Sources and environmental controls of microbial membrane lipids in soils and groundwater Dissertation (Kumulativ) zur Erlangung des Doktorgrades der Naturwissenschaften - Dr. rer. nat. - Vorgelegt dem Rat der Chemisch-Geowissenschaftlichen Fakultät der Friedrich-Schiller-Universität Jena Su Ding Geboren am 12.02.1988 in China I Gutachter: 1. Prof. Dr. Gerd Gleixner Max Plank Institute for Biogeochemistry, Jena, Germany 2. Prof. Dr. Georg Pohnert Friedrich-Schiller-Universität, Jena, Germany Tag der Verteidigung: 24.07.2019 II Table of contents Acknowledgements ................................................................................................................... V List of abbreviations ............................................................................................................... VII 1. Introduction ........................................................................................................................... 1 1.1 Tree of life ....................................................................................................................... 2 1.2 Biogeochemical importance of microorganisms in the environment .............................. 3 1.3 Tools to study microorganisms ....................................................................................... 4 1.3.1 Microbial membrane lipids – diversity in structures and functions.......................... 5 1.3.2 Lipidomics based biomarkers ................................................................................. 11 1.4 Scope and Outline ......................................................................................................... 12 Part I. GDGTs in lake sediments, groundwater and potential recharge surface soils.............. 15 2. Identification of novel 7-methyl and cyclopentanyl branched glycerol dialkyl glycerol tetraethers in lake sediments .................................................................................................... 16 3. In situ production of core and intact bacterial and archaeal tetraether lipids in groundwater ................................................................................................................................................. 33 Part II. Full lipid profile and their affect environmental parameters in soils .......................... 49 4. Characterization of intact polar lipids in soils for assessing their origin ............................. 50 5. Discussion and outlook........................................................................................................ 89 Constraining the uncertainties of brGDGT derived proxies ............................................... 89 Sources and fate of intact polar and core GDGTs in groundwater .................................... 89 Composition of intact polar membrane lipids in soils and their environmental factors ..... 90 6. Summary ............................................................................................................................. 93 Zusammenfassung ................................................................................................................... 96 III Table of contents References ............................................................................................................................... 99 Curriculum Vitae ................................................................................................................... 121 Selbständigkeitserklärung...................................................................................................... 122 IV Acknowledgements Acknowledgements Gerd, thank you for your unconditional support, guidance and giving me the freedom and good resources to work on these exciting projects. As a supervisor, you are not only guiding me on the way of science, but also telling me the truth of life to help me to be a better man. Georg, every time I encountered the bottleneck of the experiment and felt depressed, you can always find a smart solution to refresh my mind and help me out of the woods. I will never forget those inspiring scientific discussions with you. Valerie, thank you for letting me develop my own ideas and contributing significantly to my work. I’m deeply grateful for your great patience, endless support and for teaching me in the noble arts of liquid chromatography. Markus, thank you for sharing countless ideas, data and extensive discussions on the project. Without your consistent and illuminating guidance, my part of the jena experiment could not have reached its present form. I’ve really enjoyed working with you for the past 3 years. I thank Susan for your continuous support from the start of my Ph.D. study. I would like to express my deeply gratitude to Prof. Kai-Uwe Hinrichs and his lab. I’ve really learned a lot and enjoyed the time that I spent my research stay in Bremen. Particular thanks to Julius Lipp who supported a great part of my work. You are so talented in mass spectrometry and liquid chromatography. Thank you for answering the countless questions and guiding me into a whole new world of membrane lipids. I am sincerely grateful to Prof. Ruth Welti and her group. Thank you for so many constructive comments and suggestions on the work. You provide me so many good opportunities to talk to the experts in different field, treating me like your own student and let me feel at home. I would also like to thank Mary Roth who shared her lipidomic experience with me. V Acknowledgements Thank you, Vanessa, Franzi, Somak, Stefan, Carsten, Simon, Natalie, Kasun for sharing your ideas and discussions with me. I’m also appreciated for the help of Nico, Steffen, Uta, Robert, Ines, Heiko, Iris, Maria, Cassandre, Yinghui, Wenjie, Shangzhe, Xiu for your support of this work. I’m grateful for all the institute members that are not mentioned here for such a nice working atmosphere. I want to thank our secretaries Steffi, John and Kerstin. You are always there when I need your help. My big thanks would go to our Chinese family, Haiyang, Yan, Jianbei, Yunpeng, Dapeng, Zhigang, Biao Huai, Dechang, Jingyuan, Feng Peng, you made me feel like home here. Last but not least, thanks to all my friends and my family for their support of last three years. Chunjiang, thank you for your encouragement and accompany in this long way journey. VI Abbreviations List of abbreviations AEG acyletherglycerol APCI atmospheric pressure chemical ionization brGDGT branched glycerol dialkyl glycerol tetraether CDP cytidine diphosphate CL (cardiolipin) diphosphatidylglycerol Cren crenarchaeol Cren’ crenarchaeol regioisomer DAG diacylglycerol DEG dietherglycerol DGDG digalactosyldiacylglycerol DGTS diacylglycerylhydroxymethyltrimethyl-(N,N,N)- homoserine DMPE phosphatidyl-(N,N)-dimethylethanolamine GC gas chromatography GDGT glycerol dialkyl glycerol tetraether GTGT glycerol trialkyl glycerol tetraether HILIC hydrophilic interaction liquid chromatography HPH hexose-phosphohexose HPLC high performance liquid chromatography IPL intact polar lipid isoGDGT isoprenoid glycerol dialkyl glycerol tetraether MGDG monogalactosyldiacylglycerol MMPE phosphatidyl-(N)-methylethanolamine m/z mass to charge ratio MS mass spectrometer/spectrometry NP normal phase OL ornithine lipid VII Abbreviations OM organic matter PA phosphatidic acid PC phosphatidylcholine PE phosphatidylethanolamine PG phosphatidylglycerol PI phosphatidylinositol PL phospholipid PS phosphatidylserine qToF-MS quadrupole time-of-flight mass spectrometer RI ring index RP reverse phase Sph sphingolipid SPM suspended particle matter TLE total lipid extract TOC total organic carbon VIII Introduction 1. Introduction Lipids are essential components of microbial membranes (Op den Kamp, 1979). They play critical roles in microbial functions, including signal transportation, cellular barriers, energy repository and membrane architectures (Cronan, 1978; Cronan and Gelmann, 1975). Membrane lipids are very complex and highly dynamic, there are hundreds of molecular species and they are always changing with physiological and environmental changes (Dowhan, 1997; Nikaido and Vaara, 1985; Woese, 1987). It is not clear why nature created so diverse types of lipids. Recently, lipidomics, a novel discipline has emerged to study membrane lipids based on analytical chemical tools, particularly mass spectrometry (Brügger, 2014; Han and Gross, 2003, 2005; Yang and Han, 2016). Lipidomics can help us to identify new lipid molecules, reveal the mechanisms underlying responsible for physiological or environmental conditions, discover potential biomarkers to understand climate change, organism interaction and evolution (Han et al., 2012; Shevchenko and Simons, 2010; Wenk, 2005). Besides, stable isotope probing of certain lipid types reveals the activity and function of distinct microbial community in the environment (Wegener et al., 2016). Accordingly, with lipidomics, our understanding of the microorganisms in the complex ecosystem will be undoubtedly accelerated. In this introduction, first I briefly introduced the classification of life and the importance of microorganisms in the environments. Then I summarized the tools to study microorganisms and compared them to the mass spectrometry-based lipidomic techniques. In addition, the type and function of archaeal and bacterial membrane lipids were introduced for better understanding lipidomic technics. Finally, I discussed the advantages and limitations of recently used lipidomics derived biomarkers and highlighted the aim of this thesis.