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Lake Sediment Microbial Communities in the Anthropocene

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Lake Sediment Microbial Communities in the Anthropocene Lake sediment microbial communities in the Anthropocene Matti Olavi Ruuskanen A thesis submitted in partial fulfillment of the requirements for the Doctorate in Philosophy degree in Biology with Specialization in Chemical and Environmental Toxicology Department of Biology Faculty of Science University of Ottawa © Matti Olavi Ruuskanen, Ottawa, Canada, 2019 Abstract Since the Industrial Revolution at the end of the 18th century, anthropogenic changes in the environment have shifted from the local to the global scale. Even remote environments such as the high Arctic are vulnerable to the effects of climate change. Similarly, anthropogenic mercury (Hg) has had a global reach because of atmospheric transport and deposition far from emission point sources. Whereas some effects of climate change are visible through melting permafrost, or toxic effects of Hg at higher trophic levels, the often-invisible changes in microbial community structures and functions have received much less attention. With recent and drastic warming- related changes in Arctic watersheds, previously uncharacterized phylogenetic and functional diversity in the sediment communities might be lost forever. The main objectives of my thesis were to uncover how microbial community structure, functional potential and the evolution of mercury specific functions in lake sediments in northern latitudes (>54ºN) are affected by increasing temperatures and Hg deposition. To address these questions, I examined environmental DNA from sediment core samples and high-throughput sequencing to reconstruct the community composition, functional potential, and evolutionary responses to historical Hg loading. In my thesis I show that the microbial community in Lake Hazen (NU, Canada) sediments is structured by redox gradients and pH. Furthermore, the microbes in this phylogenetically diverse community contain genomic features which might represent adaptations to the cold and oligotrophic conditions. Finally, historical Hg pollution from anthropogenic sources has likely affected the evolution of microbial Hg resistance and this deposition can be tracked using sediment DNA on the Northern Hemisphere. My thesis underscores the importance of using culture-independent methods to reconstruct the structure, functional potential and evolution of environmental microbial communities. ii Acknowledgements First, I would like to thank both of you, Alex and Stéphane. You have been such great supervisors from the beginning and helped me grow as a scientist over these years. You have both pushed me to do better work, but also been always there for me and available when I needed assistance. While being co-supervised by two ambitious professors with sometimes diverging scientific focuses and views has not always been easy, it certainly has been very rewarding. Conducting my doctoral studies in Ottawa was overall a wonderful experience, and I am honored to have worked with you two during this time. In Ottawa I shared my time between the Poulain and Aris-Brosou labs. I would like to thank my friends and colleagues for spending countless hours in the office and lab with me (depending on the group!), and our inspiring discussions: Dan, Jonathan, Martin, Ben, Mija, Galen, Graham, Emmanuel, Phil, Aaron, Neke, Danielle and Noémie. It has been a great pleasure and very inspiring working with you, and I hope to see you all again soon. I would also like to thank the members of my thesis committee, Jules Blais and Alex Wong for helping me polish my ideas and the original proposal for this thesis. My committee members together with Linda Bonen also made my comprehensive examination a pleasant and inspiring experience – contrary to its reputation! Furthermore, I would like to thank Jules Blais, Linda Bonen, Marina Cvetkovska and Jesse Shapiro for their thoughtful comments on this thesis that improved its quality and for the engaging discussion at my thesis defense. I feel privileged to have been able to study High Arctic environments in Canada in my thesis. Specifically, I would like to thank Vince and Kyra for this amazing opportunity and the great time we had when sampling at Lake Hazen. iii At least once a year, I was also visiting back home in Finland. During these (sometimes long) visits I was fortunate enough to have a second academic home at the Virta lab at University of Helsinki in Viikki. Marko, Johanna, Christina, Kata and Windi, thank you so much for hosting me, and showing fresh perspectives and giving new ideas for my research in our discussions. In addition to my lab mates, I also consider myself lucky to have met so many new friends in Ottawa. Special thanks to the Marginally Significant and other people in the PIZZA crew for making my studies in Ottawa thoroughly enjoyable. Maybe we can have another sittning sometime? Thanks also to my other friends from the international crowd in Ottawa for being so supportive and welcoming. A large part of my life in Canada were the Cape Breton Session and various other music groups in Ottawa. Music has always been an important part of my life and playing and singing with you really helped me to take my mind off the thesis. You have all left such a positive impression of Canada and Canadians to me. Lastly, I would like to thank my family and friends in Finland. It has been hard living away from you for such a long time, and I have tried to make time to see you whenever I have been visiting back home. Thank you all for being so supportive over the years and believing in me. I will now make sure to see you all more often. Ja viimeiset mutta ei vähäisimmät kiitokset. Kiitos jatkuvasta tuestanne ja ymmärryksestä, Äiti ja Isä. iv Table of Contents Lake sediment microbial communities in the Anthropocene .......................................................... i Abstract ............................................................................................................................... ii Acknowledgements ........................................................................................................................ iii Table of Contents ............................................................................................................................ v List of Figures ............................................................................................................................... x List of Tables ............................................................................................................................... x Abbreviations .............................................................................................................................. xi Chapter 1: General introduction...................................................................................................... 1 1.1 Anthropocene and its effects on environmental microbial communities .............................. 1 1.1.1 Climate change............................................................................................................... 3 1.1.2 Anthropogenic impacts on the global mercury cycle .................................................... 5 1.2 Microbial ecology of lake sediments and their use as environmental archives .................... 8 1.2.1 Physicochemical conditions in lake sediments .............................................................. 8 1.2.2 Lake sediments as environmental archives .................................................................. 10 1.3 High-throughput sequencing in the study of microbial communities ................................. 11 1.3.1 Current sequencing technologies ................................................................................. 12 1.3.2 Use of high-throughput sequencing in microbiology .................................................. 13 1.4 Bioinformatics in microbial ecology .................................................................................. 14 1.4.1 Analysis of microbial ecology data .............................................................................. 17 1.5 Rationale and objectives for the thesis................................................................................ 18 Chapter 2: Physicochemical drivers of microbial community structure in sediments of Lake Hazen, Nunavut, Canada............................................................................................................... 22 2.1 Abstract ............................................................................................................................... 23 2.2 Introduction ......................................................................................................................... 24 v 2.3 Material and methods .......................................................................................................... 26 2.3.1 Collection of sediment cores and associated chemistry ............................................... 26 2.3.2 Sequencing and data preprocessing ............................................................................. 29 2.3.3 Data analyses ............................................................................................................... 30 2.4 Results and discussion ........................................................................................................ 35 2.4.1 Sediment microbial communities are similar to other arctic lakes .............................. 35 2.4.2 Both redox chemistry and pH drive community diversity and structure ..................... 39 2.4.3 Taxonomic
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