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Caractérisation Et Identification Des Champignons Filamenteux Par Spectroscopie Vibrationnelle

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Année 2013 N° UNIVERSITE DE REIMS CHAMPAGNE-ARDENNE ECOLE DOCTORALE SCIENCES TECHNOLOGIE SANTE THESE Présentée pour obtenir le grade de DOCTEUR DE L’UNIVERSITE DE REIMS CHAMPAGNE-ARDENNE Discipline : Biologie-Biophysique Soutenue publiquement le 02/12/2013 Par Aurélie LECELLIER Née le 18 mars 1983 à Issy les Moulineaux Titre : Caractérisation et identification des champignons filamenteux par spectroscopie vibrationnelle JURY Président : Dr. Jérôme MOUNIER (Brest, France) Rapporteurs : Pr. Boualem SENDID (Lille, France) Pr. Olivier SIRE (Vannes, France) Examinateurs : Dr. Wilfried ABLAIN (Rennes, France) Dr. Caroline AMIEL (Caen, France) Pr. Michel MANFAIT (Reims, France) Directeurs de thèse : Pr. Ganesh SOCKALINGUM (Reims, France) Dr. Dominique TOUBAS (Reims, France) « Le rôle de l’infiniment petit est infiniment grand. » Louis Pasteur Remerciements Remerciements A Messieurs le Professeur Michel Manfait et le Professeur Olivier Piot, Je vous remercie sincèrement pour m’avoir accueillie et pour m’avoir permis de réaliser ce travail au sein de votre unité que vous avez dirigée successivement lors de ces trois années de thèse. Je vous suis très reconnaissante pour m’avoir donné l’occasion de présenter mon travail dans des congrès nationaux et internationaux. A Monsieur le Professeur Boualem Sendid, Je vous suis très reconnaissante d’avoir accepté d’être rapporteur de cette thèse, je vous remercie pour votre participation au Jury de soutenance et pour l’intérêt que vous avez porté à mon travail. A Monsieur le Professeur Olivier Sire, Je vous suis très reconnaissante d’avoir accepté d’être rapporteur de cette thèse, je vous remercie pour votre participation au Jury de soutenance et pour l’intérêt que vous avez porté à mon travail. A Monsieur le Docteur Wilfried Ablain, Je vous remercie sincèrement d’avoir accepté de faire partie du Jury de soutenance. Je vous remercie également pour votre contribution à l’élaboration de ce travail. A Madame le Docteur Caroline Amiel, Je vous exprime toute ma reconnaissance de m’avoir initié à la spectroscopie vibrationnelle lors de mon passage au sein de votre équipe pour y effectuer mon stage de Master 2 ainsi que pour avoir guidé mes premiers pas dans le monde de la recherche. Je vous remercie pour votre soutien et vos encouragements que vous m’avez apporté. Je n’oublie pas que c’est grâce à vous si j’ai pu réaliser cette thèse. Cela me fait extrêmement plaisir que vous ayez accepté d’examiner mon travail et de me faire l’honneur de participer au Jury de soutenance. A Monsieur le Professeur Michel Manfait, Je vous adresse mes remerciements les plus respectueux pour avoir accepté d'être membre du Jury de soutenance. Je vous remercie pour l'intérêt que vous avez porté à ce travail, ainsi que pour votre sympathie. 1 Remerciements A Monsieur le Docteur Jérôme Mounier, Je tiens à t’exprimer toute ma gratitude pour l’aide précieuse que tu m’as apporté tout au long de cette thèse et ainsi que pour ta disponibilité malgré la distance. Je te remercie pour ton implication dans ce projet, pour tes conseils avisés et ta sympathie à mon égard. Enfin, je te remercie énormément pour m’avoir fait l’honneur de participer au Jury de soutenance. A Monsieur le Professeur Ganesh Sockalingum, Je vous suis sincèrement reconnaissante d’avoir encadré ce travail de thèse. Je vous remercie pour la confiance que vous m’avez accordée pendant ces trois années et pour avoir cru en mes capacités tout au long de ce travail. Je vous remercie pour tous vos conseils stimulants, votre patience, ainsi que pour la gentillesse que vous avez manifestée à mon égard. J'ai beaucoup apprécié travailler à vos côtés tant sur le plan scientifique que sur le plan humain. Je garde toujours beaucoup de plaisir à discuter avec vous et à bénéficier de votre expérience. A Madame le Docteur Dominique Toubas, Je vous adresse mes plus sincères remerciements pour votre encadrement durant cette thèse. Je suis ravie d’avoir travaillé en votre compagnie tout au long de ces années durant lesquelles j’ai pu apprécier vos qualités tant pédagogiques et scientifiques qu’humaines. Je vous remercie également pour votre disponibilité, ainsi que pour votre aide et vos précieux conseils que vous m’avez apportés lors de l’élaboration de cette thèse. Pour tout ce que vous m'avez appris, je vous remercie très sincèrement. A Monsieur le Docteur Vincent Gaydou, Je te remercie sincèrement pour toute l’aide que tu m’as apportée durant ma dernière année de thèse. L’aboutissement de ce travail est le fruit de la complémentarité de nos compétences respectives. Je te remercie pour ton soutien et tes encouragements ainsi que pour ta patience. 2 Remerciements A Monsieur le Docteur Jayakrupakar Nalalla, Nuvvu naku chesina prathi daniki am forever gratefull to you. Nenu neku eppatiki runapadiuntanu. Nevichina encouragement, advices ki chala thanks. Nrnnu opikaga vinnaduku neku ela thanks cheppalo ardam avvatledu. Nuvvu naa work environment ni fun environment ga marchavu with your humor. Mana madhyalo oka viluvaina sambandham erpadindi. Mana projects aipoiundochu kani mana friendship will last forever. Je tiens à remercier également : Stéphane Huet et Nadia Leden pour leur collaboration au sein de ce projet. Les discussions que nous avons pu avoir lors des réunions de projets m’ont beaucoup apporté. L’équipe Médian et plus particulièrement : Céline, Christophe, Cyril, David, Denise Pisani, Goutam, Imane, Irène, Julien, Joan, Laurence, Mathieu, Mickaël, Mireille Cousina, Mohammed, Nathalie, Qué et Valérie. Georges Barbier, Loïc Castrec, Marie-Anne Le Bras, Valérie Vasseur, Amélie Weill et Olivia Le Bourhis de l’équipe du Lubem pour leur contribution à l’élaboration de ce travail. Un grand merci à tous mes amis : Caroline, Georges, Hadrien, Jean-Claude, Lucie, Mai-Ahn, Marie, Mathilde, Sunny, Teddy et The Thuong, pour tous les bons moments que l’on a passé ensemble. Ces trois années passées à Reims n’auraient pas été les mêmes sans votre présence, votre sympathie et votre bonne humeur. Je remercie respectueusement mes parents, Catherine et Didier, pour leur soutien sans faille et leurs encouragements, non seulement au cours de ces trois années mais aussi tout au long de mon parcours, et sans lesquels je n’en serais pas là aujourd’hui. Vous m’avez donné toutes les chances pour réussir et c’est grâce à vous que je suis ce que je suis maintenant. Je remercie sincèrement ma sœur Aurore pour son aide précieuse et pour avoir toujours été à mes cotés durant ces années. Enfin, je remercie Arnaud, mon mari, pour son soutien indéfectible, et pour avoir fait preuve de compréhension et d’écoute malgré l’éloignement. Merci à Cannelle pour sa tendresse et son réconfort. Je ne pourrais vous remercier assez... Ces remerciements ne peuvent s’achever sans une pensée pour Alexandre Mazine. Je dédie cette thèse à Claude Grimoult. 3 Sommaire Sommaire Liste des abréviations................................................................................................................. 7 Liste des figures et des tableaux................................................................................................. 9 Avant-propos............................................................................................................................ 11 Chapitre I : Introduction....................................................................................................... 14 I.1- Les champignons filamenteux ....................................................................................... 15 I.1.a- Définition................................................................................................................. 15 I.1.b- Caractéristiques morphologiques des champignons filamenteux ........................... 15 I.1.c- Développement des champignons filamenteux ....................................................... 17 I.1.d- Phylogénie des champignons filamenteux .............................................................. 19 I.1.e- Habitat et conditions de développement.................................................................. 21 I.1.f- Problèmes liés aux champignons filamenteux et à leurs métabolites ...................... 22 - secteur agroalimentaire ............................................................................................... 22 - secteur pharmaceutique et médical ............................................................................. 24 I.1.g- Méthodes d’identification des champignons filamenteux....................................... 26 - Analyse macroscopique .............................................................................................. 26 - Analyse microscopique............................................................................................... 26 - Analyse moléculaire.................................................................................................... 27 I.2- La spectroscopie infrarouge à transformée de Fourier (IRTF) ..................................... 29 I.2.a- Principe.................................................................................................................... 29 - Rayonnement infrarouge............................................................................................. 29 - Interaction rayonnement-matière................................................................................ 31 - Absorption du rayonnement IR par l’échantillon ....................................................... 33 - Modes de vibration ....................................................................................................
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    ISSN 0031 - 9465 PHYTOPATHOLOGIA MEDITERRANEA PHYTOPATHOLOGIA PHYTOPATHOLOGIA MEDITERRANEAVolume 58 • No. 2 • August 2019 Plant health and food safety Volume 58 • Number 2 • Iscritto al Tribunale di Firenze con il n° 4923del 5-1-2000 - Poste Italiane Spa Spedizione in Abbonamento Postale 70% DCB FIRENZE di Firenze Iscritto al Tribunale August 2019 Pages 219-449 FIRENZE The international journal of the UNIVERSITY Mediterranean Phytopathological Union PRESS PHYTOPATHOLOGIA MEDITERRANEA Plant health and food safety Te international journal edited by the Mediterranean Phytopathological Union founded by A. Ciccarone and G. Goidànich Phytopathologia Mediterranea is an international journal edited by the Mediterranean Phytopathological Union The journal’s mission is the promotion of plant health for Mediterranean crops, climate and regions, safe food production, and the transfer of knowledge on diseases and their sustainable management. The journal deals with all areas of plant pathology, including epidemiology, disease control, biochemical and physiological aspects, and utilization of molecular technologies. All types of plant pathogens are covered, including fungi, nematodes, protozoa, bacteria, phytoplasmas, viruses, and viroids. Papers on mycotoxins, biological and integrated management of plant diseases, and the use of natural substances in disease and weed control are also strongly encouraged. The journal focuses on pathology of Mediterranean crops grown throughout the world. The journal includes three issues each year, publishing Reviews,
  • Phylogeny of Penicillium and the Segregation of Trichocomaceae Into Three Families

    Phylogeny of Penicillium and the Segregation of Trichocomaceae Into Three Families

    available online at www.studiesinmycology.org StudieS in Mycology 70: 1–51. 2011. doi:10.3114/sim.2011.70.01 Phylogeny of Penicillium and the segregation of Trichocomaceae into three families J. Houbraken1,2 and R.A. Samson1 1CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; 2Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. *Correspondence: Jos Houbraken, [email protected] Abstract: Species of Trichocomaceae occur commonly and are important to both industry and medicine. They are associated with food spoilage and mycotoxin production and can occur in the indoor environment, causing health hazards by the formation of β-glucans, mycotoxins and surface proteins. Some species are opportunistic pathogens, while others are exploited in biotechnology for the production of enzymes, antibiotics and other products. Penicillium belongs phylogenetically to Trichocomaceae and more than 250 species are currently accepted in this genus. In this study, we investigated the relationship of Penicillium to other genera of Trichocomaceae and studied in detail the phylogeny of the genus itself. In order to study these relationships, partial RPB1, RPB2 (RNA polymerase II genes), Tsr1 (putative ribosome biogenesis protein) and Cct8 (putative chaperonin complex component TCP-1) gene sequences were obtained. The Trichocomaceae are divided in three separate families: Aspergillaceae, Thermoascaceae and Trichocomaceae. The Aspergillaceae are characterised by the formation flask-shaped or cylindrical phialides, asci produced inside cleistothecia or surrounded by Hülle cells and mainly ascospores with a furrow or slit, while the Trichocomaceae are defined by the formation of lanceolate phialides, asci borne within a tuft or layer of loose hyphae and ascospores lacking a slit.