MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Qiuyuan Huang Candidate for the Degree: Doctor of Philosophy _______________________________________ Hailiang Dong, Director ________________________________________ Yildirim Dilek, Reader ________________________________________ Jonathan Levy, Reader ______________________________________ Chuanlun Zhang, External examiner ______________________________________ Annette Bollmann, Graduate School Representative ABSTRACT GEOMICROBIAL INVESTIGATIONS ON EXTREME ENVIRONMENTS: LINKING GEOCHEMISTRY TO MICROBIAL ECOLOGY IN TERRESTRIAL HOT SPRINGS AND SALINE LAKES by Qiuyuan Huang Terrestrial hot springs and saline lakes represent two extreme environments for microbial life and constitute an important part of global ecosystems that affect the biogeochemical cycling of life-essential elements. Despite the advances in our understanding of microbial ecology in the past decade, important questions remain regarding the link between microbial diversity and geochemical factors under these extreme conditions. This dissertation first investigates a series of hot springs with wide ranges of temperature (26-92oC) and pH (3.72-8.2) from the Tibetan Plateau in China and the Philippines. Within each region, microbial diversity and geochemical conditions were studied using an integrated approach with 16S rRNA molecular phylogeny and a suite of geochemical analyses. In Tibetan springs, the microbial community was dominated by archaeal phylum Thaumarchaeota and four bacterial phyla (Firmicutes, Proteobacteria, Cyanobacteria, Chloroflexi). In the Philippines hot springs, the archaeal community mainly consisted of phyla Crenarchaeota, Euryarchaeota, and unclassified Archaea, while the bacterial community was predominated by phyla Aquificae and Firmicutes. Sulfur metabolisms appear to be key physiological functions in these hot springs. Saline lake on high elevation represents another extreme environment where various microorganisms thrive. In this study, the taxonomic and functional diversity of the microbial community in a saline lake (Qinghai Lake, China) was characterized using metagenomes and metatranscriptomes techniques. Metagenomic data showed that microbial communities in two water columns of Qinghai Lake were mainly dominated by Bacteria (mainly phyla Cyanobacteria, Proteobacteria, Verrucomicrobia, Actinobacteria, etc), while metatranscriptomics was performed to study the functional gene expression in elemental cycles (e.g., carbon and nitrogen cycles). Lastly, an artificial extreme environment was studied, where trichloroethylene (TCE) in bedrock aquifer was a major contaminant. In situ chemical oxidation (ISCO) was a commonly used strategy to oxidize TCE, but how strong oxidants such as permanganate diffuses into solid rocks and its interaction with rock matrices remain poorly known. A series of diffusion experiments were conducted that measured the permanganate diffusion and reaction in four different types of sedimentary rocks (dark gray mudstone, light gray mudstone, red sandstone, and tan sandstone). Various Mn minerals formed as surface coatings as a result of the permanganate reduction coupled with total organic carbon (TOC) oxidation, and the extent of permanganate diffusion and reaction depended on rock properties. GEOMICROBIAL INVESTIGATIONS ON EXTREME ENVIRONMENTS: LINKING GEOCHEMISTRY TO MICROBIAL ECOLOGY IN TERRESTRIAL HOT SPRINGS AND SALINE LAKES A DISSERTATION Submitted to the Faculty of Miami University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Geology and Environmental Earth Science by Qiuyuan Huang Miami University Oxford, Ohio 2014 Dissertation Advisor: Hailiang Dong TABLE OF CONTENTS CHAPTER 1: INTRODUCTION ............................................................................... 1 REFERENCES .............................................................................................................. 5 CHAPTER 2: ARCHAEAL AND BACTERIAL DIVERSITY IN HOT SPRINGS ON THE TIBETAN PLATEAU, CHINA ............................................. 10 ABSTRACT ................................................................................................................. 11 INTRODUCTION ....................................................................................................... 12 REFERENCES ............................................................................................................ 26 CHAPTER 3: ARCHAEAL AND BACTERIAL DIVERSITY IN ACIDIC TO CIRCUMNEUTRAL HOT SPRINGS IN THE PHILIPPINES ........................... 44 ABSTRACT ................................................................................................................. 45 INTRODUCTION ....................................................................................................... 46 REFERENCES ............................................................................................................ 62 CHAPTER 4: METAGENOMIC AND METATRANSCRIPTOMIC ANALYSIS OF TAXONOMIC AND GENETIC DIVERSITY IN SALINE QINGHAI LAKE, CHINA ........................................................................................................................ 80 CHAPTER 5: PERMANGANATE DIFFUSION AND REACTION IN SEDIMENTARY ROCKS ...................................................................................... 110 ABSTRACT ............................................................................................................... 111 INTRODUCTION ..................................................................................................... 112 REFERENCES .......................................................................................................... 125 CHAPTER 6: SUMMARY ..................................................................................... 142 APPENDIX: PUBLICATIONS .............................................................................. 143 ii LIST OF TABLES CHAPTER 1: INTRODUCTION ............................................................................... 1 CHAPTER 2: ARCHAEAL AND BACTERIAL DIVERSITY IN HOT SPRINGS ON THE TIBETAN PLATEAU, CHINA ............................................. 10 TABLE 1. LOCATION AND DESCRIPTION OF THE INVESTIGATED SOIL AND TEN HOT SPRINGS ON THE TIBETAN PLATEAU, CHINA .............................................................. 33 TABLE 2. ECOLOGICAL ESTIMATES AND MAJOR GROUP AFFILIATION OF THE BACTERIAL 16S RRNA GENE CLONE SEQUENCES RETRIEVED FROM THE SOIL AND TEN HOT SPRINGS ON THE TIBETAN PLATEAU. .................................................................. 34 TABLE 3. ECOLOGICAL ESTIMATES AND MAJOR GROUP AFFILIATION OF THE ARCHAEAL 16S RRNA GENE CLONE SEQUENCES RETRIEVED FROM THE SOIL AND TEN HOT SPRINGS ON THE TIBETAN PLATEAU. .................................................................. 35 CHAPTER 3: ARCHAEAL AND BACTERIAL DIVERSITY IN ACIDIC TO CIRCUMNEUTRAL HOT SPRINGS IN THE PHILIPPINES ........................... 44 TABLE 1. GEOGRAPHIC PARAMETERS AND WATER GEOCHEMISTRY OF THE SIX INVESTIGATED HOT SPRINGS IN THE PHILIPPINES. ...................................................... 70 TABLE 2. ABUNDANCE OF ARCHAEAL AND BACTERIAL 16S RRNA GENES FOR THE SIX SPRING SEDIMENT SAMPLES FROM THE PHILIPPINES .................................................. 71 TABLE S1. DIVERSITY ESTIMATES OF 454 PYROSEQUENCES RETRIEVED FROM SIX HOT SPRINGS IN THE PHILIPPINES ...................................................................................... 77 CHAPTER 4: METAGENOMIC AND METATRANSCRIPTOMIC ANALYSIS OF TAXONOMIC AND GENETIC DIVERSITY IN SALINE QINGHAI LAKE, CHINA ........................................................................................................................ 80 TABLE 1. SAMPLE LOCATIONS AND GEOCHEMISTRY. ............................................... 100 TABLE 2. STATISTIC RESULTS OF METAGENOME AND METATRANSCRIPTOME SEQUENCES FROM SITES B AND E IN QINGHAI LAKE. .............................................. 101 CHAPTER 5: PERMANGANATE DIFFUSION AND REACTION IN SEDIMENTARY ROCKS ...................................................................................... 110 TABLE 1. CHARACTERIZATION OF ROCK PROPERTIES .............................................. 130 TABLE 2. DOBS VALUES AND EFFECTIVE DIFFUSION COEFFICIENTS FOR DIFFERENT ROCK TYPES ............................................................................................................. 131 TABLE 3. DEFF VALUES PRIOR TO OXIDANT EXPOSURE COMPARED TO DEFF AFTER EXPOSURE TO OXIDANT ........................................................................................... 132 TABLE 4. MINERALOGY ON PERMANGANATE REACTIVE SURFACES OF SEDIMENTARY ROCKS. .................................................................................................................... 133 CHAPTER 6: SUMMARY .................................................................................... 142 iii LIST OF FIGURES CHAPTER 1: INTRODUCTION ............................................................................... 1 CHAPTER 2: ARCHAEAL AND BACTERIAL DIVERSITY IN HOT SPRINGS ON THE TIBETAN PLATEAU, CHINA ............................................. 10 FIGURE 1. .................................................................................................................. 37 FIGURE 2A. ............................................................................................................... 38 FIGURE