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Microbial Diversity, Activity, and Ecology of a Hypersaline High Arctic Spring System

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Microbial Diversity, Activity, and Ecology of a Hypersaline High Arctic Spring System Microbial Diversity, Activity, and Ecology of a Hypersaline High Arctic Spring System Chih-Ying Lay Department of Natural Resource Sciences McGill University, Montreal August, 2013 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of PhD. ©2013 Although we have no rational grounds for believing in an objective reality, we also have no choice but to act as if it is true. - David Hume 2 ACKNOWLEDGEMENTS First of all, I would like to thank Dr. Lyle G. Whyte, my supervisor, who let me study in his lab and supported me with his resources to complete my PhD research. From his supervision, I acquired a lot of knowledge of experiment design, planning field trips, interpreting research results, and building academic networks. His enthusiasm on unique microbiology topics and desires of using newly-developed technologies always encouraged me to face all the trendiest topics in the frontline of environmental microbiology. He let me to attend the unforgettable field trip to the Canadian High Arctic to perform field works. Without his help, I will not finish this thesis. I also would like to thank all the support from Dr. Charles Greer, Dr. Brian Driscoll, Dr. Donald Niven, and Dr. Sébastien Faucher. They always kindly gave me many useful and professional advices to overcome research problems. I would like to thank Dr. Thomas Niederberger, Dr. Nadia Mykytczuk and Dr. Étienne Yergeau. When I had in situ questions or problems for my research, they always offered me the most immediate helps. My lab mates, Guillaume Lamarche-Gagnon, Sara Sheibani, Roland Wilhelm, Kris Radtke, Jen Allan, Jackie Goordial, Diana Popa, Sara Klemm, Dr. Christine Martineau, Dr. Ofelia Ferrera Rodriquez, Dr. Jennifer Ronholm, Dr. Olga Onyshchenko, and Dr. Helen Vrionis were very friendly and helpful to me. In the last five years, when I needed their friendship, advices, or help, they always offered me much more than I expected. They helped me to adapt to the life and work style at Macdonald campus. I also would like to thank all the members of the Microbiology Division. They enriched my microbiology knowledge through seminars and conversations. I would also like to thank NRS support staff, Dave Meek, Marie Kubecki, Ann Gossage, and Marlene Parkinson. They tried their best to keep me in line and guided me when I feel confused with the school system. I would like to thank Dr. Joann Whalen and Hélène Lalande for the soil/sediment analyses. I also would like to thank Dr. Anthony Cushing for doing a final English edition for my thesis and Patricia Görner-Potvin for translating my abstract into French. The Polar Continental Shelf Project, the Canadian Astrobiology Training Program, National Sciences and Engineering Research Council of Canada, Canadian Space Agency, and Northern Scientific Training Program all contributed to making this thesis possible. During the past five years, I had enormous friendship support from Ting-Heng Yu, Chia-Chen Chang, Ming-Yueh Wu, James Wang, Dr. Eric Huang, Li-Jen Chen, Gengrui Wang, Chen Chen, Seamus McClare, Nathaniel Fink, Timothy Schwinghamer, Arturo Mayorga, Claude Gravel, and members from Sainte Anne Singers, Musica Orbium, and McGill Taiwanese Graduate Student Association. Finally, I would like to thank my parents, Jiunn-Yuan Lay and Dr. Pen-Ho Yeh, who encouraged me to study in Canada. Thank you! i TABLE OF CONTENTS ABSTRACT ...................................................................................................................... vi RÉSUMÉ ......................................................................................................................... viii CONTRIBUTIONS TO KNOWLEDGE ............................................................................ x LIST OF TABLES ............................................................................................................. xi LIST OF FIGURES .......................................................................................................... xii LIST OF ABBREVIATIONS .......................................................................................... xiii CHAPTER 1 ........................................................................................................................ 1 Introduction and Literature Review ..................................................................................... 1 1.1 Introduction .................................................................................................. 1 1.2 Terrestrial saline water body ecosystems in Polar regions .......................... 2 1.2.1 Definitions of terrestrial saline water bodies ...................................... 2 1.2.2 Saline lakes in the Polar regions and the microbiology studies on them ……………… ............................................................................................. 4 1.2.3 Saline springs in Polar regions ............................................................ 7 1.3 Challenges to microbial life in Polar saline water bodies .......................... 11 1.3.1 The availability of liquid water in cryoenvironments ....................... 11 1.3.2 The adaptation of microorganisms to cryoenvironments .................. 12 1.3.2.1 Cold adaptations of microorganisms ..................................................... 13 1.3.2.2 Saline adaptation of microorganisms .................................................... 16 1.4 Applications and astrobiology aspects of the study ................................... 18 1.4.1 Potential applications of microorganisms from cold saline environments ..................................................................................................... 18 1.4.2 Astrobiological aspects ..................................................................... 20 1.5 Objectives .................................................................................................. 22 CONNECTING TEXT ...................................................................................................... 24 CHAPTER 2 ...................................................................................................................... 24 Microbial Diversity and Activity in Hypersaline High Arctic Spring Channels ............... 24 ABSTRACT ...................................................................................................................... 25 2.1 Introduction .......................................................................................................... 26 2.2 Materials and Methods ......................................................................................... 29 2.2.1 Sample site description and geochemical analyses .................................. 29 2.2.2 CO 2 and CH 4 concentrations and flux measurements .............................. 31 2.2.3 Microscopy and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) ............................................................................ 32 2.2.4 Microbial cultivation and characterization .............................................. 33 ii 2.2.5 Bacterial and Archaeal 16S rRNA gene clone libraries ........................... 35 2.2.6 Biodiversity indices and statistical analysis of 16S rRNA gene clone libraries ............................................................................................................. 36 2.2.7 Microbial activity at cold temperatures ................................................... 37 2.2.8 Nucleotide accession numbers ................................................................. 37 2.3 Results .................................................................................................................. 38 2.3.1 Geochemical analyses .............................................................................. 38 2.3.2 CO 2 and CH 4 concentrations and flux measurements .............................. 39 2.3.3 Cell enumeration ...................................................................................... 40 2.3.4 Identification and characterization of isolates ......................................... 40 2.3.5 Bacterial and Archaeal 16S rRNA gene clone libraries ........................... 41 2.3.6 Microbial activity at cold temperatures ................................................... 44 2.4 Discussion ............................................................................................................ 44 2.5 Acknowledgements .............................................................................................. 52 CONNECTING TEXT ...................................................................................................... 62 CHAPTER 3 ...................................................................................................................... 62 Defining the Functional Potential and Active Community Members of a Sediment Microbial Community in a High Arctic Hypersaline Subzero Spring ............................... 62 ABSTRACT ...................................................................................................................... 63 3.1 Introduction .......................................................................................................... 64 3.2 Materials and Methods ......................................................................................... 68 3.2.1 Study site and sample collection .............................................................. 68 3.2.2 Metagenomic DNA extraction and sequencing ......................................
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