MICROBIAL COMMUNITY AND BIOGEOCHEMICAL CHARACTERISTICS IN RECLAIMED SOILS AT PT BUKIT ASAM COAL MINE, SOUTH SUMATRA, INDONESIA A thesis presented to the faculty of the Graduate School of Western Carolina University in partial fulfillment of the requirements for the degree of Master of Science in Biology By Kyle Bryce Corcoran Co-Directors: Dr. Jerry R. Miller, Dr. John P. Gannon Department of Geosciences and Natural Resources Committee Members: Dr. Sean P. O’Connell, Department of Biology Dr. Thomas H. Martin, Department of Biology March 2018 ACKNOWLEDGEMENTS I would like to express my sincere gratitude to my thesis co-advisors, Dr. Jerry Miller and Dr. JP Gannon for their dedication, and encouragement throughout my graduate school experience. If it weren’t for the many hours spent helping me build the framework of this project, and critiquing my work, I would have never built the confidence that I have now. I would also like to thank all of my committee members: Dr. Sean P. O’Connell, Dr. Thomas H. Martin for the time you took to teach me new techniques regarding microbial and statistical analyses. In addition, thank you so much Micky Aja, Amar Amay, and Adi Arti Elettaria for accompanying me during my stay in Indonesia. I truly appreciate the friendships I have built with you all throughout this time and will never forget how much you all helped me throughout this experience. Trip Krenz, you have watched over me and seen me grow over the last several years. Thank you for always telling me to hold my head high and to look at the positive things that were meant to come my way. I truly appreciate your support and watching over me as an older brother. To Joe Brazelton who has helped and supported me from the start of my master’s project in the humid tropics of South Sumatra, Indonesia up until the very end. You have no idea how much your support and guidance has meant to me over the years, thank you for everything bud. To all my friends and family who always believed in me, and watched me grow as an individual. I can not express how much your support has meant to me over the last several years. The amount of time each and everyone one of you took to give me advice and pick me up in a time of need makes me forever grateful. Lastly, to my father who passed away. I promise to hold on to my dreams for you. Thank you all very much! ii TABLE OF CONTENTS List of Tables ................................................................................................................................. iv List of Figures ..................................................................................................................................v List of Abbreviations ..................................................................................................................... vi Abstract ........................................................................................................................................ vii Chapter One: Introduction ...............................................................................................................1 Chapter Two: Methods and Materials..............................................................................................6 2.1: Study Area ...........................................................................................................................6 2.2: Sample Collection and Well Installation .............................................................................8 2.3: Soil Microbial Analysis .....................................................................................................12 2.3.1: DNA Extraction ...........................................................................................................12 2.3.2: Polymerase Chain Reaction (PCR) ..............................................................................13 2.3.3: DGGE and 16S rDNA Sequencing ..............................................................................14 2.4: Water Analysis ...................................................................................................................14 2.5: Soil Analysis ......................................................................................................................15 2.5.1: CNS Analysis ...............................................................................................................15 2.5.2: Acid Digestion and ICP Analysis ................................................................................15 2.5.3: Grain Size Analysis ......................................................................................................16 2.6: Statistical Analysis .............................................................................................................16 Chapter Three: Results ...................................................................................................................17 3.1: Soil Microbial Analysis .....................................................................................................17 3.1.1: Polymerase Chain Reaction (PCR) ..............................................................................17 3.1.2: DGGE and 16S rDNA Sequencing ..............................................................................17 3.1.3: Principal Components Analysis (PCA)........................................................................19 3.2: Water Analysis ...................................................................................................................27 3.3: Soil Analysis ......................................................................................................................31 3.3.1: Total Carbon ................................................................................................................31 3.3.2: Total Metal Concentrations in Soil ..............................................................................33 3.3.3: Grain Size Distribution ................................................................................................42 Chapter Four: Discussion ...............................................................................................................45 4.1: 16S rDNA Sequence Descriptions .....................................................................................45 4.2: Total Major and Trace Metal Concentrations in Soils .......................................................48 4.3: Potential Age Effect(s) on Soil Characteristics and Microbiology ....................................50 4.4: Major and Trace Metal Mobility in Soils and Subsurface Waters ....................................53 Chapter Five: Conclusions .............................................................................................................56 References ......................................................................................................................................58 Appendix ........................................................................................................................................72 iii LIST OF TABLES Table 1. Naming scheme and locations of monitoring wells and samples collected at PTBA ......12 Table 2. DNA sequence matches to genus for 16S rRNA gene fragments for isolates .................19 Table 3. DNA sequence matches to species for 16S rRNA gene fragments for isolates ..............19 Table 4. Principal components analysis (PCA) results of sediment samples and median .............21 Table 5. Principal components analysis (PCA) correlation results of total metal .........................24 Table 6. Principal components analysis (PCA) correlation results of total metal .........................25 Table 7. Principal components analysis (PCA) correlation results of total metal .........................27 Table 8. Correlation matrix for metal concentrations in subsurface water samples ......................28 Table 9. Metal concentrations (medians, means [standard deviations]) in subsurface water ........31 Table 10. Percent carbon (medians, means [standard deviations]) in topsoil and subsoil.............33 Table 11. Metal concentrations (medians, means [standard deviations]) for (A) topsoil and .......34 Table 12. Percent silt plus clay (medians, means [standard deviations]) in topsoil and subsoil ...42 Table 13. Correlation matrix for metal concentrations in soil samples. Bold values ....................44 Table A1. DNA sequence matches for partial 16S rRNA gene fragments for isolates .................72 iv LIST OF FIGURES Figure 1. PT Bukit Asam coal mine is located in South Sumatra, Indonesia ..................................7 Figure 2. Photograph depicting monitoring wells that were installed in the Agrotourism ............10 Figure 3. Conceptual model based on soil profiles observed in the field in reforested .................11 Figure 4. Denaturing gradient gel electrophoresis (DGGE) gel of bacterial communities ...........18 Figure 5. Principal components analysis (PCA) of sediment samples and median metal .............20 Figure 6. (A) Principal components analysis (PCA) of all surface samples and denaturing .........23 Figure 7. Principal components analysis (PCA) of surface samples and denaturing gradient ......26 Figure 8. Concentrations of (A) aluminum (ng/mL), (B) iron (ng/mL), (C) manganese ..............30 Figure 9. Percent carbon in sediment collected from (A) topsoil and (B) subsoil .........................32 Figure 10. Concentrations of Al (mg/Kg) in sediment collected from the