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Proteogenomic and Physiologic Characterization of New Members of Roseobacter Lineage from Mallorca Harbors

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Proteogenomic and Physiologic Characterization of New Members of Roseobacter Lineage from Mallorca Harbors DOCTORAL THESIS 2017 PROTEOGENOMIC AND PHYSIOLOGIC CHARACTERIZATION OF NEW MEMBERS OF ROSEOBACTER LINEAGE FROM MALLORCA HARBORS Maria Mas Lladó DOCTORAL THESIS 2017 Doctoral Program of “Microbiologia Ambiental i Biotecnologia” PROTEOGENOMIC AND PHYSIOLOGIC CHARACTERIZATION OF NEW MEMBERS OF ROSEOBACTER LINEAGE FROM MALLORCA HARBORS Maria Mas Lladó Thesis Supervisor: Dr. Rafael Bosch Thesis Supervisor: Dra. Balbina Nogales Doctor by the Universitat de les Illes Balears A la meva família. Especialment, als meus pares. Agraïments AGRAÏMENTS A la fi puc donar aquesta tesis per acabada! Ha arribat el moment de tancar una etapa, un capítol de la meva vida i de seguir i millorar amb el que he començat. Per això, ha arribat també el moment d’agrair a tots aquells que d’una manera o d’una altra han contribuït a que aquesta etapa fos exitosa. En primer lloc, vull donar les gràcies al Dr. Rafael Bosch, per donar-me l’oportunitat de fer els meus estudis doctorals amb ell. Gràcies per haver-me ensenyat tantes coses del món de la microbiologia i de la bioinformàtica, i gràcies també per tenir sempre el teu bon humor i caràcter que et caracteritza. També agrair a la Dra. Balbina Nogales els seus ensenyaments i consells. Gràcies per ser sempre tan perfeccionista ja que m’ha ajudat a ser més meticulosa. En resum, gràcies a tots dos per ensenyar-me el que és fer recerca i a madurar científicament. Gràcies també als altres professors de la UIB relacionats amb el món de la microbiologia. Principalment gràcies al Dr. Jordi Lalucat, a la Dra. Elena García-Valdés, al Dr. Toni Bennàsar i al Dr. Sebastià Albertí, que han sabut donar-me consells i fer-me suggeriments quan ha estat oportú i sempre amb l’objectiu de millorar en la meva recerca. Especialment, vull destacar el Dr. Toni Bennàsar i la Dra. Elena García-Valdés, que van ser professors meus quan vaig cursar el màster de microbiologia avançada i varen fer que la meva curiositat envers la microbiologia cresqués. En referència als amics que han fet feina amb jo al laboratori i amb els que he dinat cada dia durant aquests anys, mil gràcies a tots per l’ajuda que m’heu donat sempre. No hagués pogut tenir mai millors companys de feina que vosaltres. Als del “cuartito”, que són amb els que sempre he passat més temps...gràcies Toni Busquets i Arantxa Peña per donar-me consells, solucionar problemes, brindar-me moments de desconnexió amb discussions sobre temes intranscendents, escoltar-me quan ho he necessitat...heu estat un gran suport immillorable durant aquests 4 anys. A les altres dues del “cuartito”, heu estat les meves companyes de viatge, sempre fent feina colze amb colze, sempre seguint les passes que l’altre feia. Gràcies Cati Alejandro, la meva companya de congressos, per donar-me una mà quan ho he necessitat. I gràcies Bel Brunet, per ensenyar-me tot el que m’has ensenyat i per compartir penes i alegries. Als del laboratori, gràcies Magdalena Mulet, Claudia Prince, Cristina Ramon, David Sánchez i Dani Jaén per escoltar-me quan em desesperava amb els experiments i per ajudar- me sempre que vos ha estat possible. També vull donar les gràcies a na Lady Suárez, que em va ensenyar a treballar amb els aparells d’HPLC i de la que rebia ajuda quan la necessitava. Agrair també el suport de na Marga Gomila, sempre disposada a escoltar, a respondre dubtes i a aportar solucions. Als tècnics de laboratori (Xisco, Àngel i Guillem) per facilitar la meva feina. Gràcies a na Mati pel seu bon humor matiner. I també a na Trinitat, dels Serveis Científico- Tècnics per la seva bona disponibilitat. Pens que els companys de feina són essencials perquè els projectes puguin sortir endavant, i amb vosaltres tot ha estat més fàcil. Agraïments Vull agrair a en Joseph les seves ensenyances en el món de la microbiologia i la proteòmica. Gràcies a ell vaig tenir l’oportunitat de conèixer un nou laboratori i una altre forma una mica diferent de treballar de la que estava acostumada. A banda de la part professional, li vull donar les gràcies a ell, a na Mar i a la seva família per la seva hospitalitat i amabilitat durant la meva estància a Coventry. Thanks to Sue, Alex and Cleidiane for teaching and helping me in the field of proteomics. I also want to thank my friends at Warwick University, Despoina, Amandeep, Satya and Matthias. With your friendship I could fully enjoy my stay. Además quiero agradecer la amistad y ayuda que me brindaron mis amigos españoles que conocí en Inglaterra, sobre todo a Miriam, Kike y Alfredo. Con vosotros, en cierta parte, era como estar como en casa. I sincerely hope to see you all again. Durant aquesta etapa (i sempre) han estat molt importants les meves amigues. Encara que moltes vegades no entenien molt bé el que feia o quin tipus d’experiments desenvolupava, m'ha ajudat molt el seu suport per desconnectar de la feina. Gràcies Marga Fullana, Maria Francisca Roca, Carme Ferrari i Catalina Maria Mas per la vostra amistat. Gràcies també a n’en Jaume Llorens i na Marga Barceló, per ser grans amics. També vull agrair als amics llucmajorers de la meva parella, que ara també consider els meus, el seu interès pel que estudiava i pels seus ànims. Infinites gràcies a mon pare i a ma mare. Tot l’agraïment que sent cap a vosaltres no es pot expressar en paraules. Gràcies per ser sempre al meu costat i per animar-me a tirar cap endavant. Sempre m’heu donat l’empenta que he necessitat a l’hora de prendre decisions, ja ho sabeu. Donar-vos les gràcies per la vostra comprensió i ajuda en tot moment. Gràcies també a la meva germana, sobretot per quedar a Mallorca amb nosaltres; has estat un gran suport sempre. Gràcies als meus padrins, que sempre m’heu donat molts d’ànims per continuar cap endavant. Gràcies a la meva parella, en Joan Miquel, que a pesar d’estar a quilòmetres de distància hem pogut fer-nos costat l’un a l’altre quan ho hem necessitat. Igual que tu, desig que no haguem de tornar a separar-nos mai i puguem emprendre el camí junts d’aprop. A tots vosaltres, gràcies mils, sou els pilars de la meva vida. Finalment, donar les gràcies a na Sebastiana i en Biel per preocupar-se per jo i donar-me coratge. Agraeixo també l’ajuda i costat que he rebut dels meus estimats cunyats, na Xisca i en Pere Guillem; gràcies per tot. Per acabar, vull donar les gràcies a les diferents entitats que han aportat els fons necessaris per fer possible la realització d’aquesta tesis. En primer lloc, a la Universitat de les Illes Balears per concedir-me una beca de postgrau l’any 2012. Posteriorment al “Ministerio de Educación, Cultura y Deporte” per concedir-me la beca de Formació de Personal Universitari (2012-2016) (referència FPU12/01449). També al projecte CTM2011-24886 (del “Ministerio de Economía, Indústria y Competitividad”), amb cofinançament FEDER. Finalment, al “European Molecular Agraïments Biology Organization” per concedir-me una beca per a poder fer una estada a “The University of Warwick” on vaig fer els anàlisis de proteòmica. Index TABLE OF CONTENTS LIST OF FIGURES ............................................................................................................................. I LIST OF TABLES ............................................................................................................................. III LIST OF ABBREVIATIONS ................................................................................................................ V ABSTRACT .................................................................................................................................... VII INTRODUCTION ............................................................................................................................. 1 1. The Roseobacter lineage ....................................................................................................... 3 1.1. Phylogeny, habitat and lifestyle ..................................................................................... 3 1.2. Relevant features of Roseobacter cultured isolates ...................................................... 5 1.3. Horizontal gene transfer (HGT) in the Roseobacter lineage .......................................... 8 1.3.1. Gene transfer agents ............................................................................................... 9 1.3.2. Extrachromosomal elements ................................................................................ 10 1.3.3. Transposase fluxes ................................................................................................ 12 2. Importance of the Roseobacter lineage in chronically-polluted marine environments ..... 12 3. Hydrocarbons and aromatic compounds degradation ....................................................... 14 3.1. Degradation of aromatic compounds .......................................................................... 14 3.2. Degradation of aliphatic hydrocarbons ........................................................................ 18 HYPOTHESIS AND OBJECTIVES .................................................................................................... 21 MATERIALS AND METHODS ........................................................................................................ 25 1. DNA extraction .................................................................................................................... 27 2. Genome sequencing and assembly ..................................................................................... 27 3. Identification and phylogeny of isolates based on genome data ......................................
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