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1 Diversity of Oomycetes Associated with Soybean DIVERSITY OF OOMYCETES ASSOCIATED WITH SOYBEAN SEEDLING DISEASES By Jorge Alejandro Rojas Flechas A DISSERTATION Submitted to Michigan State University in partial fulfillment of the requirements for the degree of Plant Pathology – Doctor of Philosophy Ecology, Evolutionary Biology and Behavior – Dual Major 2016 1 ABSTRACT DIVERSITY OF OOMYCETES ASSOCIATED WITH SOYBEAN SEEDLING DISEASES By Jorge Alejandro Rojas Flechas In the United States, soybeans are produced on 76 million acres of highly productive land, but can be severely impacted by diseases caused by oomycetes. Oomycetes are part of the microbial community that is associated with plant roots and the rhizosphere, which is a dynamic and complex environment subject to the interaction of different microbes and abiotic factors that could affect the outcome of the phytobiome interaction. Depending on environmental and edaphic conditions, some oomycete species will thrive causing root and seedling rot. The identity and distribution of these pathogen species is limited. Therefore, the main questions driving my research are what oomycetes are associated with soybean seedlings and what are the roles of these species causing disease? What factors increase or reduce the impact of these species on the soybean production system? With these questions in mind, the goals of my research are: (1) to characterize the oomycete diversity associated with seedling and root rot diseases of soybean; (2) determine the role of environmental and edaphic factors on the distribution of oomycete species; (3) develop molecular diagnostic tools for Phytophthora sojae and P. sansomeana and (4) evaluate the community structure of the oomycete species associated with soybean root diseases under different conditions. We initially utilized a two-year culture-based survey to study oomycetes associated with soybean seedlings from 11 states in the Midwest, characterizing the communities and profiling phenotypic traits such as pathogenicity and aggressiveness. With this approach, a total of 84 oomycete species were identified and characterized. Of those 84 oomycete species, 43 species 2 had detrimental effects on soybean seedlings being pathogenic and 17 of those pathogenic species also caused disease on soybean seeds. In addition, the ecology of oomycetes was studied by correlating abundance and diversity of oomycetes with different environmental and edaphic parameters. Our main findings were that the community structure of oomycetes (presence/absence) associated with soybean seedlings was similar geographically, but their abundances differed. By using the environmental and edaphic data, it was observed that latitude was correlated with oomycete diversity with increasing diversity observed in samples from higher latitudes. Other parameters such as temperature and precipitation affected community composition within and across years. Soil parameters like pH, clay content and cation exchange capacity also influenced the oomycete community structure. The survey served as a basis to develop markers for diagnostics, providing a collection of Phytophthora sojae isolates, a major soybean pathogen, and at the same time identifying and providing cultures for Phytophthora sansomeana as a threat for soybean. A hierarchical detection system for quantitative PCR and isothermal amplification was developed to identify these pathogens at the genus and species-specific level. Both assays were validated under laboratory and field conditions. Finally, an amplicon-based community analysis was adapted and developed to further investigate and characterize oomycete species and communities associated with agricultural systems. The loci targeted were the ITS of the rDNA, the D1-D3 regions of the 28S and the coxI gene. The data generated from the amplicon-based approach, in conjunction with the phenotype (pathogenicity/virulence) and species distribution, is being used to evaluate the role of climatic, edaphic and biotic factors on the oomycete community structure. Improved understanding of the oomycete community, especially in the root system, and the factors that influence it will enable improved disease management and enhance plant health. 3 ACKNOWLEDGEMENTS I would like to thank to Dr. Martin Chilvers, my advisor, for giving me the opportunity to be part of his lab and contribute to his program. His advice, guidance, and the freedom to explore topics on my own, and the same time the vote of confidence when I needed it. I also would like to acknowledge my committee: Dr. George Sundin, Dr. Andy Jarosz and Dr. Jim Smith, for all their discussions, feedback and advice. Also thanks to Jie, my Chinese brother who helped me on the way and we grew together in the process and Janette, for always helping out and looking out for us. To rest the of Chilvers lab members, thanks for the talks and feedback. I also would like to thank USDA National Institute for Food and Agriculture, United Soybean Board, North Central Research Program for the funding research and Michigan State Graduate School and the College of Agriculture for the scholarships the helped with the completion of my research and degree. Finally, I would like to thank my friends for their support and the good moments, and thanks to my family, my parents Jorge and Nancy for their unwavering support and love, my brothers and my extended family, and to the most important people in my life, my wife Luisa for her support, love and patience; Gaby and Sammy, they are my life and the reason to work hard every day. iv TABLE OF CONTENTS LIST OF TABLES ..................................................................................................................... viii LIST OF FIGURES ..................................................................................................................... xi Chapter 1 Literature Review ...................................................................................................... 1 Problem statement ...................................................................................................................... 2 Oomycete community ecology: tools and challenges from a plant pathology perspective ....... 5 Introduction ................................................................................................................................ 5 Traditional molecular tools to study oomycete diversity and ecology .................................... 10 Next-generation sequencing (NGS) to study oomycete diversity and ecology ....................... 16 Barcodes for identification of oomycetes ................................................................................ 20 Species definition and number of species in oomycetes .......................................................... 24 Applications of NGS to study the ecology of oomycetes ........................................................ 26 Perspectives of oomycete ecology ........................................................................................... 29 REFERENCES ......................................................................................................................... 33 Chapter 2 Oomycete species associated with soybean seedlings in North America – Part I: Identification and pathogenicity characterization ................................................................... 48 ABSTRACT ............................................................................................................................. 49 Introduction .............................................................................................................................. 50 Materials and methods ............................................................................................................. 52 Sample collection and isolation ............................................................................................ 52 Isolate storage and DNA extraction ...................................................................................... 54 Identification of isolates ........................................................................................................ 55 Seed pathogenicity assay ...................................................................................................... 56 Seedling root rot assay .......................................................................................................... 57 Koch’s postulates and SSCP confirmation ........................................................................... 58 Root area and root length image analysis ............................................................................. 59 Data analysis for root measurements .................................................................................... 59 Results ...................................................................................................................................... 62 Sample collection .................................................................................................................. 62 Seed pathogenicity ................................................................................................................ 65 Seedling root rot assay .......................................................................................................... 68 Comparison of seed and seedling root rot assays ................................................................. 75 Discussion ...............................................................................................................................
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