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Manipulating Wild and Tamed Phytobiomes: Challenges and Opportunities Terrence H Masthead Logo Plant Pathology Presentations and Posters Plant Pathology and Microbiology 3-13-2019 Manipulating Wild and Tamed Phytobiomes: Challenges and Opportunities Terrence H. Bell The Pennsylvania State University Gwyn A. Beattie Iowa State University, [email protected] Kurt P. Kowalski U.S. Geological Survey Amy T. Welty Iowa State University, [email protected] et al. Follow this and additional works at: https://lib.dr.iastate.edu/plantpath_conf Part of the Agriculture Commons, Ecology and Evolutionary Biology Commons, and the Plant Sciences Commons The ompc lete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ plantpath_conf/7. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Conference Proceeding is brought to you for free and open access by the Plant Pathology and Microbiology at Iowa State University Digital Repository. It has been accepted for inclusion in Plant Pathology Presentations and Posters by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Manipulating Wild and Tamed Phytobiomes: Challenges and Opportunities Abstract This white paper presents a series of perspectives on current and future phytobiome management, discussed at the Wild and Tamed Phytobiomes Symposium in University Park, PA, USA, in June 2018. To enhance plant productivity and health, and to translate lab- and greenhouse-based phytobiome research to field applications, the academic community and end-users need to address a variety of scientific, practical, and social challenges. Prior discussion of phytobiomes has focused heavily on plant-associated bacterial and fungal assemblages, but the phytobiomes concept covers all factors that influence plant function. Here we discuss various management considerations, including abiotic conditions (e.g. soil, nutrient applications), microorganisms (e.g. bacterial and fungal assemblages, bacterial and fungal inoculants, viruses), macroorganisms (e.g. arthropods, plant genetics), and societal factors (e.g. communication approaches, technology diffusion). An important near-term goal for this field should be to estimate the potential relative contribution of different components of the phytobiome to plant health, as well as the potential and risk of modifying each in the near-future. Disciplines Agriculture | Ecology and Evolutionary Biology | Plant Sciences Comments This is a manuscript of a proceeding published as Bell, Terrence H., Kevin Hockett, Ricardo Ivan Alcalá- Briseño, Mary Barbercheck, Gwyn A. Beattie, Mary Ann Bruns, John Carlson et al. "Manipulating Wild and Tamed Phytobiomes: Challenges and Opportunities." Phytobiomes Journal (2019). doi: 10.1094/ PBIOMES-01-19-0006-W. Rights Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The onc tent of this document is not copyrighted. This conference proceeding is available at Iowa State University Digital Repository: https://lib.dr.iastate.edu/plantpath_conf/7 Page 1 of 112 1 Manipulating Wild and Tamed Phytobiomes: Challenges and 2 Opportunities 3 Terrence H. Bell1,2,3 †, Kevin L. Hockett1,2,3 †, Ricardo I. Alcalá-Briseño4,5,6, Mary 4 Barbercheck7,8, Gwyn A. Beattie9, Mary Ann Bruns2,3,10, John E. Carlson3,10, Taejung Chung3,11, 5 Alyssa Collins1, Bryan Emmett12, Paul Esker1,8, Karen A. Garrett4,5,6, Leland Glenna3,8,13, Beth 6 K. Gugino1, María del Mar Jiménez-Gasco1,8, Linda Kinkel14, Jasna Kovac3,11, Kurt P. 7 Kowalski15, Gretchen Kuldau1,8, Johan H.J. Leveau16, Matthew J. Michalska-Smith14,17, Jessica 8 Myrick18, Kari Peter1, Maria Fernanda Vivanco Salazar8,13, Ashley Shade19,20,21,22, Nejc 9 Stopnisek19,20,21, Xiaoqing Tan3,11, Amy T. Welty9, Kyle Wickings23, Etienne Yergeau24 10 † authors co-chaired the symposium and contributed equally to this manuscript 11 12 Affiliations: 13 1- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State 14 University, University Park, PA, USA 15 2- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, 16 University Park, USA 17 3- Microbiome Center, The Huck Institutes of the Life Sciences, The Pennsylvania State 18 University, University Park, PA, USA 19 4- Plant Pathology Department, University of Florida, Gainesville, FL, USA 20 5- Institute for Sustainable Food Systems, University of Florida, Gainesville, FL, USA 21 6- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA 22 7- Department of Entomology, The Pennsylvania State University, University Park, PA, 23 USA Page 2 of 112 24 8- International Agriculture and Development Graduate Program, College of Agricultural 25 Sciences, The Pennsylvania State University, University Park, PA, USA 26 9- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA 27 10- Department of Ecosystem Science and Management, The Pennsylvania State University, 28 University Park, USA 29 11- Department of Food Science, The Pennsylvania State University, University Park, PA, 30 USA 31 12- Boyce Thompson Institute, Ithaca, NY, USA 32 13- Agricultural Economics, Sociology, and Education Department, The Pennsylvania State 33 University, University Park, PA, USA 34 14- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA 35 15- U.S. Geological Survey, Great Lakes Science Center, Ann Arbor, MI, USA 36 16- Department of Plant Pathology, University of California, Davis, CA, USA 37 17- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, 38 MN, USA 39 18- Bellisario College of Communications, The Pennsylvania State University, University 40 Park, PA, USA 41 19- Department of Microbiology and Molecular Genetics, Michigan State University, East 42 Lansing, MI, USA 43 20- The Plant Resilience Institute, Michigan State University, East Lansing, MI, USA 44 21- The DOE Great Lakes Bioenergy Research Center, Michigan State University, East 45 Lansing, MI, USA Page 3 of 112 46 22- Department of Plant, Soil and Microbial Sciences; and Program in Ecology, Evolutionary 47 Biology and Behavior, Michigan State University, East Lansing MI, USA 48 23- Department of Entomology, Cornell University, Cornell AgriTech at the New York State 49 Agricultural Experiment Station, Geneva, NY, USA 50 24- Centre INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, 51 Laval, QC, Canada 52 53 54 55 ABSTRACT 56 This white paper presents a series of perspectives on current and future phytobiome 57 management, discussed at the Wild and Tamed Phytobiomes Symposium in University Park, PA, 58 USA, in June 2018. To enhance plant productivity and health, and to translate lab- and 59 greenhouse-based phytobiome research to field applications, the academic community and end- 60 users need to address a variety of scientific, practical, and social challenges. Prior discussion of 61 phytobiomes has focused heavily on plant-associated bacterial and fungal assemblages, but the 62 phytobiomes concept covers all factors that influence plant function. Here we discuss various 63 management considerations, including abiotic conditions (e.g. soil, nutrient applications), 64 microorganisms (e.g. bacterial and fungal assemblages, bacterial and fungal inoculants, viruses), Page 4 of 112 65 macroorganisms (e.g. arthropods, plant genetics), and societal factors (e.g. communication 66 approaches, technology diffusion). An important near-term goal for this field should be to 67 estimate the potential relative contribution of different components of the phytobiome to plant 68 health, as well as the potential and risk of modifying each in the near-future. 69 70 ABBREVIATIONS AND GLOSSARY 71 2,4-DAPG: 2,4-diacetylphloroglucinol. 72 Biocontrol: The use of living organisms to suppress pests. 73 C: Carbon. 74 CBC: Conservation biological control. Biocontrol that exploits natural enemies through 75 modification of the environment or management practices. 76 CMD: Cassava mosaic disease. 77 Dormancy: Period in which an organism’s function is slowed, which is reversible under certain 78 conditions. 79 Endophyte: Organisms (generally fungi, bacteria, and viruses) that colonize internal plant tissue 80 without causing obvious visible symptoms. 81 HIPV: Herbivore-induced plant volatile. 82 Holobiont: Host and all of its associated partners. 83 ITS: Internal transcribed spacer. 84 Microbiome: All of the microorganisms found in a particular environment. The boundaries on 85 microbiomes are often challenging to define and depend on individual study parameters. 86 N: Nitrogen. 87 P: Phosphorous. Page 5 of 112 88 PapMV: Papaya mosaic virus. 89 Phytobiome: All of the biotic and abiotic factors that jointly determine a plant’s health and 90 growth. 91 PRSV: Papaya ringspot virus. 92 PVX: Potato virus X. 93 PVY: Potato virus Y. 94 SCMV: Sugarcane mosaic virus. 95 SynComs: Synthetic microbial communities. Groups of microorganisms assembled for 96 experimentation by combining multiple isolates. 97 98 INTRODUCTION 99 Phytobiomes are not simply the collection of microorganisms associated with a plant, 100 but all of the biotic and abiotic factors that influence the health and productivity of plants in a 101 defined biome. Many living components of the environment shape plant productivity, including 102 other plants, large animals, and various microorganisms, such as viruses, bacteria, fungi, 103 oomycetes, amoebae, and algae. Abiotic factors such
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