.. ................................................................................................................................. ii TABLE OF CONTENTS .............................................................................................................. iii LIST OF TABLES ........................................................................................................................ vii LIST OF FIGURES ..................................................................................................................... viii LIST OF ABBREVIATIONS AND NOMENCLATURE ......................................................... x ACKNOWLEDGMENTS ............................................................................................................. xi CO-AUTHORSHIP STATEMENT............................................................................................ xii CHAPTER 1: INTRODUCTION .................................................................................................. 1 1.1 BACKGROUND ....................................................................................................... 1 1.2 LITERATURE REVIEW .......................................................................................... 3 1.2.1 MME Treatment Systems ........................................................................................... 3 1.2.2 Design and Performance of Anaerobic Treatment Systems ................................... 5 1.2.3 Choice of a Suitable Organic Substrate .................................................................... 8 1.2.4 Geochemistry and Microbial Interactions in Sulfate-Rich Environments ........... 9 1.2.5 Sulfur Cycle ................................................................................................................ 10 1.2.6 Background on the Sulfate-Reducing Bacteria ...................................................... 11 1.2.7 Rates of Sulfate Reduction and SRB Distribution ................................................. 11 1.2.8 Mathematical Modeling of SRR .............................................................................. 13 1.2.9 Organic Matter Degradation in Passive Treatment Systems ................................ 15 1.2.10 Molecular Techniques Used in Microbial Ecology ............................................... 16 1.3 RESEARCH OBJECTIVES .................................................................................... 17 1.4 RESEARCH HYPOTHESES .................................................................................. 18 1.5 THESIS OUTLINE ................................................................................................. 19 1.7 REFERENCES ........................................................................................................ 28 CHAPTER 2: PHYLOGENETIC DIVERSITY OF TRANSITION AND ANOXIC ZONE BACTERIAL COMMUNITIES WITHIN A NEAR-SHORE ANOXIC BASIN: NITINAT LAKE ................................................................. 34