Diatom metabolomics [Elektronische Ressource] / von Charles Vidoudez

Charles Barnard

Sujets

• Biologie

Informations

• Publié par: friedrich-schiller-universitat_jena
• Publié le: 01 janvier 2010
• Nombre de lectures: 31
• Langue: English
• Poids de l'ouvrage: 16 Mo

Extrait

Diatom Metabolomics






Dissertation

zur Erlangung des akademischen Grades
doctor rerum naturalium (Dr. rer. nat.)


vorgelegt dem Rat der Chemisch-Geowissenschaftlichen
Fakultät der Friedrich-Schiller-Universität Jena


von
Diplom Biologe Charles Vidoudez
geboren am 22.01.1982 in Lausanne (Schweiz)














Gutachter:
1. Prof. Dr. Pohnert Institut für Anorganische und Analytische Chemie
Friedrich Schiller Universität, 07743 Jena

2. Prof. Dr. Hertweck Departement of Molecular and Applied Microbiology
HKI, Beutenbergstr. 11a, 07745 Jena

3. Prof. Dr. Kroth Plant Ecophysiology Group
Universität Konstanz, 78457 Konstanz

Tag der öffentlichen Verteidigung: 28.04.2010


















Une herbe marine, qui flotte en ondulant, un bout de planch e, dont on voudrait deviner l'histoire,
un brin de sargasses, dont le léger sillage zèbre la surface des flo ts, il n'en faut pas davantage.

Un Capitaine de 15 ans, Jules Verne
















To my family

Acknowledgements
Four years ago I started this thesis work as a biologist in an, at that time, essentially chemist’s lab.
Many people helped me to adapt to this environment, and I also adapted this environment to me.
These interdisciplinary interactions, though sometimes difficult for both sides, have been a source
of an invaluable enrichment. These interactions, in conjunction with the hurdles of working on a
thesis, have taught me a lot about science and have hopefully made me a better scientist. There are
many people that I would like to thank for their help during these four years, and I hope that the
persons I omit will understand.
First I would like to express all my gratitude to Prof. Dr. Pohnert, for accepting me in his research
group. He granted me the opportunity to fulfil my dream of researching algae. His support, help,
and advices throughout these years made the accomplishment of this thesis possible.
Completing this thesis would not have been possible without the unflagging support of my parents,
Pierre and Christine Vidoudez, and my brother Philippe. Even though geographically separated for
the past three years, their support and frequent visits helped me get through the difficulties inherent
to the PhD student life.
I am extremely grateful to the entire Pohnert group for their help in the laboratory. First I want to
thank Dr. Alexandra Barofsky, with whom I have been working for three years on diatoms. We
have shared many frustrations and successes; she has taught me to be a bit more of a chemist, and I
hope I taught her to be a bit more of a biologist. I give a great thanks to Dr. Emily Prince and
Jennifer Sneed. Not only they have been an invaluable source of advice and thoughtful discussion,
but they have also supported me during the numerous frustrations that occur when working on
biological systems. In addition, I thank them for accomplishing the tedious task of correcting my
English in all my publications, including this thesis. Thanks to Carsten Paul for his help, his
insatiable curiosity, and the many discussions about experiments and results, which have helped me
to keep a critical view. I thank also Dr. Matthew Welling for his friendliness and helpfulness during
the four years in which he was my lab mate. Thanks to Dr. Wichard, for introducing me to the PUA
world and for the hour5long discussions on this subject. Finally thanks to Jan Grüneberg, Martin
Rempt, Astrid Spielmeyer, Jerrit Weissflog, and Theresa Wiesemeyer for their help with chemistry
and GC5MS, and to Andrea Bauer, Katharina Grosser, Hannes Richter, and Caroline Kurth for their
help in the lab and discussions.
I would like to acknowledge the many people who helped me collect samples and conduct
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experiments in the field. Thanks to Dr. Raffaella Casotti and Dr. François Ribalet from the Stazione
Anton Dorhn for inviting me on the two research cruises on the north Adriatic Sea and for the long
successful cooperation. I would also like to thank Dr. Mauro Bastianini from the Istituto di Scienze
Marine5Venezia for the help and phytoplankton species and density determination during these
cruises, and to the captains and crew of the RSV Dellaporta and Urania who made these cruises
possible.
Many thanks to Dr. Jens Nejstgaard from the Bergen University in Norway, for giving us the
opportunity to conduct mesocosm experiments, and for the help and support during this cooperation;
to Dr. Hans H. Jackobsen of the National Institute for Aquatic Resources in Denmark for the cell
counts of the mesocosms; and to all the other participants of these experiments.





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Table of content
Acknowledgements ...................................................................................................... 1
Table of content ........... 3
List of figures ............... 5
List of tables ................................................................................................................. 6
Zusammenfassung/ abstract ....................... 7
Abbreviations ............. 11
1. Introduction ......................................................................................................... 13
2. Results and Discussion ....................... 29
2.1 Polyunsaturated aldehydes .......... 29
2.1.1 Occurrence of PUA in the natural environment ........................................................... 30
2.1.2 Laboratory studies ........................................................................................................ 36
2.1.3 Discussion .................................................................................................................... 42
2.2 Development of a metabolomic method for diatoms .................................. 49
2.3 Metabolic survey of a S. marinoi culture .................................................... 59
2.3.1 Experiment design ........................................................................................................ 60
2.3.2 Overview of the cultures .............................................................................................. 61
2.3.3 Polyunsaturated aldehydes and fatty acids ................................................................... 63
2.3.4 Cell metabolites ............................................................................................................ 67
2.3.5 Metabolites released in the medium ............................................................................. 82
2.3.6 Discussion .................................................................................................................... 88
2.4 Mesocosms ................................................................................................ 101
Experiment design .................................................................................................................... 102
2.4.1 Bloom development ................................................................................................... 103
2.4.2 PUA ............................................................................................................................ 104
2.4.3 Dissolved metabolites ................................................................................................ 107
2.4.4 Discussion .................................................................................................................. 110
2.5 Decadienal treatment on Phaeodactylum tricornutum .............................. 113
2.5.1 ESTs preliminary analysis .......................................................................................... 114
2.5.2 Metabolomic profiling ................................................................................................ 115
2.5.3 Discussion .................................................................................................................. 117
3. Conclusion ......................................................................................................... 119
4. Materials and Methods ..................... 123
4.1 Culturing .... 124
4.1.1 Strains ......................................................................................................................... 124
4.1.2 Media .......................................................................................................................... 124
4.1.3 Culture conditions ...................................................................................................... 124
4.1.4 Microscopy ................................................................................................................. 125
4.1.5 Large volume cultures (10 L and 25 L) ...................................................................... 125
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4.2 GC-MS specification ................................................................................. 127
4.3 PUA, genera