Molecular ecological analysis of methanogenic communities in terrestrial and submarine permafrost deposits of Siberian Laptev Sea area Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften - Dr. rer. nat. - dem Fachbereich Biologie Universität Potsdam vorgelegt von Katharina Feige geb. Koch Potsdam, den 09.06.2009 Die Untersuchungen zur vorliegenden Dissertation wurden am Alfred-Wegener- Institut für Polar- und Meeresforschung in Potsdam durchgeführt. Einzelne Analysen erfolgten zusätzlich an der Technischen Universität Berlin im Fachbereich für Umweltmikrobiologie (Prof. Ulrich Szewzyk). 1. Gutachter: PD Dr. habil. Dirk Wagner 2. Gutachter: Prof. Dr. Antje Boetius 3. Gutachter: Dr. German Jurgens What we know is a drop What we don’t know is an ocean Isaac Newton Published online at the Institutional Repository of the University of Potsdam: URL http://opus.kobv.de/ubp/volltexte/2009/3799/ URN urn:nbn:de:kobv:517-opus-37998 http://nbn-resolving.org/urn:nbn:de:kobv:517-opus-37998 TABLE OF CONTENTS PREFACE................................................................................................................................................ II ACKNOWLEDGEMENTS....................................................................................................................... II ABBREVIATIONS..................................................................................................................................IV SUMMARY ..............................................................................................................................................V ZUSAMMENFASSUNG .........................................................................................................................VI 1. INTRODUCTION ................................................................................................................................. 1 1.1 SCIENTIFIC BACKGROUND ........................................................................................................... 1 1.1.1 ARCTIC CLIMATE CHANGE AND METHANE EMISSION.......................................................... 1 1.1.2 PERMAFROST – A SENSITIVE INDICATOR FOR GLOBAL CLIMATE CHANGE.................... 1 1.1.3 TERRESTRIAL PERMAFROST – STRESSED WITH SEVERAL PROCESSES......................... 3 1.1.5 METHANOGENS IN PERMAFROST – ROBUST MICROORGANISMS ..................................... 5 1.2 OBJECTIVES.................................................................................................................................... 8 1.3 STUDY SITE ..................................................................................................................................... 9 1.4 OVERVIEW OF PUBLICATIONS ................................................................................................... 11 2. PUBLICATIONS................................................................................................................................ 14 2.1 FIRST PUBLICATION: METHANOGENIC COMMUNITY COMPOSITION AND ANAEROBIC CARBON TURNOVER IN SUBMARINE PERMAFROST SEDIMENTS OF THE SIBERIAN LAPTEV SEA......................................................................................................................................... 16 2.2 SECOND PUBLICATION: COMPARISON OF MICROBIAL COMMUNITIES IN TERRESTRIAL AND SUBMARINE PERMAFROST SEDIMENTS FROM THE SIBERIAN LAPTEV SEA AREA ........ 26 2.3 THIRD PUBLICATION: METHANOGENIC COMMUNITIES ANALYSED BY IN VITRO USING DENATURING GRADIENT GEL ELECTROPHORESIS ON TERRESTRIAL AND SUBMARINE PERMAFROST SAMPLES OF THE SIBERIAN LAPTEV SEA SHELF AREA..................................... 50 3. SYNTHESIS AND CONCLUSION .................................................................................................... 66 3.1 SYNTHESIS .................................................................................................................................... 66 3.1.1 INTRODUCTION.......................................................................................................................... 66 3.1.2 ARCHAEAL COMMUNITY ABUNDANCE AND STRUCTURE.................................................. 66 3.1.3 IN VITRO EXPERIMENT WITH METHANOGENIC COMMUNITIES.......................................... 68 3.2 CONCLUSIONS .............................................................................................................................. 70 3.3 FUTURE RESEARCH..................................................................................................................... 72 APPENDIX: FOURTH PUBLICATION: METHANE CYCLE IN TERRESTRIAL AND SUBMARINE DEPOSITS OF THE LAPTEV SEA REGION........................................................................................ 73 REFERENCES ...................................................................................................................................... 78 I PREFACE & ACKNOWLEDGEMENT PREFACE This work was part of the joint research project “Process studies of permafrost dynamics in the Laptev Sea” financed by the German Federal Ministry of Education and Research (BMBF) and of the Russian-German Cooperation “System Laptev Sea”. The main focus of the Laptev Sea System Project was the formation of the submarine permafrost within the near-shore zone of the shallow shelf. Studies of permafrost evolution in the coastal zone allow us to understand the on-shore/off- shore permafrost system evolution more precisely (Overduin et al., 2007). The coastal drilling transect campaign was conducted in spring 2005 in the Cape Mamontov Klyk area (Siberian Laptev Sea Shelf area, Russia). Cores were drilled along an 11.5 km transect from terrestrial to submarine permafrost. Field research and sampling were carried out during the expedition COAST I 2005. This study is presented in English as a cumulative Ph.D. thesis at the University of Potsdam, Institute of Biochemistry and Biology. This thesis includes an introduction of the particular research field including the scientific background and descriptions of the study area. The main part of this thesis contains three publications as first author. The first was published (under my maiden name Koch). The second has been submitted and the third is in preparation for submission (both under my married name Feige). The final part of my thesis comprises a publication as co-author and a synthesis representing the conclusions and future perspectives of the work. ACKNOWLEDGEMENTS I would like to express my very sincere thanks to Dr. habil. Dirk Wagner for accepting me into his working group. He gave me the opportunity to conduct research freely in the natural sciences. I have profited greatly from his experience and expertise in structuring and representing complex relationships in a clear and transparent manner. Thank you, Dirk, for your consistent treatment of me with respect and dignity and for your comments on this thesis. I would like to thank Prof. Dr. Antje Boetius and Dr. German Jurgens cordially a being the reviewer of this thesis. I thank Prof. Dr. Hans-Wolfgang Hubberten as head of AWI Research Unit Potsdam for his ever positive thoughts and patience. I also thank him for permitting my participation in the LENA 2008 expedition and for supporting my attendance at various national and international conferences. I would like to thank all the current and former members of the working group “GEOMICS“ and naturally also “GEOCHEMICS“ (Ute, Antje) for the excellent group II PREFACE & ACKNOWLEDGEMENT work and the always friendly and humorous atmosphere. Special thanks goes to Lars Ganzert alias Larsen, Juliane Griess alias Jule, Esther Rickert, Hugues Lantuit, and Georg Schwamborn for the deep, useful, and upbeat discussions and exchanges we have had. Both at and outside of work, I had a great time with you. The same goes for Dr. Daria Morozova and Dr. Susanne Liebner, who are no longer at our institute. Dear Susi and Daria, I thank you for your fond encouragement and for listening. Thank you to all my colleagues in the periglacial department! I thank Dr. Christian Knoblauch and Dr. Paul Overduin for their chemical analyses, willingness to be co-authors, and upbeat sense of humor. Christian, it was great being with you on the expedition in Samoylov. Paul, I enjoyed our time on the trip to Bremerhaven in preparation for the expedition. Our talks, Paul, with you as lay- microbiologist and me as lay-geologist were very enlightening. Thanks you both! I thank the laboratory of the Department of Environmental Microbiology at the Technical University in Berlin for my use of their Rotor 6000 and the support of Prof. Dr. Ulrich Szewzyk and his assistants. In particular, I thank Katharina Knobel for her help with the Real-Time PCR. A very special thanks goes to my sign language interpreter Joanna Martin who has interpreted for me at conferences and the GEO-Treff meetings. I hope she continues to accompany me in my professional life. I thank her children for their patience and understanding during the times of her absence. I also thank you for your correction of and comments on this thesis, Joanna. My special thanks go to my parents and my small extended family who have always believed in me and supported and encouraged me. Not only are you proud of me, but I am proud of you, my dear parents. And last but not least my thanks go to my most humorous husband, Henrik. I treasure your humour, your love, your encouragement, and our wonderful conversations. III ABBREVIATIONS ABBREVIATIONS bp base pairs