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Grappling Extremes: Molecular Methods Combined with Cultivation

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Grappling Extremes: Molecular Methods Combined with Cultivation Grappling extremes: Molecular methods combined with cultivation reveal the composition and biology of space- relevant microbial communities Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr.rer.nat.) der Fakultät für Biologie und Vorklinische Medizin der Universität Regensburg vorgelegt von Alexandra Kristin Perras aus München im Jahr 2017 Das Promotionsgesuch wurde eingereicht am: 13.01.2017 Diese Arbeit wurde angeleitet von: Prof. Dr. Christine Moissl-Eichinger Prüfungsausschuss: Vorsitzender Prof. Dr. Peter Poschlod 1.Gutachter: Prof. Dr. Christine Moissl-Eichinger 2.Gutachter: Prof. Dr. Reinhard Wirth 3. Prüfer: Prof. Dr. Rainer Merkl Unterschrift: Alexandra K. Perras - 2 - Grappling extremes: Molecular methods combined with cultivation reveal the composition and biology of space- relevant microbial communities Dissertation for achieving the doctoral degree of natural sciences (Dr.rer.nat.) at the faculty of Biology and Preclinical Medicine at the University of Regensburg by Alexandra Kristin Perras from Munich 2017 Key words: Mars-analogues, microbial ecology, Archaea, Candidatus Altiarchaeum hamiconexum, hami, extreme environments, the ISS microbiome, MASE - 3 - The dissertation was performed under the supervision of Prof. Dr. Christine Moissl-Eichinger (PhD supervisor) Prof. Dr. Reinhard Wirth (1st mentor) Prof. Dr. Charles Cockell (2nd mentor) At the Naturwissenschaftliche Fakultät 3, Biology and Preclinical Medicine and the Medical University of Graz under fulfilment of all requirements of the Regensburger Graduate School of Life Sciences (RIGeL). - 4 - Table of Contents Danksagung ................................................................................................................................................... 7 List of publications ......................................................................................................................................... 8 I. Abstract ............................................................................................................................................... 10 II. General Introduction ........................................................................................................................... 11 1. Tackling the dogma of microbial diversity ........................................................................................ 11 2. A grappling archaeon: Traits of the SM1 Euryarchaeon ................................................................... 17 3. The era of astrobiology ..................................................................................................................... 25 4. Scope and publication guide ............................................................................................................ 32 III. Manuscripts and publications ............................................................................................................. 34 III.1. Grappling archaea: ultrastructural analyses of an uncultivated, cold-loving archaeon, and its biofilm ......................................................................................................................................................... 35 Abstract ....................................................................................................................................................... 36 Introduction ................................................................................................................................................. 36 Material and methods ................................................................................................................................. 39 Results ......................................................................................................................................................... 39 Discussion .................................................................................................................................................... 48 III.2. S-layers at second glance? Altiarchaeal grappling hooks (hami) resemble archaeal S-layer proteins in structure and sequence................................................................................................................... 52 Abstract ....................................................................................................................................................... 53 Introduction ................................................................................................................................................. 53 Material and methods ................................................................................................................................. 55 Results ......................................................................................................................................................... 58 Discussion .................................................................................................................................................... 66 III.3. Resilient microorganisms in dust samples of the International Space Station – Survival of the adaptation specialists ...................................................................................................................... 71 Abstract ....................................................................................................................................................... 72 Introduction ................................................................................................................................................. 72 Materials and methods................................................................................................................................ 74 Results ......................................................................................................................................................... 79 Discussion .................................................................................................................................................... 93 III.4. Mars exploration begins on Earth: Systematic comparison of the anaerobic, intact and cultivable microbiome of extreme, anoxic, Mars-analogue environments .................................................. 100 Abstract ..................................................................................................................................................... 101 Introduction ............................................................................................................................................... 101 - 5 - Materials and methods.............................................................................................................................. 103 Results ....................................................................................................................................................... 105 Discussion .................................................................................................................................................. 122 IV. General Discussion ............................................................................................................................ 125 1. Small size matters! Recent findings on the grappling SM1 Euryarchaeon ..................................... 125 2. Survival specialists deriving from the ISS ....................................................................................... 133 3. Terrestrial extreme, Mars-like habitats: Implications for extraterrestrial life? ............................. 136 V. Zusammenfassung ............................................................................................................................. 144 VI. Bibliography....................................................................................................................................... 146 VII. Content of supporting CD .................................................................................................................. 167 VIII. Eidesstattliche Erklärung ................................................................................................................... 168 - 6 - Danksagung Danksagung An erster Stelle möchte ich mich ganz herzlich und besonders bei meiner Doktormutter Prof. Christine Moissl- Eichinger bedanken. Sie hat mir nicht nur die Möglichkeit gegeben, unglaublich spannende Themen zu bearbeiten, sondern mich auch immer wieder begeistern, motivieren, und bei Rückschlägen aufmuntern können. Vielen Dank für das offene Ohr und die vielen Ratschläge in allen Lebenslagen! Christine, du warst und wirst immer ein Vorbild für mich sein! Ganz besonders möchte mich ich mich auch bei Prof. Reinhard Wirth bedanken! Sie haben mich vor Jahren in meinem allerersten Projekt in der Mikrobiologie betreut und mich nachhaltig für die Mikrobiologie begeistern können. Vielen Dank für das Übernehmen der Mentorenschaft und des Gutachters auch in dieser Arbeit, die ausgezeichneten Ratschläge und wissenschaftlichen Inspirationen. Auch bei meinem dritten Mentor und Leiter des MASE-Projektes, Prof. Charles Cockell, möchte ich herzlichst für die Betreuung während der letzten drei Jahre bedanken! Die Arbeit im MASE-Projekt hat sehr viel Spaß gemacht und mir die wertvolle Erfahrung gegeben, mit sehr vielen, internationalen Wissenschaftlern gemeinsam an einem Projekt zu arbeiten. An dieser Stelle ein großes Dankeschön an alle MASE-Teammitglieder für die ausgezeichnete
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