Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung Helmholtz-Zentrum Potsdam Deutsches GeoForschungsZentrum Methane distribution and oxidation across aquatic interfaces: case studies from Arctic water bodies and the Elbe estuary Kumulative Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften „doctor rerum naturalium“ -Dr. rer. Nat.- in der Wissenschaftsdisziplin „Mikrobiologie“ Eingereicht an der Mathematisch-Naturwissenschaftlichen Fakultät der Universität Potsdam Von Roman Osudar Potsdam, Mai 2016 Published online at the Institutional Repository of the University of Potsdam: URN urn:nbn:de:kobv:517-opus4-96799 http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-96799 Preface Preface This work represents a joint project between Helgoland and Potsdam units of The Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research and also between The GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam. The work was supervised by Prof. Dr. Dirk Wagner (GFZ, section 5.3: Geomicrobiology) and Dr. Ingeborg Bussmann (AWI, Helgoland, section: Shelf Sea System Ecology). The aim of the project was to extent our knowledge about environmental controls of methane distribution and aerobic methane oxidation in aquatic ecosystems which are subject to pronounced interaction with bordering environments. Arctic water bodies and estuaries were chosen as study sites which exemplify these aquatic interfaces. The field sampling campaigns took place in the Elbe estuary from 2011 to 2013 and in the Lena Delta in July 2012 (expedition LENA 2012), with a personal participation. The laboratory work was performed at the three mentioned institutes (AWI Helgoland, AWI Potsdam and GFZ) and also partly in the Winogradsky Institute of Microbiology, Russian Academy of Science, Moscow, Russia with the support of Prof. Dr. Nikolay Pimenov. Sampling campaign in the Lena Delta was financially supported by the European cooperation for long-term monitoring (PERGAMON) [COST STSM Reference Number: ECOST-STSM-ES0902-290811-008783]. The workshop and conference attendances were supported by the Helmholtz Graduate School for Polar and Marine Research (POLMAR) and the Association for General and Applied Microbiology (VAAM). This thesis is written in English and submitted as a cumulative dissertation to the Faculty of Mathematics and Natural Science at the University of Potsdam. The main body of the thesis consists of: (1) general introduction to the research topic with the particular objectives of the study and the description of the study area; (2) manuscripts, which describe the carried out research; and (3) synthesis, which summarizes the obtained results. The “Manuscripts” section is composed of three manuscripts with first authorship, two of which are published or accepted for publication in peer- reviewed scientific journals and one is presented as a final draft. i Acknowledgments Acknowledgments I am happy to acknowledge everybody who contributed to the success of my work. I wish to particularly thank… … my supervisors: Prof. Dr. Dirk Wagner and Dr. Ingeborg Bussmann for the invaluable help, support and patience generously granted to me during the whole period of my study. ... heads of the AWI Helgoland, AWI Potsdam and GFZ: Prof. Dr. Karen Helen Wiltshire, Prof. Dr. H.- W. Hubberten, and Prof. Dr. Dr. h.c. R. Hüttl and Dr. S. Schwartze, respectively for the opportunity to work in a great scientific and collegial atmosphere. ... all my colleagues at all three Institutes, Geomicrobiology section and especially: Dr. Mashal Alawi, Prof. Dr. Susanne Liebner, Andrea Kiss, Janine Heise, Dr. Felizitas Bajerski, Dr. Paloma Serrano, Dr. Sizhong Yang, Julia Magritz and Steffi Genderjahn for the scientific contribution and simply for always “being there for me”. … Günther ‘Molo’ Stoof, Waldemar Schneider and all the others involved in the expedition LENA 2012 for a wonderful Arctic summer. … my family and my friends for believing in me. ii Table of contents TABLE OF CONTENTS PREFACE ............................................................................................................................................. i ACKNOWLEDGMENTS ....................................................................................................................... ii TABLE OF CONTENTS ......................................................................................................................... iii SUMMARY ......................................................................................................................................... v ZUSAMMENFASSUNG ........................................................................................................................ vii I. INTRODUCTION .............................................................................................................................. 1 1.1 Methane cycle ............................................................................................................................. 1 1.2 Methane distribution and cycling in bordering aquatic and terrestrial environments .............. 5 1.2.1 Arctic water bodies ............................................................................................................ 5 1.2.2 Estuaries ............................................................................................................................. 6 1.3 Aerobic methanotrophic bacteria (MOB) ................................................................................... 8 1.3.1 Classification of MOB ......................................................................................................... 8 1.3.2 Environmental controls and biogeography of MOB .......................................................... 10 1.3.3 Taxon-specific activity of MOB .......................................................................................... 13 1.3.4 Aquatic MOB ...................................................................................................................... 14 1.4 Molecular tools for the study of MOB ........................................................................................ 15 1.5 Aims and objectives .................................................................................................................... 17 1.6 Study area .................................................................................................................................... 17 1.6.1 The Lena Delta ................................................................................................................... 18 1.6.2 The Elbe estuary ................................................................................................................. 19 1.7 Overview of the publications and manuscripts .......................................................................... 21 II. MANUSCRIPTS ............................................................................................................................... 24 Manuscript I “Methane turnover and methanotrophic communities in Arctic aquatic ecosystems of the Lena Delta, Northeast Siberia” ............................................................................ 24 Manuscript II “Environmental factors affecting methane distribution and bacterial methane oxidation in the German Bight (North Sea)” ....................................................................... 49 Manuscript III “Effect of salinity and light on aerobic bacterial methane oxidation in the marine and freshwater” ..................................................................................................................... 72 III. SYNTHESIS .................................................................................................................................... 87 3.1 Discussion .................................................................................................................................... 87 iii Table of contents 3.2 Conclusion ................................................................................................................................... 92 3.3 Final remarks ............................................................................................................................... 93 IV. REFERENCES ................................................................................................................................. 95 V. APPENDIX ...................................................................................................................................... 108 Additional manuscript I “Assessment of the radio 3H‐CH4 tracer technique to measure aerobic methane oxidation in the water column” ............................................................................ 108 Additional manuscript II “Methane distribution and methane oxidation in the water column of the Elbe estuary, Germany” .......................................................................................................... 138 iv Summary Summary The increase in atmospheric methane concentration, which is determined by an imbalance between its sources and sinks, has led to investigations of the methane cycle in various environments. Aquatic environments are of an exceptional interest due to their active involvement in methane cycling worldwide and in particular in areas sensitive to climate change. Furthermore, being connected with each other aquatic environments form networks that can be spread on vast areas