3. Aerobic Gammaproteobacterial Methanotrophs Mitigate Methane Emissions from Oxic and Anoxic Lake Waters

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3. Aerobic Gammaproteobacterial Methanotrophs Mitigate Methane Emissions from Oxic and Anoxic Lake Waters Research Collection Doctoral Thesis Methane oxidation in suboxic and anoxic zones of freshwater lakes Author(s): Oswald, Kirsten Publication Date: 2016 Permanent Link: https://doi.org/10.3929/ethz-a-010708140 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO. 23298 METHANE OXIDATION IN SUBOXIC AND ANOXIC ZONES OF FRESHWATER LAKES A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (Dr. sc. ETH Zurich) presented by KIRSTEN OSWALD M.Sc. Applied Environmental Geoscience, Eberhard Karls Universität Tübingen born on 09.03.1983 citizen of Germany accepted on the recommendation of Prof. Dr. Bernhard Wehrli, examiner Dr. Carsten J. Schubert, co-examiner Prof. Dr. Marcel M. M. Kuypers, co-examiner Prof. Dr. Martin Ackermann, co-examiner 2016 TABLE OF CONTENTS ACKNOWLEDGEMEMTS .................................................................................................................... 3 SUMMARY ............................................................................................................................................ 5 ZUSAMMENFASSUNG ........................................................................................................................ 7 1. INTRODUCTION ........................................................................................................................... 9 1.1. Methanogenesis ..................................................................................................................... 10 1.2. Methane oxidation ................................................................................................................. 11 1.3. Methane production and emission from lakes ....................................................................... 16 1.4. Methane oxidation dynamics in lakes ................................................................................... 17 1.5. Study sites ............................................................................................................................. 19 1.6. Overview of methods ............................................................................................................ 21 1.7. Objectives and outline ........................................................................................................... 24 1.8. Contribution to related publications ...................................................................................... 25 2. LIGHT-DEPENDENT AEROBIC METHANE OXIDATION REDUCES METHANE EMISSIONS FROM SEASONALLY STRATIFIED LAKES ............................................................. 27 2.1. Abstract ................................................................................................................................. 28 2.2. Introduction ........................................................................................................................... 28 2.3. Materials and Methods .......................................................................................................... 30 2.4. Results ................................................................................................................................... 37 2.5. Discussion ............................................................................................................................. 42 2.6. Acknowledgments ................................................................................................................. 49 2.7. Supporting Information ......................................................................................................... 49 3. AEROBIC GAMMAPROTEOBACTERIAL METHANOTROPHS MITIGATE METHANE EMISSIONS FROM OXIC AND ANOXIC LAKE WATERS ............................................................ 53 3.1. Abstract ................................................................................................................................. 54 3.2. Introduction ........................................................................................................................... 54 3.3. Methods ................................................................................................................................. 56 3.4. Results ................................................................................................................................... 63 3.5. Discussion ............................................................................................................................. 71 3.6. Acknowledgements ............................................................................................................... 78 3.7. Supplementary Information ................................................................................................... 78 4. CRENOTHRIX POLYSPORA: AN IMPORTANT OVERLOOKED PLAYER IN FRESHWATER METHANE OXIDATION ........................................................................................ 83 4.1. Summary ............................................................................................................................... 84 4.2. Results and Discussion .......................................................................................................... 84 4.3. Methods ................................................................................................................................. 89 4.4. Acknowledgements ............................................................................................................... 90 I Table of Contents 4.5. Extended Data ....................................................................................................................... 91 4.6. Supplementary Information ................................................................................................... 92 5. METHANE OXIDATION IN THE FERRUGINOUS LAKE LA CRUZ (SPAIN) .................... 97 5.1. Abstract ................................................................................................................................. 98 5.2. Introduction ........................................................................................................................... 98 5.3. Methods ............................................................................................................................... 100 5.4. Results ................................................................................................................................. 106 5.5. Discussion ........................................................................................................................... 114 5.6. Acknowledgements ............................................................................................................. 121 5.7. Supplementary Information ................................................................................................. 122 6. CONCLUSIONS AND OUTLOOK ........................................................................................... 125 6.1. Methane, isotopes and oxidation dynamics ......................................................................... 125 6.2. Methanotrophic community ................................................................................................ 126 6.3. A novel methanotroph in lake water ................................................................................... 127 6.4. Photosynthesis fueled methanotrophy ................................................................................. 127 6.5. Methane oxidation and alternative electron acceptors ........................................................ 128 REFERENCES .................................................................................................................................... 131 II ACKNOWLEDGEMEMTS First and foremost, I would like to express my gratitude to my supervisors, Dr. Carsten Schubert and Prof. Bernhard Wehrli, for giving me the opportunity to complete my PhD studies in their groups. I really appreciate your guidance, trust, encouragement and advice. I am especially thankful for the freedom and resources I was able to benefit from. I would like to thank my co-examiner and collaborator, Prof. Marcel Kuypers, for his valuable input, expertise and for hosting me at the MPI for several scientific visits. I greatly appreciate the chance to have worked in partnership with another institute. I am grateful to Prof. Martin Ackermann for co-examining my thesis and for his helpful comments. A special thank you goes to Dr. Jana Milucka and Dr. Andreas Brand, who offered their support and proficiency in the lab and during field work. Thank you for countless discussions, ideas and motivation. I am immensely thankful to all technicians and staff at Eawag and the MPI for their continuous assistance and patience in the lab, in the field and with various analyses: Dr. Sten Littmann, Serge Robert, Daniela Tienken, Patrick Kathriner, Karin Beck, Alois Zwyssig, Daniela Nini, David Kistler, Irene Brunner, Gijs Nobbe, Francisco Vásquez, Gabriele Klockgether and Kirsten Imhoff. In particular, I would like to acknowledge Christian Dinkel for all his expert support during field campaigns. Thank you for making everything run smoothly on the boat, your fun company and positive disposition. Dr. Prosper Zigah, I am grateful for your help and skills, especially during the Lake Kivu campaign,
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