Unicentre CH-1015 Lausanne http://serval.unil.ch Year : 2015 Environmental activity of bacteria degrading aromatic pollutants Moreno Forero Silvia Carina Moreno Forero Silvia Carina, 2015, Environmental activity of bacteria degrading aromatic pollutants. Originally published at : Thesis, University of Lausanne Posted at the University of Lausanne Open Archive http://serval.unil.ch Document URN : urn:nbn:ch:serval-BIB_A58E1EDC611D1 Droits d’auteur L'Université de Lausanne attire expressément l'attention des utilisateurs sur le fait que tous les documents publiés dans l'Archive SERVAL sont protégés par le droit d'auteur, conformément à la loi fédérale sur le droit d'auteur et les droits voisins (LDA). A ce titre, il est indispensable d'obtenir le consentement préalable de l'auteur et/ou de l’éditeur avant toute utilisation d'une oeuvre ou d'une partie d'une oeuvre ne relevant pas d'une utilisation à des fins personnelles au sens de la LDA (art. 19, al. 1 lettre a). 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Département de Microbiologie Fondamentale       Environmental activity of bacteria degrading aromatic pollutants Thèse de Doctorat ès Sciences de la vie (PhD) presentée à la Faculté de Biologie et de Médecine de l’Université de Lausanne Par Silvia Carina Moreno Forero Biologiste  marine  de  l’Université  Jorge  Tadeo  Lozano,  Colombie    et  Master  en  systématique  et  gestion  de  la  biodiversité     de  l’Université  de  Lausanne   Thesis Director Jan Roelof van der Meer Committee of thesis: Prof. Pierre Goloubinoff, President Prof. Johan Leveau, Expert Dr. Fabrice Martin-Laurent, Expert Lausanne, Juin 2015 ii ii What  am  I,  Life?  A  thing  of  watery  salt   Held  in  cohesion  by  unresting  cells   Which  work  they  know  not  why,  which  never  halt,   Myself  unwitting  where  their  master  dwells.   I  do  not  bid  them,  yet  they  toil,  they  spin;   A  world  which  uses  me  as  I  use  them,   Nor  do  I  know  which  end  or  which  begin,   Nor  which  to  praise,  which  pamper,  which  condemn.   So,  like  a  marvel  in  a  marvel  set,   I  answer  to  the  vast,  as  wave  by  wave   The  sea  of  air  goes  over,  dry  or  wet,   Or  the  full  moon  comes  swimming  from  her  cave,   Or  the  great  sun  comes  north,  this  myriad  I   Tingles,  not  knowing  how,  yet  wondering  why.     (Poem II of Seven Poems from ‘Lollingdon Downs’ by John Masefield, 1917) We are drowning in information but starved for knowledge –John Naisbitt       iii iv Acknowledgments I would like to thank several persons that contributed to complete my doctoral thesis: First of all, Jan, who gave me the opportunity to work in his group in this very interesting topic. He always had a word of encouragement and positive mind to go forward and I loved to work with him. David Johnson, Nicolas Pradevand, Edith Coronado and people from the Genomic Technologies facility (GTF), Floriane Consales, Alex Paillusson et Melanie Dupasquier for their help with bioanalayser, microarrays and the software Genespring for the treatment of transcriptome data. Diego Gonzales, Marta Rosikiewicks and Erica Yashiro for their help with scripts for data management. Yoann Le Digabel and Mathias Humery for their help with subtleties of French… Sara Mitri for final English corrections. Siham Beggah for her unconditional friendship that I hope endlessly. People from Jan’s group, DMF and from the BACSIN consortium for their encouragements, nice environment and suggestions. To all those anonymous poets/artists who gave me emotions and feelings to go through the final path of this thesis. And finally, to my dear husband and beautiful children for their huge understanding and support during all this time.   v vi TABLE OF CONTENTS SUMMARY ix RESUME xi CHAPTER I 1 General Introduction 2 Sphingomonas wittichii RW1 3 Arthrobacter chlorophenolicus A6 4 Pseudomonas veronii 1YdBTEX2 6 Bioremediation 6 Water stress 8 Transcriptomic approach 9 Aim 11 Outline of the thesis 13 References 15 CHAPTER II 21 Comparison of genome-wide responses to water stress 22 Abstract 22 Introduction 23 Materials and Methods 25 Bacterial strains and growth media 25 Growth rate reduction as function of water availability 26 Genome-wide expression analysis of induced drought stress 26 RNA isolation (hot phenol protocol) 27 Microarray hybridisations 28 Data analysis 28 Results and discussion 30 Comparative growth under induced water stress 30 Transcriptional responses to water stress 33 Gene Ontology Interpretation of changes observed under solute stress 37 GO terms enriched under matric stress 41 Stress-induced protein orthologs among the three strains 43 Concluding remarks 45 References 48 Suplementary Tables 52 CHAPTER III 87 Genome-Wide Analysis of Sphingomonas wittichii RW1 Behaviour During Inoculation and Growth in Contaminated Sand 88(150)   vii