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Metagenomic and Metatranscriptomic Analyses of Lake Vostok Accretion Ice

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Metagenomic and Metatranscriptomic Analyses of Lake Vostok Accretion Ice METAGENOMIC AND METATRANSCRIPTOMIC ANALYSES OF LAKE VOSTOK ACCRETION ICE Yury M. Shtarkman A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY December 2015 Committee: Scott O. Rogers, Advisor Rober W. Midden Graduate Faculty Representative Vipaporn Phuntumart Paul F. Morris Robert Michael McKay © 2015 Yury M Shtarkman All Rights Reserved iii ABSTRACT Scott O. Rogers, Advisor Lake Vostok (Antarctica) is the 4th deepest lake on Earth, the 6th largest by volume, and 16th largest by area, being similar in area to Ladoga Lake (Russia) and Lake Ontario (North America). However, it is a subglacial lake, constantly covered by more than 3,800 m of glacial ice, and has been covered for at least 15 million years. As the glacier slowly traverses the lake, water from the lake freezes (i.e., accretes) to the bottom of the glacier, such that on the far side of the lake a 230 m thick layer of accretion ice collects. This essentially samples various parts of the lake surface water as the glacier moves across the lake. As the glacier enters the lake, it passes over a shallow embayment. The embayment accretion ice is characterized by its silty inclusions and relatively high concentrations of several ions. It then passes over a peninsula (or island) and into the main basin. The main basin accretion ice is clear with almost no inclusions and low ion content. Metagenomic/metatranscriptomic analysis has been performed on two accretion ice samples; one from the shallow embayment and the other from part of the main lake basin. Ice from the shallow embayment contains a variety of Bacteria as well as a few Archaea and several types of Eukarya. Most are related to species that are psychrophilic, marine, aquatic, or live in lake/ocean sediments, or a combination of these. However, sequences identified as originating from many different thermophiles were found, suggesting the presence of hydrothermal activity in the lake. In contrast to the embayment ice, the ice from the main basin yielded only about 5-6% of the number of sequences. Here again, molecular signatures of psychrophiles, marine, aquatic, a few sediment-dwelling organisms, and a few thermophiles were found. Because of the extreme iv conditions, it has been hypothesized that Lake Vostok is sterile, or that very few types of organisms inhabit the lake. Our results indicate that it contains a diverse set of organisms, and the number and taxonomic composition varies with position in the lake. v This dissertation is dedicated to Irina Vasilkova and Mikhail Shtarkman - my wonderful parents, my amazing sister Alexandra and my sweet grandma. vi ACKNOWLEDGMENTS I would like to express my sincere appreciation to Dr. Scott O. Rogers, my advisor, for giving me this opportunity. He was always the one encouraging me to move forward in my project, learn more and gain a broader scientific view. I am very thankful for the knowledge I gained and the skills I learned from him. I am grateful for his supervision, guidance, constructive criticism, and the amazing patience he had for my work, especially writing. He helped me to become a better scientist and without him this work would not have been completed and published. This work was partially funded by the National Science Foundation. I would also like to thank Bowling Green State University and especially the Department for Biological Sciences for providing financial support and a great research environment. I would also like to thank my incredible committee: Dr. Paul Morris for his support, guidance and suggestions on this project; Dr. Vipaporn Phuntumart for her comments and suggestions; Dr. R. Michael L. McKay for his support and cheers, and Dr. W. Robert Midden for his interest in our research area. I would like to thank a former member of my committee, Dr. Carmen Fioravanti, for his support and constructive criticism. I am also thankful to all my committee members for the passion and interest the devoted to preliminary examination, proposal defense, and while serving in my dissertation committee. I appreciate all their valuable ideas and feedback on my dissertation defense examination. This work would not have been possible without the support and advice of many people. I would like to acknowledge former members from our laboratory: Tom D’Elia, Ram Satish 9HHUDSDQHQLDQG=H\QHS.RऊHUIRUWKHLUZRUNRQWKHGHVLJQRIWKLVSURMHFWDQGRQWKHLFHFRUHV and Caitlin Knowlton for her work on the control samples. I am also thankful to Robyn Edgar, vii Dr. Morris’s former student, for her help with bioinformatics software and database. I am also grateful to all of them for their comments and suggestions in preparation of the manuscripts. I would also like to thank my former lab mates, Farida Sidiq and Lorena Harris for their help and dedication during my first months in the lab. Special thanks go to Chen Xing, Seiguk Shin, Caitlin Knowlton and Sammy Juma for their support and the fun times we had together. They helped me during rough times and we had a lot of fun working together. Thank you guys big time. I would like to mention Dr. George Bullerjahn, Dr. Neocles Leontis and former vice provost for research and Dean of the Graduate College Heinz Bulmahn for letting me be a part of the BGSU graduate school and believing in my capabilities. My heart is full of friends back home in Russia and those who support me here at Bowling Green. Among hundreds, I especially want to thank Dr. Yury Ivanov, Dr. Vasiliy Morosov, Pavel Moroz and Natalia Kholmicheva, we shared a lot together as scientists and as roommates. Thank you for putting up with me for such a long time. I would also like to share my sincere thanks to my great friends Astha Malik and Jigar Patel for always being there for me when I needed support. Lastly, I would like to thank my family for supporting me 100% and believing in me. I would not be able to do this without their love, care and encouragement. viii TABLE OF CONTENTS Page CHAPTER I .................................................................................................................................. 1 Introduction to methods .................................................................................................... 1 Ribosomal genes as metagenomic targets ........................................................................ 3 Culturing and phylogenetic analysis ............................................................................... 6 Cold environments .......................................................................................................... 7 Genomic sequencing overview ....................................................................................... 10 Lake Vostok accretion ice ............................................................................................... 11 Lake Vostok samples preparation..................................................................................... 13 Software overview ........................................................................................................... 14 Summary.......................................................................................................................... 15 References for the Chapter I ............................................................................................ 18 CHAPTER II ............................................................................................................................... 22 Introduction ..................................................................................................................... 22 Lake Vostok origin .............................................................................................. 26 Antarctic drilling project .................................................................................... 28 Microbial composition of the lake ....................................................................... 31 Accretion ice type I ............................................................................................. 32 Accretion ice type II ............................................................................................ 36 Cold stress mechanisms ...................................................................................... 39 Other planets ........................................................................................................ 40 Research statement .......................................................................................................... 43 ix Materials and methods ..................................................................................................... 45 Molecular analysis ............................................................................................... 45 Sequence analyses................................................................................................ 46 Taxonomy identification and database construction ........................................... 49 Metabolic map reconstruction ............................................................................. 51 Water control samples ......................................................................................... 54 Results.............................................................................................................................. 54 Psychrophiles ....................................................................................................... 83 Thermophiles
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