Environmental activity of bacteria degrading aromatic pollutants

251 Pages·2015·13.2 MB·English

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

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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