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UNIVERSITY of CALIFORNIA RIVERSIDE Effects of in Situ UNIVERSITY OF CALIFORNIA RIVERSIDE Effects of in situ Bioremediation Strategies on the Biodegradation of Polycyclic Aromatic Hydrocarbons and Microbial Community Dynamics in Soil A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Environmental Toxicology by Douglas Carl Wolf September 2019 Dissertation Committee: Dr. Jay Gan, Chairperson Dr. Samantha Ying Dr. Peter Homyak Copyright by Douglas Carl Wolf 2019 The Dissertation of Douglas Carl Wolf is approved: Committee Chairperson University of California, Riverside ACKNOWLEDGEMENTS I would like to thank everyone who has been a part of my graduate research the past five years at the University of California, Riverside. Graduate school has been a challenging, yet extremely gratifying time of my life and this would not have been possible without the support and guidance I received throughout the years. I would like to thank Dr. Jay Gan for his valuable mentorship and support. I am grateful for the freedom and responsibility to pursue research interests that I was truly passionate about, even if they were not previously studied in the lab. I am also thankful for the opportunity to present my research internationally at locations I never imagined I would visit and creating once in a lifetime experiences that I will forever cherish. I would also like to thank my committee members Dr. Peter Homyak and Dr. Samantha Ying for generously serving on my dissertation committee and providing thoughtful advice in a positive environment that helped me navigate the many ups and downs of this journey. I am also thankful for numerous students and visiting scholars in our lab that have been an absolute pleasure to work with. I would like to specifically acknowledge Jaben Richards, Jie Wang, and Qiuguo (Rachel) Fu for their indispensable advice during my first few years in the graduate program. I could not have been successful in graduate school if not for the love and support from family and friends. I would like to thank my parents Duane and Nancy Wolf for always believing in me without hesitation in whatever path I chose in life. Thank you for your unconditional love and for giving me the hope and courage to pursue graduate school. Thank you Sara Santos for moving across the iv country to California with me and starting a life together. You are my cornerstone and I would not have been able to get through graduate school without you. Thank you for reminding me to eat, that water is more important than coffee, and that everything happens for a reason. I would also like to thank the “Fogon Friday” crew, Zachary Cryder, Michelle McGinnis, Alex Steele, and Craig Carlan for providing a necessary break from the lab with many laughs and too much food. I would also like to thank Stacia Dudley and Allison Taylor for their friendship and support as we all entered and underwent the hardships of graduate school together. I would also like to thank Environmental Pollution and Chemosphere for publishing my research and permitting me to use the articles in this dissertation. Chapter 3 is reproduced with permission from: Wolf, D.C., and J. Gan. 2018. Influence of rhamnolipid biosurfactant and Brij-35 synthetic surfactant on 14C-pyrene mineralization in soil. Environmental Pollution 243, 1846-1853. Chapter 4 is reproduced with permission from: Wolf, D.C., Cryder, Z., and J. Gan. 2019. Soil bacterial community dynamics following surfactant addition and bioaugmentation in pyrene-contaminated soils. Chemosphere 231, 93-102. Funding for this work was provided by the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE- 1326120. v ABSTRACT OF THE DISSERTATION Effects of in situ Bioremediation Strategies on the Biodegradation of Polycyclic Aromatic Hydrocarbons and Microbial Community Dynamics in Soil by Douglas Carl Wolf Doctor of Philosophy, Graduate Program in Environmental Toxicology University of California, Riverside, September 2019 Dr. Jay Gan, Chairperson Polycyclic aromatic hydrocarbons (PAHs) are a class of compounds of environmental and public health concern because of their toxicity and environmental ubiquity that will be further exacerbated by increasing anthropogenic pollution. In situ bioremediation is a common cleanup technique for PAH-contaminated soils because it is considered to be cost-effective and environmentally-friendly. However, PAHs are often bound to nonpolar soil domains and become resistant to microbial degradation, the primary PAH removal pathway. This dissertation addresses these limitations by evaluating bioremediation- enhancement technologies such as biosurfactant amendment, bioaugmentation, and phytoremediation to increase PAH bioavailability and/or soil microbial activity. The use of biosurfactants to increase PAH bioavailability has the potential to be an environmental alternative to synthetic surfactants. Therefore, rhamnolipid biosurfactant was compared to Brij-35 surfactant in two soils contaminated with 14C-pyrene that were also bioaugmented with a PAH-degrading microbe, Mycobacterium vanbaalenii PYR-1. The effect of the surfactants and bioaugmentation on PAH biodegradation and soil microbial vi community dynamics was evaluated. The addition of Brij-35 increased 14C-pyrene mineralization in both soils, but the rhamnolipid biosurfactant inhibited PAH degradation in a dose-dependent manner, which was likely due to preferential utilization of the biosurfactant as an easier carbon source by the degrading microorganisms. The bioaugmentation of M. vanbaalenii PYR-1 resulted in efficient 14C-pyrene dissipation. Using 16S rRNA analysis, it was determined that the pyrene biodegradation was associated with changes in the soil microbial communities. The addition of pyrene resulted in a large increase in Bacillus, a genus associated with PAH degradation. However, the addition of rhamnolipid biosurfactant decreased the abundance of Bacillus microorganisms, which was reflected in 14C-pyrene mineralization. These bioremediation-enhancement technologies were further assessed in a phytoremediation setting in PAH-contaminated soil from a shooting range site due to the accumulation of clay target fragments. Bermudagrass and switchgrass enhanced soil enzyme activity and PAH biodegradation. The bioaugmentation of M. vanbaalenii PYR-1 enhanced high- molecular-weight PAH biodegradation. The decrease in PAH concentrations was also reflected in lettuce seed germination toxicity assays. Overall, this research highlights the importance of physical and biological mechanisms in the evaluation and implementation of in situ bioremediation-enhancement technologies for successful PAH remediation of contaminated soils. vii Table of Contents Chapter 1 Introduction..................................................................................................... 1 1.1 Physicochemical Properties and Toxicity of Polycyclic Aromatic Hydrocarbons ... 1 1.2 Sources and Environmental Fate of PAHs ................................................................ 7 1.2.1 Soil Microbial Degradation of PAHs ............................................................... 13 1.3 Bioremediation of PAH-contaminated Soils ........................................................... 17 1.4 Strategies to Improve Bioremediation Efficacy of PAH-contaminated Soils ......... 20 1.4.1 Bioaugmentation ............................................................................................... 21 1.4.2 Biostimulation .................................................................................................. 23 1.4.3 Surfactant Amendment ..................................................................................... 23 1.4.4 Phytoremediation .............................................................................................. 28 1.4.5 Integrated Bioremediation Approaches ............................................................ 31 1.5 Summary ................................................................................................................. 32 1.6 Research Objectives ................................................................................................ 33 1.7 Dissertation Organization ........................................................................................ 34 1.8 References ............................................................................................................... 35 Chapter 2 Influence of Rhamnolipid Biosurfactant and Brij-35 Synthetic Surfactant on 14C-Pyrene Mineralization in Soil ............................................................................ 49 2.1 Introduction ............................................................................................................. 49 2.2 Materials and Methods ............................................................................................ 51 2.2.1 Chemicals ......................................................................................................... 51 2.2.2 Soil and Surfactant Properties .......................................................................... 52 2.2.3 Microbial Incubation ........................................................................................ 53 2.2.4 Pyrene Mineralization Experiments ................................................................. 54 2.2.5 Quality Assurance and Quality Control............................................................ 56 2.3 Results and Discussion ...........................................................................................
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