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Microbial Communities and Their Impact on Bioenergy Crops in Dynamic Environments South Dakota State University Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange Electronic Theses and Dissertations 2018 Microbial Communities and Their mpI act on Bioenergy Crops in Dynamic Environments Brandon Monier South Dakota State University Follow this and additional works at: https://openprairie.sdstate.edu/etd Part of the Biology Commons, and the Plant Sciences Commons Recommended Citation Monier, Brandon, "Microbial Communities and Their mpI act on Bioenergy Crops in Dynamic Environments" (2018). Electronic Theses and Dissertations. 2659. https://openprairie.sdstate.edu/etd/2659 This Dissertation - Open Access is brought to you for free and open access by Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. For more information, please contact [email protected]. MICROBIAL COMMUNITIES AND THEIR IMPACT ON BIOENERGY CROPS IN DYNAMIC ENVIRONMENTS BY BRANDON MONIER A dissertation submitted in partial fulfillment of the requirements for the Doctor of Philosophy Major in Biological Sciences Specialization in Plant Molecular Biology South Dakota State University 2018 iii ACKNOWLEDGEMENTS First, I would like to thank the Department of Biology and Microbiology and also the Department of Agronomy, Horticulture and Plant Science for their continued support of this program. To my thesis advisors, Drs. Heike Bücking and Jose Gonzalez- Hernandez, thank you for your support and providing the necessary help and motivation to complete this project. To Drs. Xijin Ge and Qin Ma, thank you for giving me the chance to pursue other facets of research and turning my hobbies into avenues of discovery. To my advisory committee, thank you for giving me additional guidance and challenging me to become a better scientist. Since science is a collaborative effort, I would like to the thank the following people (in alphabetical order) for helping me out with various projects over the years: Don Auger, Karen Barthel, Arvid Boe, Merritt Burch, Jerry Cordero-Sepulveda, April DeMell, Sam Dwire, Janice Eibensteiner, Carl Fellbaum, Kevin Garcia, Kristene Gedye, Nina Herrera, Arjun Kafle, Elliot Liepold, Bingqiang Liu, Jan Matson, Adam McDermaid, Jerry Mensah, James Monier, Brian Moore, Mandy Orth, Vincent Peta, Cankun Wang, Hadley Wickham, and Jing Zhao. I would also like to acknowledge the Sun Grant Initiative, the W.M. Keck Center, and the Joint Genome Institute for providing me the necessary resources and insight to accomplish this project. iv TABLE OF CONTENTS LIST OF ABBREVIATIONS .......................................................................................... vii LIST OF FIGURES ........................................................................................................ viii LIST OF TABLES ......................................................................................................... xvii ABSTRACT .................................................................................................................. xxiii Chapter 1: General Introduction .........................................................................................1 1.1 Prairie Cordgrass and its Benefits as a Potential Biofuel ......................................1 1.2 Mycorrhizal Endosymbiotic Interactions ..............................................................3 1.3 The Need for Further Research, Genetic Tools and Systems ...............................4 1.4 References .............................................................................................................6 Chapter 2: Microbiome analysis of Upper Midwest prairie cordgrass populations ...........9 2.1 Introduction ...........................................................................................................9 2.2 Materials and Methods ........................................................................................12 2.2.1 Sample Collection ....................................................................................... 12 2.2.2 DNA Extraction .......................................................................................... 12 2.2.3 Amplicon Sequencing ................................................................................. 13 2.2.4 Data QC, Alignment, and Analysis............................................................. 13 2.3 Results .................................................................................................................15 2.3.1 Primer metrics ............................................................................................. 15 2.3.2 Alpha diversity ............................................................................................ 15 2.3.3 Taxonomic abundance ................................................................................ 17 2.3.4 Beta diversity .............................................................................................. 19 2.4 Discussion ...........................................................................................................21 2.5 Figures .................................................................................................................27 2.6 Tables ..................................................................................................................45 2.7 References ...........................................................................................................57 Chapter 3: Impact of the arbuscular mycorrhizal symbiosis on the biomass potential of the bioenergy crop prairie cordgrass ..................................................................................63 3.1 Introduction .........................................................................................................63 3.2 Materials and Methods ........................................................................................65 3.2.1 Plant and fungal culture .............................................................................. 65 v 3.2.2 Experimental design.................................................................................... 66 3.2.3 Biomass, responsiveness, and AM fungi colonization analyses ................. 68 3.2.4 Phosphate and nitrogen analysis ................................................................. 69 3.2.5 Statistical analysis ....................................................................................... 69 3.3 Results .................................................................................................................70 3.3.1 Biomass ....................................................................................................... 70 3.3.2 Root colonization ........................................................................................ 72 3.3.3 P and N nutrition ......................................................................................... 73 3.4 Discussion ...........................................................................................................75 3.5 Figures .................................................................................................................79 3.6 Tables ..................................................................................................................97 3.7 References .........................................................................................................106 Chapter 4: Transcriptome analysis of Prairie Cordgrass, Switchgrass, and Brachypodium under AM Symbiosis .......................................................................................................111 4.1 Introduction .......................................................................................................111 4.2 Materials and Methods ......................................................................................114 4.2.1 Plant material and fungal culture .............................................................. 114 4.2.2 Experimental design.................................................................................. 114 4.2.3 AM colonization analysis and RNA extraction ........................................ 115 4.2.4 Alignments and de novo assembly ........................................................... 116 4.2.5 RNA-seq analysis and functional annotation ............................................ 117 4.3 Results ...............................................................................................................118 4.3.1 Mycorrhizal colonization .......................................................................... 118 4.3.2 Read metrics and de novo assembly overview ......................................... 118 4.3.3 RNA-seq overview.................................................................................... 118 4.3.4 Significant DEG activity ........................................................................... 119 4.3.5 Carbohydrate metabolism ......................................................................... 119 4.3.6 Photosynthetic pathways ........................................................................... 120 4.3.7 Abiotic and biotic stress ............................................................................ 120 4.3.8 Hormone metabolism ...............................................................................
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