Studies on the Effects of Plant Variety and Root Exudate Compounds on the Soil Microbial Community

University of Kentucky UKnowledge Theses and Dissertations--Plant and Soil Sciences Plant and Soil Sciences 2015 STUDIES ON THE EFFECTS OF PLANT VARIETY AND ROOT EXUDATE COMPOUNDS ON THE SOIL MICROBIAL COMMUNITY Márton Szoboszlay University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Szoboszlay, Márton, "STUDIES ON THE EFFECTS OF PLANT VARIETY AND ROOT EXUDATE COMPOUNDS ON THE SOIL MICROBIAL COMMUNITY" (2015). Theses and Dissertations--Plant and Soil Sciences. 71. https://uknowledge.uky.edu/pss_etds/71 This Doctoral Dissertation is brought to you for free and open access by the Plant and Soil Sciences at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Plant and Soil Sciences by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known. I agree that the document mentioned above may be made available immediately for worldwide access unless an embargo applies. I retain all other ownership rights to the copyright of my work. I also retain the right to use in future works (such as articles or books) all or part of my work. I understand that I am free to register the copyright to my work. REVIEW, APPROVAL AND ACCEPTANCE The document mentioned above has been reviewed and accepted by the student’s advisor, on behalf of the advisory committee, and by the Director of Graduate Studies (DGS), on behalf of the program; we verify that this is the final, approved version of the student’s thesis including all changes required by the advisory committee. The undersigned agree to abide by the statements above. Márton Szoboszlay, Student Dr. Luke A. Moe, Major Professor Dr. Mark S. Coyne, Director of Graduate Studies STUDIES ON THE EFFECTS OF PLANT VARIETY AND ROOT EXUDATE COMPOUNDS ON THE SOIL MICROBIAL COMMUNITY DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Agriculture, Food, and Environment By Márton Szoboszlay Director: Dr. Luke A. Moe, Associate Professor of Plant and Soil Sciences Co-Director: Dr. Elisa M. D’Angelo, Associate Professor of Plant and Soil Sciences Lexington, Kentucky, USA 2015 Copyright © Márton Szoboszlay 2015 ABSTRACT OF DISSERTATION STUDIES ON THE EFFECTS OF PLANT VARIETY AND ROOT EXUDATE COMPOUNDS ON THE SOIL MICROBIAL COMMUNITY Plants modify the soil environment through their root system, changing its physical properties and exuding compounds that promote or inhibit the growth of certain microorganisms. Therefore the structure of the soil microbial community is different in the rhizosphere than in the bulk soil. This dissertation introduces three research projects that investigated the effects of specific root exudate compounds on the soil microbial community structure, and plant cultivar specific differences in the rhizosphere microbiota. The progenitor of maize is Balsas teosinte (Zea mays subsp. parviglumis). In a greenhouse experiment we compared the structure and function of its bacterial and fungal rhizosphere community with that of domesticated corn cultivars sweet corn and popping corn by terminal restriction fragment length polymorphism, fatty acid methyl ester analysis, and soil enzyme assays. The results allude to functional and structural differences in the rhizosphere microbial communities of the corn varieties that could lead to useful discoveries on how corn domestication has altered rhizosphere processes. To study how root exudate flavonoids 7,4′-dihydroxyflavone and naringenin influence the soil bacterial community structure we constructed model systems to approximate the flavonoid exudation of Medicago sativa roots. Soil samples from the model systems were subjected to ATP assays and 16S rRNA gene amplicon sequencing. Our results suggest that 7,4′-dihydroxyflavone can interact with a diverse range of soil bacteria, including members of Acidobacteria subdivision 4, Gaiellales, Nocardioidaceae, and Thermomonosporaceae and may have other functions in the rhizosphere in addition to nod-gene induction in the legume–rhizobia symbiosis. Hydroxyproline is the most common amino acid in plant cell wall proteins and serves as an important carbon and nitrogen source for soil bacteria. We treated soil with the L or the D enantiomer of hydroxyproline and collected samples for 16S rRNA gene amplicon sequencing three and seven days after the treatment. The L- and D-hydroxyproline treatments induced very similar responses in the bacterial community structure, but there were several differentially abundant groups. Our results inform about the role of hydroxyproline in shaping the soil microbial community in the rhizosphere and about the catabolism of its enantiomers in the soil. Keywords: Maize rhizosphere 7,4′-dihydroxyflavone Naringenin Hydroxyproline Soil bacterial community structure Márton Szoboszlay Student’s Signature 2015. 11. 20. Date STUDIES ON THE EFFECTS OF PLANT VARIETY AND ROOT EXUDATE COMPOUNDS ON THE SOIL MICROBIAL COMMUNITY By Márton Szoboszlay Dr. Luke A. Moe Director of Dissertation Dr. Elisa M. D’Angelo Co-Director of Dissertation Dr. Mark S. Coyne Director of Graduate Studies 2015. 11. 20. DEDICATION I’d like to dedicate this dissertation to You but only if you promise to read it all. ACKNOWLEDGMENTS I owe thanks to many of my teachers, peers, and students from the University of Kentucky who helped me in my professional development. I wouldn’t have been able to do this work without them. I’m especially grateful to the members of Moe-lab: to Ran for showing me a Mongolian wedding, to Ben for teaching me how yeast can be a pet, to Audrey for the oatmeal cookie recipe that actually works, to Qing for one Chinese word a day, to Ruth for explaining why scales are on a fish and not in the media room, to Muhammad for the ride to Lisle, to Atanas for the plate, mug, and bowl I practically stole from him, and to Alison for inviting me to the house of bunnies and frogs. I also have to thank Jenny, Jola, and Abbe from AGTC for the honorary membership and the comfy chair that allowed me to fall asleep while working on the T-RFLP data. These things may seem insignificant compared to all the professional teaching and advice I received from members of our lab and department, but they helped me greatly to stay in Lexington long enough to finish this work. Last but not least, I’d like to thank Luke for betting on the unknown (i.e. hiring me). iii TABLE OF CONTENTS Acknowledgments ............................................................................................................................... iii Table of contents ................................................................................................................................. iv List of tables ......................................................................................................................................... vi List of figures ..................................................................................................................................... viii List of files ............................................................................................................................................ ix Chapter 1: Comparison of rhizosphere microbial communities of Balsas teosinte and domesticated corn cultivars ................................................................................................................ 1 Introduction ............................................................................................................................ 1 Materials and methods ........................................................................................................... 2 Maize cultivars and teosinte..................................................................................... 2 Soil properties ............................................................................................................ 3 Plant growth conditions and rhizosphere sampling ............................................. 3 T-RFLP analysis for examining bacterial and fungal community structure ..... 4 Fatty acid methyl ester (FAME) analysis ............................................................... 6 Extracellular enzyme assays ..................................................................................... 7 Statistical analysis .................................................................................................... 10 Results .................................................................................................................................... 11 Bacterial and fungal community structure via T-RFLP ..................................... 11 Microbial

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