ABSTRACT CHENG, QIWEN. Understanding Microbial
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ABSTRACT CHENG, QIWEN. Understanding Microbial Transformations of Organic Matter Under Anaerobic Conditions: Experimental Evaluation of Mediating Capabilities of Pyrogenic Carbonaceous Materials and Metagenomic Characterization of Mixed Communities (Under the direction of Dr. Douglas Call). Anaerobic microbial transformations play an essential role in organic matter degradation in the field of wastewater and solid waste treatment. Nevertheless, the application of anaerobic treatment is limited by the range of contaminants that can be targeted and the long timescales that are often required. These challenges encourage researchers to explore novel microbial pathways for contaminant degradation and energy production, and to identify microorganisms that allow engineers to shape microbial communities for environmental purposes. This dissertation provides some insights into these research areas by conducting three projects: 1) investigating the impact of amending pyrogenic carbonaceous materials (PCMs) on methane generation from anaerobic bioreactors fed with high-strength wastewater; 2) evaluating an approach to cost-effectively enrich PCM-reducing microbial communities from a PCM- amended system; and 3) characterizing the impact of temperature on structures and functions of microbial communities in landfills. The first project (Chapter 2) shows for the first time that PCM properties other than conductivity can largely explain how material amendments impact short-term batch reactor performance, which provides guidance for selecting optimal material types, sizes, and loadings for methane generation in anaerobic digesters. The second project (Chapter 3) successfully enriched an activated carbon-reducing microbial community derived from a drinking water biological activated carbon system with activated carbon as the sole electron acceptor, which proposes a novel, low-cost method to grow exoelectrogens from mixed cultures. The third project (Chapter 4) constitutes the first study to comprehensively investigate the response of microbial communities to elevated temperatures in landfills, and provides guidance for operating landfills and recovering renewable biogas. Both experimental evaluation and computational analysis were performed in this dissertation to characterize microbial reactions and identify key microorganisms associated with anaerobic microbial transformations of organic matter. © Copyright 2020 Qiwen Cheng All Rights Reserved Understanding Microbial Transformations of Organic Matter Under Anaerobic Conditions: Experimental Evaluation of Mediating Capabilities of Pyrogenic Carbonaceous Materials and Metagenomic Characterization of Mixed Communities by Qiwen Cheng A dissertation submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Civil Engineering Raleigh, North Carolina 2020 APPROVED BY: _______________________________ _______________________________ Douglas Call Francis Lajara De Los Reyes Committee Chair _______________________________ _______________________________ Morton Barlaz Detlef Knappe DEDICATION This dissertation is dedicated to my parents, Shiqing Cheng and Shumin Cheng, who always love me unconditionally and whose good examples have taught me to work hard for the things that I aspire to achieve. This dissertation is also dedicated to those who devote their lives to protecting the environment. The world will become a better place because of you. ii BIOGRAPHY Qiwen Cheng was born in Jinan, Shandong Province, China in 1991. She received her bachelor’s degree in Environmental Engineering from Shandong University, China, in 2013. She started her graduate study in the same year, and received her master’s degree in Civil Engineering from University of Washington in 2015. She then transferred to North Carolina State University to pursue a doctoral degree in Civil Engineering, with a specialization in Environmental, Water Resources and Coastal Engineering. Her research focuses on understanding the interactions between microorganisms and the environment, and exploring approaches to produce the desired microbial populations for environmental purposes. During her graduate study, she characterized microbial communities in engineered systems and investigated how their compositions and functions could be affected by environmental conditions. She also investigated electron transfer occurring in microbial communities and how it could be facilitated by amendments of pyrogenic carbonaceous materials (PCMs). In her research, she relies extensively on molecular biology techniques, metagenomics and advanced analytical approaches to characterize PCM properties as well as microbial community structures, physiology and metabolism. iii ACKNOWLEDGMENTS I am deeply grateful for my committee members who were more than generous with their expertise and precious time. My deepest gratitude goes to Dr. Douglas Call, my committee chair, for his countless hours of reflecting, reading, encouraging, and most of all patience throughout the entire process. I would also like to show my gratitude to Dr. Francis de los Reyes, Dr. Detlef Knappe, Dr. Morton Barlaz, and Dr. Owen Duckworth for serving on my committee and enlightening me with great research ideas. I would like to thank the current and former Call Group members, Dr. Juan Fausto Ortiz Medina, Dr. Fei Liu, Conner Murray, Victoria Tavares, Elvin Hossen, Sol Park, Mark Poole, Yazeed Algurainy, Dr. Shan Zhu and Hezhou Ding, for all of your support on schoolwork and research. I would also like to thank my friends in Civil Engineering at North Carolina State University, Binghui Li, Zisu Hao, Qianwen Liu, Amie McElroy, Zachary Hopkins, Asmita Narode, Arpit Sardana, Mei Sun, Joe Weaver, Yue Zhi, Chuhui Zhang, for all the fun we have had during the past five years. Special thanks to Yi-Chun Lai, who has been a constant source of kindness, strength and inspiration for me. May peace, hope and love be with you all. I would like to acknowledge the help from North Carolina State University Student Health Services for taking care of my physical and mental health. I want to give my special thanks to Sooyoung Uhm, Shauna Campbell and Dr. Heather Rogers for guiding me through the challenges in graduate school. I would also like to acknowledge the staff members at North Carolina State University, Dr. Lisa Castellano and Jake Rhoads in Civil Engineering, Chuck Mooney, Roberto Garcia, Chuanzhen Zhou and Fred Stevie at Analytical Instrumentation Facility, Hannah Jones, David Baltzegar and Kristen Fowler in Genomic Sciences Laboratory and Lisa Lentz in Environmental and Agricultural Testing Service, for their assistance in sample iv analysis. I would like to further acknowledge the staff members, Charles Cocker at South Durham Water Reclamation Facility, Jason Parker at North Cary Water Reclamation Facility, Jess Brown and Jennifer Nyfennegger at Carollo Engineers, Pamela London-Exner at Veolia North America, and Jeremy Ennis and Frederick Hughes at Dempsey E. Benton Water Treatment Plant for their kind offer of water and carbon samples. v TABLE OF CONTENTS LIST OF TABLES ....................................................................................................................... vii LIST OF FIGURES ...................................................................................................................... ix Chapter 1. Introduction .............................................................................................................. 1 Chapter 2. Amending anaerobic bioreactors with pyrogenic carbonaceous materials: the influence of material properties on methane generation ........................................................ 12 2.1. Abstract ..................................................................................................................... 12 2.2. Significance .............................................................................................................. 13 2.3. Introduction .............................................................................................................. 13 2.4. Materials and methods .............................................................................................. 15 2.5. Results and discussion .............................................................................................. 20 2.6. Conclusions .............................................................................................................. 38 2.7. References ................................................................................................................ 40 Chapter 3. Developing microbial communities containing a high abundance of exoelectrogenic microorganisms using activated carbon granules ....................................... 46 3.1. Abstract ..................................................................................................................... 46 3.2. Significance .............................................................................................................. 46 3.3. Introduction .............................................................................................................. 47 3.4. Materials and methods .............................................................................................. 49 3.5. Results and discussion .............................................................................................. 53 3.6. Conclusions .............................................................................................................