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The Role of Photoheterotrophic and Chemoautotrophic

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The Role of Photoheterotrophic and Chemoautotrophic The role of photoheterotrophic and chemoautotrophic prokaryotes in the microbial food web in terrestrial Antarctica: a cultivation approach combined with functional analysis Guillaume Tahon Promotor Prof. Dr. Anne Willems Dissertation submitted in fulfillment of the requirements for the degree of Doctor (Ph.D.) of Science: Biotechnology (Ghent University) Tahon Guillaume | The role of photoheterotrophic and chemoautotrophic prokaryotes in the microbial food web in terrestrial Antarctica: a cultivation approach combined with functional analysis Copyright © 2017, Tahon Guillaume ISBN-number: 978-94-6197-523-2 All rights are reserved. No part of this thesis protected by this copyright notice may be reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording or by any information storage or retrieval system without written permission of the author and promotor. Printed by University Press | http://www.universitypress.be Ph.D. thesis, Faculty of Sciences, Ghent University, Ghent, Belgium This Ph.D. work was supported by the Fund for Scientific Research – Flanders (project G.0146.12) Publically defended in Ghent, Belgium, May 5th, 2017 Examination committee Prof. Dr. Savvas Savvides (Chairman) L-Probe: Laboratory for protein Biochemistry and Biomolecular Engineering Faculty of Sciences, Ghent University, Belgium VIB Inflammation Research Center VIB, Ghent, Belgium Prof. Dr. Anne Willems (Promotor) LM-UGent: Laboratory of Microbiology Faculty of Sciences, Ghent University, Belgium Prof. Dr. Elie Verleyen (Secretary) Laboratory of Protistology and Aquatic Ecology Faculty of Sciences, Ghent University, Belgium Em. Prof. Dr. Paul De Vos LM-UGent: Laboratory of Microbiology Faculty of Sciences, Ghent University, Belgium Dr. Natalie Leys SCK·CEN: Environment, Health and Safety Belgian Nuclear Research Centre, Mol, Belgium Dr. Annick Wilmotte Cyanobacteria Research group and BCCM/ULC Cyanobacteria Collection Center for Protein Engineering, Liège University, Belgium iii “Antarctica, an inhospitable wasteland, but even here, on the Earth's frozen bottom, we find life. And not just any life.” Werner Herzog Dankwoord Het eerste dat ik dacht was “Een dankwoord schrijven, hoe begin je daar in godsnaam aan, want het toch is onmogelijk om mijn ‘dank’ aan zoveel mensen beknopt op papier neer te pennen.”. Na veel schrijven en vooral herschrijven ben ik uiteindelijk tot een dankwoord gekomen. Onderstaande woorden zullen en kunnen nooit alles en iedereen omvatten, maar hopelijk zeggen mijn ietwat poëtische woorden toch een beetje hoe dankbaar ik ben voor jullie steun de afgelopen vijf jaar. Beginnen kan ik niet anders dan met Prof. Anne Willems, Anne, de persoon door wie dit doctoraatsproject mogelijk was. Het is ondertussen iets meer dan vijf jaar geleden dat u mij uitnodigde voor een gesprek over een Antarcticaproject en mij ook de kans gaf om dit aan te vatten. Ik wil u niet alleen bedanken om mij deze kans te geven, maar natuurlijk ook voor alle hulp bij het opzetten van de experimenten, het analyseren van de data, het schrijven van de artikels en, last but not least, de niet-wetenschappelijke momenten. I would also like to thank the members of my examination committee for taking the time to review my dissertation and for their helpful comments. Bjorn, Helen en Pia, waar moet ik beginnen… Ooit zaten we samen op het nulde. Nu, zovele jaren later hebben jullie al alle drie andere oorden opgezocht (en blijf ik hier eenzaam en alleen achter op het labo), maar toch is het contact er niet minder op geworden. Dankjewel voor alles! Al is er ondertussen veel veranderd (Helen is nu een getrouwde vrouw) en staat veel op het punt te veranderen (Pia verwacht een klein boeleke en Bjorn begint als Verschrikkelijke Sneeuwman in Spitsbergen en Antarctica), toch hoop ik dat we nog regelmatig leuke momenten en Delicieuxlunches mogen beleven. En Pia, weet dat ik nog steeds in blijde verwachting ben van je handgemaakte en -geschilderde soepbord. Bram, Charles (aka Xavier, aka Carlos), Chris, Prem, Frédéric en Pieter-Jan (aka PJ), onze tijd samen was van korte, doch krachtige duur. Merci voor de kwart-voor-vier-lachmomentjes, het gezever en gezwans, en natuurlijk ook de professionele momenten. Onze eigenste Wall of Fame zal de toekomstige werknemers nog vele jaren herinneren (of toch zolang de verf het volhoudt…) aan hoe tof het was toen wij er waren. Velen zullen proberen, maar niemand zal vii er in slagen ons te evenaren, want onze doortocht gaat de geschiedenisboeken in als de Gouden Jaren! Anique, Yihua, Pablo, Arianna, Francesca and Maria-Francesca, thank you all for the nice moments, both in the lab and at various places in and near Ghent. Jessy, binnenkort zoem jij er vandoor op de tonen van Dalida’s grootste meesterwerk: Jessy apicoltore. Spreid je vleugels en verken de wereld, maar doe het wel niet te vroeg. September is naar het schijnt een mooie maand om het nest te verlaten. Ondertussen zal ze misschien al denken dat ik haar vergeten ben, maar niets is minder waar. Het schrijven van mijn ode aan jou lukte gewoon niet vroeger wegens het constant volschieten van mijn gemoed. Zelfs nu heb ik de grootste moeite van de wereld om de tranen niet langs mijn wangen te laten stromen. Liesbeth, mijn lama, er bestaat in feite geen enkel woord in eender welke taal om te zeggen hoe dankbaar ik ben voor al je hulp. Eerst was er, samen met Evie (nog zo’n klassevrouw), de vijfsterren sequencing service. Later volgden dan de experimenten met ons ‘beest’. Natuurlijk deed je zoveel meer dan dat. Iedereen die over jou hoort mag terecht jaloers en bedroefd zijn dat ze geen zo’n collega hebben en ooit zullen hebben. Ik ben er dan ook zeker van dat jij de muze was voor de wereldhit “Je te donne” van Jean-Jacques Goldman. Natuurlijk zijn er nog tal van andere collega’s die me de afgelopen jaren hebben bijgestaan met raad en daad en daarom niet mogen ontbreken. Jeannine, merci om altijd alle benodigdheden te bregen en om schoon te maken wat ik vuil maakte. Maarten, merci voor de gezellige momenten en de MALDI-TOF MS service. Kim en Geert H., merci voor de babbels en de hulp bij de experimenten. Mario en Bart H., merci voor technische hulp en de onnozele momenten. Marjan en de twee Sofies, merci om zo’n tijgers te zijn. Timo, Leen, Cindy en Jindrich, merci voor de vele ontspannende, uiteraard zeer hoogstaande gesprekken. Epifania, bedankt voor het helpen bij de vele adinistratie de afgelopen jaren. Daarnaast zijn er ook tal van mensen naast het werk die een belangrijke rol gespeeld hebben. Master William, Sir Rudiger en Don Thomas, het begon lang geleden aan het Boerekot. Ondertussen zovele jaren later hebben we al veel meegemaakt. Reeds enkele jaren volgen we de wijze raad van Madonna op. Tussen ons gezegd: I’ve got the feeling that if we took a holiday, took some time to celebrate, it would be so nice! Dus spread the word, want viii binnenkort is het weer time for the good times! Hannes en Jonathan, bedankt voor alle leuke momenten. Dat er nog veel mogen volgen. En natuurlijk ook alle vrienden van KSA Lo voor het bezorgen van zoveel leuke momenten en herinneringen. Uiteraard was dit alles niet mogelijk geweest zonder mijn familie, en dan in het bijzonder mijn ouders. Papa en mama, bedankt voor alles! Zonder jullie steun, motivatie en blijvend vertrouwen was dit nooit gelukt. Alles wat jullie mij gegeven hebben sinds dag één was het grootste geschenk dat iemand me ooit gegeven heeft. Mathieu, Valentine, opa en oma, jullie mogen natuurlijk ook niet ontbreken. Dikke merci voor alle steun, hulp en veelvuldige babbels de afgelopen jaren en alle jaren daarvoor. Guillaume Tahon Gent, 5 mei 2017 ix List of abbreviations A AA amino acid AAP aerobic anoxygenic photosynthetic bacteria ADP adenosine diphosphate Ala alanine anfD/AnfD iron-dependent nitrogenase α subunit gene / enzyme anfG/AnfG iron-dependent nitrogenase δ subunit gene / enzyme anfH/AnfH iron-dependent nitrogenase γ subunit gene / enzyme anfK/AnfK iron-dependent nitrogenase β subunit gene / enzyme APB anoxygenic phototrophic bacteria Arg arginine ATP adenosine triphosphate B bchB/BchB dark-operative protochlorophyllide oxidoreductase B subunit gene / enzyme Bchl bacteriochlorophyll bchL/BchL dark-operative protochlorophyllide oxidoreductase L subunit gene / enzyme of anoxygenic phototrophs bchLNB/BchLNB dark-operative protochlorophyllide oxidoreductase L, N and B subunits genes / enzymes of anoxygenic phototrophs bchN/BchN dark-operative protochlorophyllide oxidoreductase N subunit gene / enzyme bchX/BchX chlorophyllide oxidoreductase X subunit gene / enzyme bchXYZ/BvhXYZ chlorophyllide oxidoreductase X, Y and Z subunits genes / enzymes bchY/BchY chlorophyllide oxidoreductase Y subunit gene / enzyme bchZ/BchZ chlorophyllide oxidoreductase Z subunit gene / enzyme BLAST basic local alignment tool bp base pair BP before present BSA bovine serum albumin xi C C2H2 acetylene C2H4 ethylene C2H6 ethane CBB Calvin-Benson-Bassham cbbL type I ribulose bisphosphate carboxylase large subunit gene cbbM type II ribulose bisphosphate carboxylase large subunit gene Chl chlorophyll Chlide chlorophyllide chlL/ChlL dark-operative protochlorophyllide oxidoreductase L subunit gene / enzyme of oxygenic phototrophs chlLNB/ChlLNB dark-operative protochlorophyllide oxidoreductase L, N and B subunits genes / enzymes of oxygenic phototrophs CN- cyanide CO2 carbon dioxide COR chlorophyllide oxidoreductase D D1 photosystem 2 D1 subunit gene / enzyme in Cyanobacteria D2 photosystem 2 D2 subunit gene
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