Enhanced Microbial Sulfate Removal Through a Novel Electrode-Integrated Bioreactor A THESIS SUBMITTED TO THE FACULTY OF THE UNIVERSITY OF MINNESOTA BY DANIEL C TAKAKI IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE DR. CHAN LAN CHUN JUNE 2018 © Daniel C Takaki 2018 Acknowledgements Academic support came from my major advisor Dr. Chan Lan Chun, as well as my thesis research committee members, Dr. Daniel S. Jones and Dr. Adrian Hanson. Additionally, the faculty of the University of Minnesota Water Resources Science program and the University of Minnesota – Duluth Civil Engineering Department. Laboratory support for this project came from Tobin Deen, Tyler Untiedt, Adelle Schumann, Sara Constantine, Thomas Vennemann, Jacob Daire, Kristofer Isaacson, and Brock Anderson of the Chun Research Group, University of Minnesota – Duluth, and Sophie LaFond-Hudson and Amber White of the Johnson Group, University of Minnesota - Duluth. This project would not have been possible without the financial support from a number of sources including the University of Minnesota College of Food, Agricultural, and Natural Resources Science (CFANS) Diversity Scholars – Graduate Student Fellowship, the United States Geological Survey (USGS) Water Resource Center Annual Grant Competition, and the Mining Innovation Grant. Technical support for this project was provided from the University of Minnesota Genomics Center and Dr. Daniel S. Jones, University of Minnesota College of Science and Engineering, for assisting in microbial community genomic sequencing and data composition. Steven Johnson, University of Minnesota-Duluth, Natural Resources Research Institute, helped to create the flow-through column reactors. i Dedication This thesis is dedicated to my parents, Pam and Steve Takaki, and my siblings Jeff and Marissa for their unyielding support and to my close friends who kept me humble and motivated while working on this project. ii Abstract In northeast Minnesota, elevated levels of sulfate in freshwater systems is a topic of great interest, due to potential adverse impacts to wild rice ecosystems. Sulfate may contribute to methylmercury production and eutrophication in certain conditions. Increased interest has emerged for developing low cost and efficient technologies to treat high levels of sulfate in mining and industrial waste water. The use of biological sulfate reduction is a promising and economically viable plan for maintaining low levels of sulfate and sulfide, but its performance is highly variable. This project developed a sediment bioelectrochemical batch reactor that used a low electrical potential to enhance and sustain biological sulfate reduction by continuously supplying electron donor substrates (electrolytic hydrogen) to sulfate reducing bacteria. The project aims to understand the effect of a low applied voltage on the efficacy of sulfate reduction and iron sulfide formation. Reactors contained creek sediment (Second Creek, MN) and an artificial mine water with a sulfate concentration of ~1000 ppm. The sulfur chemistry in the pore water of the reactors was assessed to determine sulfate reduction, resulting in over 90% reduction in porewater sulfate at the cathode in batch reactors, where electrolytic hydrogen gas was generated at a rate of 4.14 mmol/day. Simultaneously, ferrous iron was released into the reactor via iron electrodissolution and reacted with reduced sulfide ions to form iron sulfide precipitates. This level of hydrogen generation was sustained over a 14-day period and successfully showed that the application of a low voltage to sediment bioreactors is a promising technology to treat sulfate contaminated waste waters. iii The microbial community structure and relative abundance of different species associated with sulfate reduction were also examined. It was shown that relative abundance of sulfate reducing bacteria, specifically Desulfovibrio, a genus of deltaproteobacteria positively associated with sulfate reduction, which utilize hydrogen as their preferred electron donor, increased throughout batch reactor operation when operated at 2V. Finally, the sediment bioelectrochemical batch reactor served as a proof of concept for the application of low electrical potential to enhance and sustain biological sulfate reduction. The outcomes of this reactor operation laid the groundwork to develop a prototype flow-through bioelectrochemical reactor designed to handle larger volumes of waste water for an extended period of time. Preliminary results from this flow-through reactor demonstrated the ability to generate a constant supply of electrolytic hydrogen used by sulfate reducing bacteria. Through these experiments, recommendations have been made to improve efficacy of flow-through reactors. iv Table of Contents Acknowledgements i Dedication ii Abstract iii Table of Contents v List of Tables vi List of Figures vii Chapter 1. Introduction 1.1 Sulfate in Freshwater Ecosystems 1 1.2 Treatments of Sulfate Contaminated Waste Waters 3 1.3 Biological Sulfate Reduction as a Treatment Method 5 1.4 Project Scope 6 1.5 Project Hypothesis and Objectives 8 Chapter 2. Sediment Bioelectrochemical Batch Reactor for Sulfate Treatment 2.1 Sediment Bioelectrochemical Batch Reactor Configuration and Design 9 2.2 Operation and Sampling 10 2.3 Chemical Analysis 11 2.3.1 Physiochemical Analysis 11 2.3.2 Sulfur Chemistry Analysis 12 2.4 Sediment Bioelectrochemical Batch Reactor Results 13 2.5 Summary 20 Chapter 3. Microbial Community Analysis of Sediment Bioelectrochemical Batch Reactor 3.1 Sediment Collection and DNA Extraction Methods 24 3.2 Quantification of SRB populations using qPCRs 24 3.3 Amplicon Sequencing and Bioinformatics 26 3.4 Results 27 3.4.1 Quantification of SRB populations using qPCR 27 3.4.2 Microbial Community Diversity Analysis 31 3.5 Discussion 40 Chapter 4. Flow-Through Bioelectrochemical Reactor for Sulfate Treatment 4.1 Packed-Bed Bioelectrochemical Reactor Design 43 4.2 Reactor Operation and Analysis 44 4.3 Results 45 4.4 Discussion 54 4.5 Recommendations 56 Bibliography 60 Appendix A. Sediment Microbial Community Taxa 64 v List of Tables Table 1-1. Summary of costs and efficiencies associated with sulfate treatment processes adopted from Bowell 2004 and MPCA 2017. 4 Table 2-1. Chemical composition of artificial mine water 10 Table 3-1. Primers sets targeting the dsrAB gene tested for use in polymerase chain reaction and quantitative polymerase chain reaction. 26 Table 4-1. Average current density and daily hydrogen production in flow through bioelectrochemical reactors operating at a range of applied voltage (2V to 4V) and flow rates (30.2 mL/day to 108 mL/day). 46 vi List of Figures Figure 1-1. Sulfate concentrations in surface water in Minnesota. 2 Figure 2-1. Schematic diagram and photograph of sediment bioelectrochemical batch reactor. 9 Figure 2-2. Change of redox potential in porewater throughout the operation of sediment bioelectrochemical batch reactors operated at 2V and 0V. 14 Figure 2-3. Change of pH in porewater throughout the operation of sediment bioelectrochemical batch reactors operated at 2V and 0V. 14 Figure 2-4. Change of total iron concentration in porewater throughout the operation of sediment bioelectrochemical batch reactors operated at 2V and 0V. 15 Figure 2-5. Change in porewater sulfate concentration at the cathode throughout the duration of sediment bioelectrochemical batch reactors operated at 2V and 0V. 16 Figure 2-6. Black band iron sulfide formation developed at the cathode in sediment bioelectrochemical reactor after 14 days of 2V applied. 17 Figure 2-7. Solid phase sulfide concentration in sediment bioelectrochemical batch reactors after 14 days of operation at 2V and 0V. 18 Figure 2-8. SEM image and elemental mapping of Fe and S in black band precipitates in 2V reactors sediment after 14 days (1000x magnification). 19 Figure 2-9. SEM image and elemental mapping of Fe and S in untreated Second Creek sediment (1000x magnification). 19 Figure 3-1. Quantification of 16S rRNA gene and the dsrA gene in the sediment bioelectrochemical reactors as a function of reactor operation duration. 29 Figure 3-2. Ratio of dsrA to 16S rRNA gene copy numbers per gram of sediment in sediment bioelectrochemical batch reactors initially. 30 Figure 3-3. Ratio of dsrA to 16S rRNA gene copy numbers per gram of sediment in sediment bioelectrochemical batch reactors after 14 days. 30 vii Figure 3-4. Distribution of the most abundant phyla relative OTUs in both the control and 2V sediment bioelectrochemical batch reactors near the cathode (sample port D). 32 Figure 3-5. Distribution of the most abundant class relative OTUs in both the control and 2V sediment bioelectrochemical batch reactors near the cathode (sample port D). 33 Figure 3-6. Changes in relative abundance of orders of sulfate reducing bacteria near the cathode, measured as a function of Relative Observed OTUs versus reactor operation time. 34 Figure 3-7. Change in relative abundance of Desulfovibrionales over time near the cathode in relation to the change in sulfate concentration near the cathode in 2V reactor. 35 Figure 3-8. Changes in relative abundance of different taxa near the cathode, measured as a function of Relative Observed OTUs versus batch reactor operation time. 36 Figure 3-9. Relative abundance of sulfate reducing bacteria, iron oxidizing bacteria, sulfide oxidizing bacteria, and methanogenic bacteria on day 14 of batch reactor operation. 37 Figure 3-10. Principle Coordinate Analyses (PCoA) ordinations