graciously sharing their space and equipment with me. Luke Hydock, the manager of the MacFarlane greenhouses, was instrumental in the design, construction, and maintenance of the growth system. He, Amber Kittle, and the rest of the MacFarlane staff kept my plants healthy and well-fed throughout this work. Victoria Schacht pruned buds, leaves, and runners. I thank the Hubbard Center for Genome Studies for their sequencing expertise. Finally, I extend my deep appreciation to my family and friends for their love and support in this, and in all things. iv TABLE OF CONTENTS ACKNOWLEDGMENTS .......................................................................................................................................................... iii LIST OF TABLES ...................................................................................................................................................................... vi LIST OF FIGURES .................................................................................................................................................................... vi ABSTRACT ................................................................................................................................................................................ vii CHAPTER 1 INTRODUCTION .............................................................................................................................................. 1 1.1. Ecological Limits and Sustainable Food System Intensification ....................................................... 1 1.2. Controlled Environment Agriculture ........................................................................................................... 3 1.2.1. Soilless Culture ................................................................................................................................................... 5 1.3. Survey of Substrates, Irrigation Systems, and Nutrient Solutions in Soilless CEA .................... 5 1.3.1. Irrigation ............................................................................................................................................................... 6 1.3.2. Substrates ............................................................................................................................................................. 7 1.3.3. Naturally Derived Nutrient Solutions ........................................................................................................ 9 1.4. Pathogens in Soilless CEA ............................................................................................................................... 13 1.4.1. Pythium ................................................................................................................................................................ 15 1.5. Microbial Communities in Soilless CEA .................................................................................................... 20 1.5.1. Organic Solutions and Microbial Communities ................................................................................... 23 1.5.2. Aquaponic Microbial Communities .......................................................................................................... 24 1.6. Research Questions ........................................................................................................................................... 27 1.6.1. Hypotheses ......................................................................................................................................................... 28 CHAPTER 2 METHODS ........................................................................................................................................................ 29 2.1. Experimental Design ......................................................................................................................................... 29 2.2. Growth Environment ........................................................................................................................................ 29 2.3. System Design and Construction ................................................................................................................. 30 2.4. Nutrient Solutions .............................................................................................................................................. 32 2.5. Plants ....................................................................................................................................................................... 34 2.6. Pythium Inoculation .......................................................................................................................................... 35 2.6.1. Inoculum .............................................................................................................................................................. 35 2.6.2. Drench Inoculation .......................................................................................................................................... 36 2.7. Plant Health Metrics .......................................................................................................................................... 36 2.7.1. Aboveground Mass .......................................................................................................................................... 36 2.7.2. Root Assessments ............................................................................................................................................ 37 2.8. Plant Health Statistical Analyses .................................................................................................................. 38 v 2.9. Sampling ................................................................................................................................................................ 38 2.9.1. Leachate ............................................................................................................................................................... 38 2.9.2. Solution ................................................................................................................................................................ 38 2.9.3. Bulk Substrate ................................................................................................................................................... 38 2.9.4.