Chapter 2 Microbially Enhanced Dissolution of Hgs in an Acid Mine

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Chapter 2 Microbially Enhanced Dissolution of Hgs in an Acid Mine Stability, Transformations, and Fate of Residual Mercury at the Inoperative New Idria Mercury Mine, New Idria, California A DISSERTATION SUBMITTED TO THE DEPARTMENT OF GEOLOGICAL AND ENVIRONMENTAL SCIENCES AND THE COMMITTEE ON GRADUATE STUDIES OF STANFORD UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPY Adam Douglas Jew January 2013 © 2013 by Adam Douglas Jew. All Rights Reserved. Re-distributed by Stanford University under license with the author. This work is licensed under a Creative Commons Attribution- Noncommercial 3.0 United States License. http://creativecommons.org/licenses/by-nc/3.0/us/ This dissertation is online at: http://purl.stanford.edu/jj799kf8676 ii I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Gordon Brown, Jr, Primary Adviser I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Scott Fendorf I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Alfred Spormann I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. James J. Rytuba Approved for the Stanford University Committee on Graduate Studies. Patricia J. Gumport, Vice Provost Graduate Education This signature page was generated electronically upon submission of this dissertation in electronic format. An original signed hard copy of the signature page is on file in University Archives. iii Abstract: Mercury mining in the California Coast Range has resulted in over a thousand mercury mines of various sizes that have yet to be remediated and are potential point sources of Hg pollution. The New Idria mine, located in San Benito County, California, was the second largest mercury mine in North America and was not remediated following its closure in 1972. Only within the past two years has it been designated as an EPA Superfund site and is currently undergoing remediation. This thesis focuses on the stability of mercury remaining at the site, the types of mercury phases present at the site as well as downstream from it, and the transport of mercury from the site. The stability of cinnabar (HgS), the primary mercury-bearing phase at the New Idria mine and other mercury mines in the California Coast Range, was investigated in the presence of microorganisms found in the acid mine drainage (AMD) system at the site. Geomicrobiological and geochemical studies of the identity and effects of these microorganisms on the solubility of HgS identified Thiomonas species and showed that the AMD bacterial consortium significantly enhances the solubility of cinnabar and metacinnabar, the two common HgS crystalline phases present. -54 -52 These two phases are very insoluble (Ksp = 10 and 10 , respectively) in the absence of these bacteria and are often considered to be relatively nonbioavailable. The phases of mercury present in the waste piles and downstream sediments were analyzed using a combination of sequential chemical extractions and synchrotron-based techniques, including a new low-temperature extended x-ray absorption fine structure (EXAFS) spectroscopy method developed in this project. This new method allows, for the first time, quantification of the amount of elemental mercury present in complex mine waste samples and associated sediments that contain a variety of Hg-bearing phases. When coupled with field- and lab-based evasion studies of Hg vapor from mine wastes, this new approach showed that high mercury evasion rates into the atmosphere from the New Idria and other Hg mine sites in the California Coast Range can be positively correlated with high levels of elemental Hg in the mine wastes. Another new discovery from this study is that freshwater diatoms in the New Idria drainage system are one of the major sinks for mercury. Selective iv chemical extraction and EXAFS studies of the species of mercury associated with diatom frustules showed that these frustules can stably sequester mercury in low bioavailability forms. These studies also showed that the abundant iron- (oxy)hydroxide (ferrihydrite) nanoparticles present in the New Idria drainage system have very little associated mercury, which contradicts long-held assumptions that sorption of Hg(II) on these nanoparticles is a major Hg sequestration and transport mechanism in the New Idria drainage system. A general conclusion from this study is that the majority of mercury in the New Idria drainage system is in relatively stable, low bioavailability forms. The understanding gained from this study of the stability, forms, and transport of mercury at the New Idria site can be extrapolated to other similar inoperative mercury mine sites in the California Coast Range and should aid in their future remediation efforts. v Acknowledgements As with any major work there are more people that deserve thanks than can be adequately expressed in the space given. First and foremost I would like to thank my advisor, Gordon E. Brown, Jr., for giving me the opportunity to work on a challenging thesis that is wide ranging in scope. I would also like to thank Gordon for allowing me the flexibility to work in scientific areas outside the general expertise of the surface and aqueous geochemistry group, full financial support for this work, and help in developing my critical reasoning skills. Besides thanking Gordon I would like to thank the rest of the Brown research group, both present and past members, for their friendship and advice over the years. I would like to thank James Rytuba of the United States Geological Survey for his help with this work through numerous meetings to discuss aspects about mercury cycling at not only the field site chosen for this work, but also mercury cycling in general. I wish to thank Mark Marvin-DiPasquale and Lisamarie Windham- Myers of the United States Geological Survey for allowing me to work in their laboratory during my first summer at Stanford where I was first introduced to ultra-trace mercury analysis which allowed me to further refine my techniques in the laboratory at Stanford University for this project. Special thanks is needed for Alfred Spormann, Sebastian Behrens, and the rest of the Spormann research group for allowing me to use of their laboratory for a portion of this work as well as teaching me laboratory techniques for working microorganisms. Thanks goes to Scott Fendorf and his research group, both present and past members, for their friendship and use of some of their equipment. I would like to thank my committee members, Gordon Brown, Jr., Scott Fendorf, James Rytuba, Alfred Spormann, and Chris Francis. Though the make- up of my committee changed prior to my defense, their direction and input on this project over the years has proven invaluable. I would also like to thank Jennifer Wilcox who served as committee chair for my thesis defense. vi Numerous collaborators over the years have given me better understanding of science as well as friendship: Mae Gustin (University of Nevada-Reno), Christopher Kim (Chapman University), Guangchao Li (Stanford University), Doug Turner (Stanford University), Bob Jones (Stanford University), Sam Webb (SSRL), John Bargar (SSRL), Joe Rogers (SSRL), Ruben Kretzschmar (ETH-Zurich), and Jan Wiederhold (ETH-Zurich). The support I have received from my friends and family over the years has been immense and greatly appreciated. My parents have given me so much help and support over the years that I cannot fully express my gratitude to them. They went above and beyond to help me through a very difficult health related issue during my time at Stanford. The guidance that my brother has offered over the years has been truly appreciated. I appreciate the support and encouragement from my grandparents, some of whom are no longer around to celebrate the completion of this dissertation. To old friends and new ones that I have gained during my time at Stanford, I thank you for friendship, guidance, and support over the years. I wish to thank the Department of Geological and Environmental Sciences at Stanford University for its support over the years. I would like to thank the various funding agencies which make research projects like mine a reality. This work has been funded by the following entities: Stanford Environmental Molecular Science Institute through NSF Grant CHE-0431425, NSF Center for Environmental Implication of Nanotechnology Grant EF-0830093, the McGee Grant, the Jahns Fellowship, and the Lokey Fellowship. vii Table of Contents Abstract iv Acknowledgements vi Table of Contents viii List of Tables xiii List of Figures xv Chapter 1: Introduction to Mercury Geology, the Inoperative New Idria Mercury Mine, and Mercury Analysis Techniques___________ 1 Introduction 2 Background 4 Mercury Geology 4 The Inoperative New Idria Mercury Mine 5 Mercury Analysis Techniques 12 Objectives 18 Summary of Thesis Research 19 Literature Cited 27 Chapter 2: Microbially Enhanced Dissolution of HgS in an Acid Mine Drainage System in the California Coast Range 33 Abstract 34 Introduction 36 Material and Methods 38 Results 48 AMD Solution Chemistry 48 Clone library, qPCR, and Bacterial Isolate 49 Bacterial Dissolution of HgS 50 viii Effects of Hg on Iron
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