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Distribution and Characterization of Bacterial Communities in Diverse Antarctic Ecosystems by High-Throughput Sequencing

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Distribution and Characterization of Bacterial Communities in Diverse Antarctic Ecosystems by High-Throughput Sequencing ––– Distribution and characterization of bacterial communities in diverse Antarctic ecosystems by high-throughput sequencing Bjorn Tytgat Promotors Prof. Dr. Anne Willems Prof. Dr. Elie Verleyen Dissertation submitted in fulfilment of the requirements for the degree of Doctor (Ph.D) in Sciences, Biology (Ghent University) Tytgat Bjorn | Distribution and characterization of bacterial communities in diverse Antarctic ecosystems by high-throughput sequencing Copyright © 2016, Bjorn Tytgat ISBN-number: 978-9-4619738-8-7 All rights reserved. No part of this thesis protected by its copyright notice may be reproduced or utilized in any form or any means, electronic or mechanical, including photocopying, recording or by any information storage or retrieval system without written permission of the author and promotors. Funding: This thesis was supported by the Special Research Fund BOF of Ghent University (grant 0J28410) and by the Belgian Science Policy Office (BelSPO) project CCAMBIO. Ph.D. Thesis, Faculty of Sciences, Ghent University, Ghent, Belgium Publicly defended in Ghent, Belgium, April 28th, 2016 ii Examination committee Prof. Dr. Koen Sabbe (Chairman) Laboratory of Protistology and Aquatic Ecology Department of Biology, Faculty of Sciences, Ghent University Prof. Dr. Olivier De Clerck (Secretary) Phycology Research Group, Ghent University Department of Biology, Faculty of Sciences, Ghent University Prof. Dr. Anne Willems (Promotor) Laboratory of Microbiology Department of Microbiology and Biochemistry, Faculty of Sciences, Ghent University Prof. Dr. Elie Verleyen (Co-promotor) Laboratory of Protistology and Aquatic Ecology Department of Biology, Faculty of Sciences, Ghent University Prof. Dr. Wim Vyverman Laboratory of Protistology and Aquatic Ecology Department of Biology, Faculty of Sciences, Ghent University Prof. Dr. Aurélien Carlier Laboratory of Microbiology Department of Microbiology and Biochemistry, Faculty of Sciences, Ghent University Prof. Dr. George A. Kowalchuk Ecology & Biodiversity Institute of Environmental Biology, Department of Biology, Utrecht University The Netherlands Dr. Arwyn Edwards Centre for Environmental Microbiology Microbiology Research Group Institute of Biological, Rural and Environmental Sciences, Aberystwyth University United Kingdom iii iv Dankwoord “I am somehow less interested in the weight and convolutions of Einstein’s brain than in the near certainty that people of equal talent have lived and died in cotton fields and sweatshops.” - Stephen J. Gould, The New Scientist, 1979 “We are like dwarfs on the shoulders of giants, so that we can see more than they, and things at a greater distance, not by virtue of any sharpness on sight on our part, or any physical distinction, but because we are carried high and raised up by their giant size.” Bernard of Chartres, 8th century BP “I speak English well, I learn it from a book” Manuel & Guillaume Niet dat ik claim om ook maar het talent van een Einstein of andere illustere onderzoekers te benaderen, verre van zelfs, maar ik ben zeer dankbaar om in een land en tijdperk te leven waarin ik – hoewel toch niet altijd zó evident – de kansen kon krijgen om de ‘fouten’ die ik als naïeve tiener gemaakt had recht te zetten, of om te studeren tout court, onafhankelijk van je afkomst of middelen. Dat ik hieraan zelfs een vervolg kon breien, met de bijkomende uitdagingen die het des te interessanter maakten, was een wens die uiteindelijk in vervulling is gegaan. Dit was echter niet mogelijk zonder de input, hulp, humor en babbels van en met verscheidene (over het algemeen ^^) betere specimens binnen onze soort. Eerst en vooral moet – en wil – ik Prof. Dr. Anne Willems bedanken, zonder wie dit alles in eerste instantie niet mogelijk was. De vacature kwam op een cruciaal moment, en de bevestiging maakte er een bijzondere verjaardag van. Bedankt voor het gestelde vertrouwen voor dit, toch wel (een beetje), pionierswerk. Je staat nu ook met naam en toenaam titel vereeuwigd in dit vodje papier, Professor Dr. Elie Verleyen. Bedankt voor de vele hulp, suggesties, discussies, avontuur Japan, en niet in het minst, het vertrouwen! Zonder jouw goedkeuren per Annes telefoontje kon ik hier niet aan beginnen. Je hebt je bureau weer (bijna) voor jou alleen ... Prof. Dr. Wim Vyverman voor de discussies en adviezen, en samen met mijn promotoren, het vertrouwen. We gaan dan eens jammen. ;) I wish to thank the members of the examination committee for their thorough review of the draft manuscript and helpful suggestions. v Het Nulde, chronologisch. Joke, mijn gids bij het betreden van de grote boze wereld, voor de babbels en de humor. Helen, voor de babbels, de discussies en de adviezen bij het eerste praktische werk. Pia, die het jaren met het prachtige uitzicht op mijn rug heeft moeten stellen. Bedankt voor de babbels en de hulp bij dat beangstigende prille labowerk (ARISA). Guillaume, partner in crime op de Ledeganck. De babbels, de discussies, de imitaties, de onbaatzuchtigheid. Een plezierige ramp om naast te zitten op conferenties ;). Anne Becker, half-en-half van het Nulde. Bedankt voor de fijne babbels en de morele steun de laatste maanden. Het Sterrevolk: Maxime, partner in crime op de S8, voor de leute en de discussies, de scripts en de figuren die de thesis toch niet gehaald hebben. (Ook een ramp om naast te zitten tijdens conferenties ;) ); Dagmar, om me te helpen bij de eerste stapjes van het NGS-verhaal; Sofie, voor de babbels (en errug interessante weetjes ;) ) en technische/logistieke ondersteuning; Tine, om in te springen voor het verwerken van de RNA-extracties. De technische back-up van het labo microbiologie: Margo, Liesbeth, Evie, Cindy, Epifania en Jeannine om me uit de nood te helpen (bij administratieve missers). Although the meta-omics studies are not included in this thesis, I would also like to thank Prof. Satoshi Imura, 伊村先生, for the generous hospitality and provisioning of the facilities for the DNA and RNA-extractions at the National Institute for Polar Research, Tachikawa, Japan, and not in the least for demonstrating his skills with the ninja chopsticks. Also Dr. Takeshi Segawa for the aid and tips with the RNA-extractions, and occasional interpreting; Watanabe-san, for his effortless helping, despite the language barrier; Dr. Megumu Tsujimoto for collecting the samples according to our much demanding protocol; Dr. Akinori Takahashi for lending me his birding books; and the kind administrative assistants for the nice food and tea ceremony! Het bestuur van Natuurpunt Haaltert, de mensen van plantenwerkgroep Allium en vogelwerkgroep Cinerea, die me de laatste twee jaar veelal hebben moeten missen tijdens activiteiten en vergaderingen, en die ik ondersteuningsgewijs nogal verwaarloosd heb. Morgen stop ik met uit te stellen! Wim en Micheline, voor de vele hulp en opvang! Opnieuw wil ik mijn moeder en jongste grote broer, Jurgen, bedanken voor de financiële en materiële steun tijdens mijn studies. Ook Dorine en Kurt voor de hulp de laatste jaren. Pa, ik hoop dat je trots zou geweest zijn. Ik mis je. En zoals altijd, last but not least: Wendy, Zij-Die-Alles-Regelt, en met wie en door wie het allemaal begon. Zonder jou was ik waarschijnlijk nooit aan het TKO begonnen, laat staan de hogere studies. Mijn steun en toeverlaat, mijn beste vriendin. Dank je voor je geloof in mij en je liefde (en toch, ge zijt zot ...). Het laatste jaar was erg zwaar, maar we zijn er geraakt! En ... Linnéa, door wie ik heel wat slaap (en waarschijnlijk deadlines ...) heb moeten missen, maar die het zonnetje in huis brengt. Je wordt een pracht van een vrouw, maar toch: you owe us! Wacht maar tot jij moet blokken ... En nu, op naar nieuwe horizonten ... (en een gazonnetje!) Bjorn vi vii viii Contents Examination committee ........................................................................................................ iii Dankwoord .............................................................................................................................v Contents ............................................................................................................................... ix List of non-standard abbreviations and acronyms................................................................ xiii Chapter 1. General introduction ..............................................................................................1 1.1. The Antarctic Region .......................................................................................................1 1.1.1 Antarctica: physical and environmental settings .........................................................1 1.1.2. Geography .................................................................................................................2 1.1.3. Climate and climate change .......................................................................................5 1.1.3.1 Ozone hole and UV-radiation ...............................................................................8 1.2. Geological and historical setting ......................................................................................9 1.3. Life on the frozen continent ........................................................................................... 11 1.3.1. Adaptations to the Antarctic environment ................................................................ 14 1.4. Antarctic ecosystems ..................................................................................................... 15 1.4.1. Terrestrial systems..................................................................................................
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