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Phd Susanne Liebner.Pdf adaptation, spatial variability, and phylogenetic characterization of methanotrophic communities in permafrost soils of the lena delta, siberia Dissertation von Susanne Liebner November 2007 Adaptation, spatial variability, and phylogenetic characterization of methanotrophic communities in permafrost soils of the Lena Delta, Siberia Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften -Dr. rer. nat.- dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Susanne Liebner Potsdam, November 2007 Die Untersuchungen zur vorliegenden Dissertation wurden hauptsächlich am Alfred- Wegener-Institut für Polar- und Meeresforschung in Potsdam durchgeführt. Einzelne Analysen erfolgten zusätzlich am Max-Planck-Institut für Marine Mikrobiologie in Bremen. 1. Gutachter: Prof. Dr. Rudolf Amann 2. Gutachter: Dr. habil. Dirk Wagner PREFACE & ACKNOWLEDGEMENTS Preface This work was integrated into the Russian-German joint venture project System Laptev Sea 2000. The focus of this project was to extent our knowledge about the Laptev Sea system in north-east Siberia obtained through previous Russian-German projects, such as the Laptev Sea System (1994-1997), and Taymyr (1994-1997). Studies on Quaternary environmental changes, Arctic coastal dynamics and recent periglacial processes including ecological studies on permafrost soils and ecosystems of the central Lena Delta were in the focus of the recent project (Schirrmeister et al., 2004). The present work contributes to the last aspect by investigating the field of methane fluxes in polygonal tundra environments of the Lena Delta. Field work and sampling of this study was conducted during the expeditions LENA 2002 and LENA 2005 (Samoylov Island, Lena Delta, Siberia) with a personal participation in the last expedition. The work was performed in the frame of the International Max Planck Research School for Marine Microbiology (MarMic) mainly at the Alfred Wegener Institute for Polar and Marine Research, Research Unit Potsdam. Some analyses were conducted at the Max Planck Institute for Marine Microbiology in Bremen. This study is presented in English as a cumulative Ph.D. thesis at the University of Bremen (Fachbereich 02). The thesis consists of a general introduction to the particular research field including the scientific background as well as aims and objectives of this study. The study area is described in an extra chapter. The main part of this thesis consists of three manuscripts with first authorship and a final synthesis representing the conclusions as well as critical remarks and future prospects of this work. Acknowledgements My particular thanks to Dr. habil. Dirk Wagner (AWI Potsdam) for promoting and encouraging me throughout all the years at AWI, for his indestructibly optimism and challenging personality and last but least for initializing my fascination for the microbial world. Special thanks also to Prof. Dr. Rudolf Amann and Dr. PD Jens Harder (MPI for Marine Microbiology) as members of my thesis committee for their scientific support and critics as well as for their contribution to the MarMic program. I also acknowledge the continuous interest and patience of the head of the AWI research department Prof. Dr. Hans-Wolfgang Hubberten concerning the demands of the GEOMICs group and that due to his support I was able to attend the expedition LENA 2005 and various national and international conferences. Also, I would like to mention that he as well as Christine Litz promoted my participation in the MarMic program. Many thanks in general to all people contributing to that program, in particular to Dr. Christiane Gloeckner as the MarMic coordinator and to the ‘MarMics’ Amelia Rotaru, i PREFACE & ACKNOWLEDGEMENTS Alberto Robador, Joanna Sawicka, and Rita Dunker sharing the same fate and many inspiring informal after work sessions. The last also applies to Regina Schauer whose diploma thesis was of great additional value for my work. Tina Treude and Imke Busse (MPI for Marine Microbiology) kindly introduced me into the radiotracer experiments. Many thanks also to Torsten Sachs (AWI Potsdam) for critically revising major parts of my thesis. Antje Eulenburg and Paul Overduin (AWI Potsdam) were of much help for the pore water analysis. Torben Stührmann (MPI for Marine Microbiology) displayed an enormous patience explaining to me the world of ARB and was very helpful providing up to date information about the scientific world and many encouraging words. Also, I want to thank the crew of the Expedition LENA 2005, in particular Günter ‘Molo’ Stoof (AWI Potsdam) for technical support as well as Alexander Yu. Dereviagin (Moscow State University), Mikhail N. Grigoriev (Permafrost Institute Yakutsk), Dmitri V. Melnitschenko (Hydro Base Tiksi), and Alexander Yu. Gukov (Lena Delta Reserve). Warmest thanks to Waldemar Schneider (AWI Potsdam) for his unique disposition to always question everything and everyone, for his experienced logistic abilities, and his sympathy. I thank all GEOMICs at the AWI Potsdam, that due to their pronounced ‘corporate identity’ always kept a warm, supporting and optimistic lab atmosphere meanwhile even in the complete absence of a technician. Particular thanks in this context to Heiko Baschek, Martin Karels, Katharina Koch, Daria Morozova, and Lars Ganzert. During the last years I was allowed to enjoy the company of numerous great AWI Ph.D. and diploma students always willing to extend the working day by either inspiring scientific discussions having a beer or just by having a beer. From time to time, some of them succeeded perfectly to lower the level beyond of what is possible. Larsen, Torsten, Dasha, Jürgen, Julia, Hugues, Katharina, Jule, Thomas, Andreas, Sebastian, and Christian: Thank’s a lot! Most of all I thank Marc for the way he is, especially to me, and my parents as well as my brother who always had faith in what I was doing although (or maybe because) I never managed to explain to them what I was actually working at. This work is dedicated to them. ii TABLE OF CONTENTS Table of contents Preface……………………………………………………………………………….... i Acknowledgements…………………………………………………………………... ii Table of contents……………………………………………………………………... iii List of abbreviations………………………………………………………………….. iv Summary………………………………………………………………………………. v Zusammenfassung…………………………………………………………………… vii 1. Introduction………………………………………………………………………. 1 1.1 Scientific background………………………………………………………... 1 1.2 Taxonomic, phylogenetic, and physiological characterization of MOB… 2 1.3 Molecular tools for the study of MOB……………………………………… 4 1.4 Eco-physiology and diversity of MOB……………………………………… 5 1.5 Estimating bacterial diversity and patterns of bacterial diversity……….. 9 1.6 Aims and objectives…………………………………………………………. 11 1.7 Overview of publications and manuscripts………………………………... 13 2. Study area………………………………………………………………………… 16 2.1 The Lena Delta as part of the continuous permafrost zone…………….. 16 2.2 Samoylov Island and its polygonal tundra environments………………... 18 3. Manuscript I: Abundance, distribution and potential activity of methane 20 oxidizing bacteria in permafrost soils from the Lena Delta, Siberia…………….. 20 4. Manuscript II: Diversity of aerobic methanotrophic bacteria in a perma- 30 frost soil of the Lena Delta, Siberia………………………………………………… 30 5. Manuscript III: Composition and diversity of soil bacterial communities in 45 polygonal tundra sites of the Lena Delta, Siberia, with particular focus on the Bacteroidetes phylum………………………………………………………………... 45 6. Synthesis…………………………………………………………………………. 64 7. References……………………………………………………………………….. 72 8. Appendix………………………………………………………………………….. 90 8.1 Manuscript IV: Temperature adaptation of microbial populations in different horizons of the active layer in permafrost soils from the Lena- Delta, Siberia……………………………………………………………………… 90 8.2 Q10-values of potential methane oxidation rates…………………………. 101 8.3 Sample list, field data, and sampling procedure during LENA 2005…… 101 8.4 Overview of clone libraries and affiliation of clones……………………… 104 8.5 Enrichment of MOB from a Siberian permafrost soil…………………….. 108 iii LIST OF ABBREVIATIONS List of abbreviations AMO ammonia monooxygenase amoA gene encoding the -subunit of the AMO bp base pairs Cy3 fluorescent dye DAPI 4’,6-diamidino-2-phenylindole DDBJ DNA database of Japan DGGE denaturing gradient gel electrophoresis DOC dissolved organic carbon EMBL nucleotide sequence database FISH fluorescence in-situ hybridization GC-content content of guanine and cytosine GenBank international genetic database IPCC Intergovernmental Panel on Climate Change kb kilo base pairs MDH methanol dehydrogenase MMO methane monooxygenase mmoX gene encoding the hydroxylase component of the sMMO MOB (aerobic) methane oxidizing bacteria mRNA messenger RNA MUSCLE multiple sequence alignment algorithm mxaF gene encoding the -subunit of the MDH NMS medium nitrate-mineral-salts medium OTU operational taxonomic unit PCR polymerase chain reaction PLFA phospholipid fatty acid pMMO particulate methane monooxygenase pmoA gene encoding the -subunit of the pMMO qPCR quantitative (real time) PCR rRNA ribosomal RNA RT reverse transcriptase SIP stable isotope probing sMMO soluble methane monooxygenase TC total organic carbon TCC total cell counts TN total nitrogen T-RFLP terminal restriction fragment length polymorphism iv SUMMARY Summary The Lena Delta, located in north-east Siberia in the zone of continuous permafrost, is the largest delta within the circum-arctic. Northern wetlands and wet polygonal tundra environments
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