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Sulfate Reducing Communities in Aquifer Systems Can Be Reliably Stimulated by Addition of Complex Nutrients

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Sulfate Reducing Communities in Aquifer Systems Can Be Reliably Stimulated by Addition of Complex Nutrients University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 8-2012 Sulfate reducing communities in aquifer systems can be reliably stimulated by addition of complex nutrients Matthew Bryan Scholz [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Bioinformatics Commons, and the Environmental Microbiology and Microbial Ecology Commons Recommended Citation Scholz, Matthew Bryan, "Sulfate reducing communities in aquifer systems can be reliably stimulated by addition of complex nutrients. " PhD diss., University of Tennessee, 2012. https://trace.tennessee.edu/utk_graddiss/1386 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Matthew Bryan Scholz entitled "Sulfate reducing communities in aquifer systems can be reliably stimulated by addition of complex nutrients." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Microbiology. Gary S. Sayler, Major Professor We have read this dissertation and recommend its acceptance: Alison Buchan, Steven W. Wilhelm, Mark Radesovich Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Sulfate Reducing Communities in Aquifer Systems can be Reliably Stimulated by Addition of Complex Nutrients A Dissertation Presented for the Doctorate of Philosophy Degree The University of Tennessee, Knoxville Matthew Bryan Scholz August 2012 ii Copyright © 2012 Matthew Bryan Scholz All rights reserved. iii Dedication First and foremost, I have to thank my wife, Jeanna Scholz for her support, care and help during this process. I am grateful to her for all the opportunities we have found during our time together. For my mother, father, grandparents and family: I am, and always will be, thankful and proud to be considered a part of all of your lives. In no small part, it would not have been possible for me to achieve this goal without all of your love and support. Finally, to my daughter: Believe me, if I can do this, you can do anything. I love you, Stella Mai Carol Scholz. iv Acknowledgements It is with gratitude that I thank my advisor, Dr. Gary Sayler for his support during my career, as well as my committee, Dr. Steve Wilhelm, Dr. Alison Buchan and Dr. Mark Radosevich for all their support, patience and advice. Thanks to Dr. Vernon McIntosh Jr. who helped me frame several important points in this dissertation. I also need to thank Hebe Dionisi, who initiated this project, Dr. Larry McKay, who was instrumental in gathering samples in Bangladesh and Dr. Alice Layton who aided in the experimental design and other vital steps to gather information from my samples. Also thanks to Tommy Mead and Dr. Jennifer DeBruyn, who helped me with protocols, design, performing protocols, and generally keeping me sane. Finally, everyone at the Center for Environmental Biotechnology at the University of Tennessee: Thank you for your help and support. v Abstract The dissertation presented below is the summation of research into the potential roles of microbial communities associated with aquifers of Bangladesh contaminated with naturally occurring arsenic, including microcosm experiments to assess the role of nutrient supplementation on both the solubility of arsenic and associated bacterial community shifts. Nutrient supplementation microcosm experiments show that any supplementation can stimulate growth of sulfate reducing microbes (SRM), which can also be associated with removal of arsenic and other minerals. The addition of both a complex carbon and sulfate source shows prolonged removal of these elements from the soluble phase. Increased SRM numbers were maintained through 96 days of incubation. A bioinformatic investigation of the identified subsystems encoded by all sequenced and annotated bacteria capable of carrying out the most conserved steps in sulfate reduction was performed. These analyses indicated that there are a number of SRM capable of directly reducing complex carbon sources, both in syntrophic communities, as well as without additional aid from the environment. Sulfate reducing microbes are present, detectable and easily stimulated to grow in aquifer sediment. These communities of SRM are able to create conditions capable of removing arsenic from the soluble phase. The rate of growth of SRM and ability to maintain this immobilization supports the theory that SRM detected in the environment are capable of growth on complex nutrients, and require additional nutrients to successfully remediate arsenic for long periods of time. vi Table of Contents Introduction and General Information ................................................................................ 1 Water Contamination: Microbial, Chemical and Biogeochemical ................................. 1 Arsenic in Bangladesh .................................................................................................... 2 Arsenic Contamination Led to Arsenic Exposure .......................................................... 3 The Importance of Groundwater to Bangladesh ............................................................. 6 Challenges to Arsenic Remediation ................................................................................ 8 The Need for in situ Remediation ................................................................................. 10 Hypotheses .................................................................................................................... 10 Literature Review.............................................................................................................. 15 Arsenic in Aquifers: Potential Sources, Cycling and Mechanisms .............................. 16 Potential Role of Iron Reducing Bacteria in Arsenic Solubility ................................... 17 Respiratory Arsenic Transformation: A Mechanism for Increased Arsenic Solubility 18 Increased Arsenic Solubility: Oxidation of Reduced Minerals .................................... 18 Immobilization or Mineralization of Arsenic by Sulfate Reduction ............................ 18 Potential Arsenic Cycling ............................................................................................. 19 Sulfate Reducing Bacteria: Mechanisms of Action ...................................................... 20 Impact and Significance ............................................................................................ 20 Overview ................................................................................................................... 30 3- Step 1: SO4 + ATP -> APS + PPi ........................................................................... 32 2- Step 2: APS -> ADP + SO3 .................................................................................... 33 2- + 2+ Step 3: SO3 + 6 H + 6 e- -> S + 3H2O ................................................................ 33 Environmental Engineering: Community Shifts as a Result of Amendment ............... 34 Sulfide Interaction with Metals ..................................................................................... 38 Arsenic: Toxicity, Microbial Resistance, and Respiratory Pathways ........................... 40 Arsenic Resistance ........................................................................................................ 41 Molecular Analysis and Detection of Sulfate Reducing Microorganisms Approach and Issues ............................................................................................................................. 44 Functional Gene Detection vs. Taxonomy.................................................................... 46 Sampling: Bias and Extraction...................................................................................... 47 qPCR as Molecular Characterization ............................................................................ 50 SRM Detection and Quantification ............................................................................... 53 Molecular Techniques ................................................................................................... 53 Microcosms: Construction, Analysis and Sampling Microcosm Design, Construction and Analysis .................................................................................................................. 55 Aquifer Sampling (Water Filtration and Sediment Collection) ................................ 58 Well Water: Well Preparation ................................................................................... 58 Well Water Filtration ................................................................................................ 59 Sediment Sampling ................................................................................................... 60 Materials and Methods ...................................................................................................... 68 Experimental Design ....................................................................................................
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