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The Association Between Bacteria, Plant Establishment and Metal(Loid) Immobilization in Metalliferous Mine Tailings

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The Association Between Bacteria, Plant Establishment and Metal(Loid) Immobilization in Metalliferous Mine Tailings Rhizosphere Bacteria and Phytostabilization Success: The Association Between Bacteria, Plant Establishment and Metal(loid) Immobilization in Metalliferous Mine Tailings Item Type text; Electronic Dissertation Authors Honeker, Linnea Katherine Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 07/10/2021 03:05:59 Link to Item http://hdl.handle.net/10150/624161 RHIZOSPHERE BACTERIA AND PHYTOSTABILIZATION SUCCESS: THE ASSOCIATION BETWEEN BACTERIA, PLANT ESTABLISHMENT AND METAL(LOID) IMMOBILIZATION IN METALLIFEROUS MINE TAILINGS by Linnea Honeker __________________________ Copyright © Linnea Honeker 2017 A Dissertation Submitted to the Faculty of the DEPARTMENT OF SOIL, WATER, AND ENVIRONMENTAL SCIENCE In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY In the Graduate College THE UNIVERSITY OF ARIZONA 2017 2 THE UNIVERSITY OF ARIZONA GRADUATE COLLEGE As members of the Dissertation Committee, we certify that we have read the dissertation prepared by Linnea Honeker, titled “Rhizosphere Bacteria and Phytostabilization Success: The Association Between Bacteria, Plant Establishment and Metal(loid) Immobilization in Metalliferous Mine Tailings”, and recommend that it be accepted as fulfilling the dissertation requirement for the Degree of Doctor of Philosophy. ___________________________________________________ Date: 2/2/17 Raina M. Maier, Ph.D. ___________________________________________________ Date: 2/2/17 Jonathan D. Chorover, Ph.D. ___________________________________________________ Date: 2/2/17 Virginia I. Rich, Ph.D. ___________________________________________________ Date: 2/2/17 Donata Vercelli, M.D. ___________________________________________________ Date: 2/2/17 Gayatri Vedantam, Ph.D. Final approval and acceptance of this dissertation is contingent upon the candidate’s submission of the final copies of the dissertation to the Graduate College. I hereby certify that I have read this dissertation prepared under my direction and recommend that it be accepted as fulfilling the dissertation requirement. ___________________________________________________ Date: 2/2/17 Dissertation Director: Raina M. Maier, Ph.D. 3 STATEMENT BY AUTHOR This dissertation has been submitted in partial fulfillment of the requirements for an advanced degree at the University of Arizona and is deposited in the University Library to be made available to borrowers under rules of the Library. Brief quotations from this dissertation are allowable without special permission, provided that an accurate acknowledgement of the source is made. Requests for permission for extended quotation from or reproduction of this manuscript in whole or in part may be granted by the head of the major department or the Dean of the Graduate College when in his or her judgment the proposed use of the material is in the interests of scholarship. In all other instances, however, permission must be obtained from the author. SIGNED: Linnea Honeker 4 ACKNOWLEDGEMENTS I have had a tremendous amount of support over the last 5 years, and couldn’t have completed this journey without some key individuals. First, I’d like to acknowledge and thank my advisor Dr. Raina Maier. Thank you for granting me the opportunity to be a graduate student in your lab and mentoring me. With patience and encouragement, you have taught me so much about the research process, writing, and how to push myself to my limits. I couldn’t have asked for a better advisor to help mold me into a professional scientist prepared for a post-graduate career and beyond. I’d also like to thank my committee members, Dr. Virginia Rich, Dr. Jon Chorover, Dr. Gayatri Vedantam, and Dr. Donata Vercelli. Thank you for making the commitment and taking the time from your busy schedules to play such a critical role in the completion of my graduate degree. I appreciate any advice and suggestions you have given me regarding my research along the way. Regarding the implementation and maintenance of the Iron King Mine and Humboldt Smelter Superfund field site, there are several people to thank. Thank you Scott White, who devoted endless hours setting up and maintaining the field site. Thank you Dr. Juliana Gil-Loaiza for all your effort in collecting and processing many samples from the field site and for the critical data I used in my research. Without the effort of these researchers, I would not have had the field site from which to collect my samples. There are many others that I appreciate for their time and effort in helping me with my research. Our lab manager Dr. Julie Neilson was vital to my success with our many talks about my research and her help in preparing and writing my manuscripts. Her brilliant ideas and input helped me tremendously. It was a pleasure working with my 5 colleague Dr. Robert Root in my first research project who did metal analysis on my root samples at the Stanford Synchrotron. Also, I’d like to thank Patricia Jansma who trained me on the confocal microscope and was always available if I needed any help or advice regarding sample analysis. And finally, I’d like to thank all my lab mates who were so much fun and made this journey more light-hearted and enjoyable. 6 DEDICATION First, I’d like to dedicate this dissertation to my mother, Diane Herbertson. Despite sometimes challenging conditions during my childood, my mom always provided for me and did whatever she could to make sure I got everything I needed and that I was in good schools so I could succeed. She instilled in me perserverance and the will to overcome challenges. During the darkest times of my life, she never left my side, and I wouldn’t have made it to where I am now if it weren’t for her. I’d also like to dedicate this dissertation to my husband Craig Honeker and daughter Audrey. My husband has been with me through all of the ups and downs of my entire graduate career, and never gave up on me. He helped me to laugh and have fun, and took me on many adventures, giving me a break from my school worries and stress. And finally, my daughter Audrey is a shining light in my life who gives me endless hope and motivation to be the best I can be. I want her to know she can acheive whatever her dreams may be. 7 TABLE OF CONTENTS ABSTRACT……………………………………………………………………………....8 CHAPTER 1: INTRODUCTION………………………………………………………..10 1. Literature Review………………………………………………………….…..10 2. Explanation of Dissertation Format…………………………………………...31 3. References………………………………………………………………….….33 4. Figure Legend…………………………………………………………………51 5. Figures………………………………………………………………………....52 APPENDIX A: EFFECT OF RE-ACIDIFICATION ON BUFFALO GRASS RHIZOSPHERE AND BULK MICROBIAL COMMUNITIES DURING PHYTOSTABILIZATION OF METALLIFEROUS MINE TAILINGS.............54 APPENDIX B: BACTERIAL ROOT COLONIZATION PATTERNS OF BUCHLOE DACTYLOIDES GROWING IN METALLIFEROUS MINE TAILINGS REFLECT PLANT STATUS AND GEOCHEMICAL CONDITIONS………………………………………………………….….......124 APPENDIX C: RESOLVING COLOCALIZATION OF BACTERIA AND METAL(LOID)S ON PLANT ROOT SURFACES BY COMBINING FLUORESCENCE IN SITU HYBRIDIZATION (FISH) WITH MULTIPLE-ENERGY MICRO-FOCUSED X-RAY FLUORESCENCE (ME μXRF)……………………………………..……………………………..173 8 ABSTRACT Phytostabilization offers a less expensive alternative to traditional cap and plant methods for containing metalliferous mine tailings to prevent wind erosion and contamination of nearby communities and the environment. However, plant establishment during phytostabilization of pyritic legacy mine tailings in semiarid regions is challenging due to particularly extreme conditions including low pH, low organic carbon, low nutrients, and high toxic metal(loid) concentrations. Microorganisms drive major biogeochemical cycles in soils, however, the roles microorganisms play at the root – soil interface during phytostabilization, particularly in relation to plant health and metal immobilization, are not yet fully understood. The aims of this dissertation are to focus on bacterial communities associated with the roots of buffalo grass used in the phytostabilization of pyritic metalliferous mine tailings to: i) characterize bacterial diversity and communities of rhizosphere and bulk substrate, ii) delineate associations between rhizoplane bacterial colonization patterns and environmental and plant status parameters, and iii) develop an in situ method to visually assess associations between roots, bacteria, and metals. Key findings indicate that after addition of a compost amendment to alleviate the plant-growth inhibiting characteristics of mine tailings, rhizosphere and bulk substrate contain a diverse, plant-growth supporting bacterial community. As substrate re-acidifies due to compost erosion, an emergence of an iron (Fe)- and sulfur (S)-oxidizer and Fe-reducer dominated, less diverse community develops in the bulk and rhizosphere substrate, thus posing a threat to successful plant establishment. However, even at low pH, some plant-growth-promoting bacteria are still evident in the rhizosphere. On the rhizoplane (root surface), the relative abundance of 9 metabolically active bacteria was positively correlated with plant health, verifying the strong association between plant health and bacteria. Furthermore, pH showed a strong association with the relative abundance of
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