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Traceability of the Mycorrhizal Symbiosis in the Controlled Production of Edible Mushrooms

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Traceability of the Mycorrhizal Symbiosis in the Controlled Production of Edible Mushrooms Traceability of the mycorrhizal symbiosis in the controlled production of edible mushrooms Traçabilitat de la simbiosi micorízica en la producció controlada de fongs comestibles Herminia De la Varga Pastor Aquesta tesi doctoral està subjecta a la llicència Reconeixement- NoComercial – SenseObraDerivada 3.0. Espanya de Creative Commons. Esta tesis doctoral está sujeta a la licencia Reconocimiento - NoComercial – SinObraDerivada 3.0. España de Creative Commons. This doctoral thesis is licensed under the Creative Commons Attribution-NonCommercial- NoDerivs 3.0. Spain License. TRACEABILITY OF THE MYCORRHIZAL SYMBIOSIS ON THE CONTROLLED PRODUCTION OF EDIBLE FUNGI Traçabilitat de la simbiosi micorízica en la producció controlada de fongs comestibles Herminia De la Varga Pastor DOCTORAL THESIS 2013 Tesi realitzada al Institut de Recerca i Programa de Doctorat en Biodiversitat: Tecnologia Agroalimentàries, Centre de 2008-2013. Facultat de Biologia de la Cabrils. Subprograma de Patologia Vegetal. Universitat de Barcelona Traceability of the mycorrhizal symbiosis in the controlled production of edible mushrooms Traçabilitat de la simbiosi micorízica en la producció controlada de fongs comestibles Memòria presentada per Herminia De la Varga Pastor per optar al grau de Doctora per la Universitat de Barcelona Doctoranda Tutor de Tesi Herminia De la Varga Pastor Jaume Llistosella Vidal (UB, Biologia) Director de Tesi Codirector de Tesi Joan Pera Álvarez (IRTA, Cabrils) Xavier Parladé Izquierdo (IRTA, Cabrils) 2 Traceability of the mycorrhizal symbiosis in the controlled production of edible mushrooms %0_+#,21 Amb aquestes línies prèvies m’agradaria mostrar el meu agraïment a totes aquelles persones que d’una manera o una altra han contribuït a que el treball realitzat durant el últims quatre anys, hagi acabat sent una realitat reflectida en aquesta tesi. En primer lloc mostrar el meu agraïment al Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) per donar-me l’oportunitat de realitzar el doctorat en atorgar-me una beca del Programa de Becas Predoctorales para la formación de personal investigador. Beca que he pogut gaudir i realitzar a l’Institut de Recerca i Tecnologia Agroalimentàries (IRTA), al Centre de Cabrils, a qui també agraeixo l’haver-me permès formar part del seu equip i fer us de les seves instal·lacions. En especial agrair l’excel·lent acollida per part de totes les persones que formen el subprograma de Patologia vegetal, tots heu contribuït d’alguna manera a aquesta tesi; però sobretot, res d’aquesta feina hagués estat possible sense el Dr. Joan Pera i el Dr. Xavier Parladé, director i codirector d’aquesta tesi doctoral. A tots dos agrair l’oportunitat de formar part del seu equip, per bolcar-me tots els seus coneixements i contagiar-me les ganes d’investigar i fer ciència així com per l’excel·lent tracte personal i totes les oportunitats que m’han obert al treballar amb ells. Al Dr. Jaume Llistosella, professor del departament de Biologia Vegetal de la Universitat de Barcelona i tutor d’aquesta tesi, per acceptar tutoritzar la tesi i per tots els bons consells que sempre he rebut d’ell. La feina feta a aquesta tesi ha estat finançada pels diferents projectes en els que he format part de l’equip investigador: RTA2006-00095-CO2-02 INIA (Ministerio de Educación y Ciencia-MEC), AGL2009-12884-C03-01 Ministerio de Ciencia e Innovación (MICINN) i RM2010-00002-C03-02 INIA (Ministerio de Economia y Competitividad-MINECO). Agrair també a tots als companys d’aquests projectes els coneixements, la feina, les mostres i les experiències compartides, en especial a Beatriz Águeda, Teresa Ágreda, al Dr. Fernándo Martínez Peña, a la Dra. Ana María De Miguel, a la Dra. Luz Marina Fernández i a la Dra. Sara Hortal gran part d’aquesta tesi no hagués estat possible sense la seva col·laboració i els seus coneixements. 3 Je veux remercier l'INRA de Nancy, Ecogenomics of Interactions Lab, de me permettre de procéder à un séjour de recherche avec eux. Une partie de ce travail a été réalisé grâce à eux. Je veux surtout remercier le Dr. Claude Murat, pour diriger mon travail là; le Dr. Francis Matrin, le Dr. Françoise Le Tacon et le Dr. Jean Garbaye, pour leur comportement exceptionnel avec moi. Je veux également remercier tous les gens avec qui j’ai partagé mon séjour à l'INRA, j'ai excellents souvenirs de vous. Agrair també a les companyes i amigues Vicky Barnés, Olga Jurado, Olga González, Bárbara López, Maria Blanco i Montse Prat pel seu suport, i també per tots aquells moments extralaborals compartits. Al tots els companys i companyes de l’IRTA així com als que han anat passant pel centre en les seves estades, treballs curts, pràctiques, etc. amb qui he compartit els migdies, els esmorzars, mil converses, rialles i molt bons moments. No em puc oblidar dels meus companys de viatge cap a l’obtenció del doctorat, els becaris que encara ho son i els que ja han passat a ser doctors: Marta, Priscila, Carolina, Manu, Georgina, Chelo, Lorena, Laura, Rafa, Amaia, Nati, Lola i Kathy. Durant aquests quatre anys de treball a l’IRTA he après moltes coses, no tant sols referents a les micorizes, els fongs comestibles, la biologia molecular… sinó a nivell personal, gracies a la gran gent que m’ha envoltat fent el treball més fàcil i agradable. Gracies a tots i a totes els que en algun moment d’aquests últims anys s’hagi creuat en la meva vida, perquè de ben segur que d’una manera o altra han influït en que aquest treball sigui avui una realitat. Per últim vull dedicar unes línies als amics, amigues i a la família (Herminia, Dionisio, Aitana i Abel) que sempre han estat al meu costat donant-me suport durant aquests anys i en l’elaboració d’aquest treball. En especial agrair a l’Alejandro el seu suport incondicional, els seus ànims i els “sacrificis” fets per aquesta tesi. 4 Traceability of the mycorrhizal symbiosis in the controlled production of edible mushrooms -,2#,21 AGRAÏMENTS 3 CONTENTS 5 List of Figures 10 List of Tables 12 GENERAL INTRODUCTION 15 1. Edible mushrooms and their importance 17 2. Species studied in this thesis 20 2.1. Boletus edulis 20 2.2. Lactarius deliciosus 21 2.3. Rhizopogon roseolus 22 2.4. Tuber melanosporum 22 3. Molecular techniques used 26 3.1. Conventional PCR 26 3.2. Real-time PCR 28 3.3. Simple sequence repeat (SSR) analysis 31 PURPOSE AND GENERAL OBJECTIVES 34 CHAPTER 1 37 Production of Boletus edulis inoculated plants in pure cultures and in nursery conditions 1. Introduction 39 2. Materials and Methods 44 2.1. Synthesis of mycorrhizas in pure culture conditions 44 2.1.1. Preparation of host plant seedlings under axenic conditions 44 2.1.2. Isolation and maintenance of B. edulis pure cultures 45 2.1.3. Synthesis of mycorrhizas in pure culture conditions 47 2.2. Synthesis of mycorrhizas in nursery conditions 47 2.2.1. Acclimatization of in vitro mycorrhizal plants 47 2.2.2. Controlled inoculations of Cistus spp. plants with species of the B. edulis complex for the production of mycorrhizal plants in nursery conditions. 50 5 Contents 2.3. Viability of B. edulis complex cultures stored in water at 4°C 52 3. Results 53 3.1. Synthesis of mycorrhizas in pure culture 53 3.2. Production of mycorrhizal plants in nursery conditions 57 3.2.1. Acclimatization of in vitro mycorrhizal plants 57 3.2.1.1. Acclimatization of plants inoculated under pure culture synthesis conditions 57 3.2.1.2. Acclimatization of plants inoculated under pure culture synthesis conditions in two different substrates 57 3.2.2. Controlled inoculations of Cistus spp. plants with species of the B. edulis complex for theproduction of mycorrhizal plants in nursery conditions. 58 3.2.2.1. Inoculations with spores suspension 58 3.2.2.2. Inoculations with mycelial inoculum 58 3.3. Viability of B. edulis complex cultures stored in water at 4°C 60 4. Discussion 62 CHAPTER 2 69 Use of molecular techniques for the traceability of ectomycorrhizal fungi: Seasonal dynamics of Boletus edulis and Lactarius deliciosus mycelium in pine forests of central Spain 1. Introduction 71 2. Materials and Methods 74 2.1. Design of B. edulis probes and primers for their mycelium detection. 74 2.1.1. Design of primers and probes 74 2.1.2. DNA extractions 74 2.1.3. Construction of standard curves 74 2.1.4. Quantification of extraradical soil mycelium of standards and samples by real-time PCR 75 2.2. Validation method by comparison of conventional PCR and quantitative real time PCR. 76 2.2.1. Study site 76 2.2.2. Boletus edulis soil mycelium quantification 78 2.2.3. Quantification of ectomycorrhizas 78 2.3. Seasonal dynamics of Boletus edulis and Lactarius deliciosus extraradical mycelium in pine forests of central Spain. 79 2.3.1. Study site 79 2.3.2. Soil sampling 81 6 Traceability of the mycorrhizal symbiosis in the controlled production of edible mushrooms 2.3.3. Soil DNA extraction 81 2.3.4. Quantification of extraradical soil mycelium by real-time PCR 81 2.4. Data analyses 82 3. Results 83 3.1. Validation by comparison of conventional PCR and quantitative real time PCR. 83 3.2. Seasonal dynamics of Boletus edulis and Lactarius deliciosus extraradical mycelium in pine forests of central Spain. 86 3.3. Quantification and dynamics of Boletus edulis and Lactarius deliciosus ectomycorrhizas. 91 3.4. Relation of extraradical mycelium and ectomycorrhiza of Boletus edulis and Lactarius deliciosus. 94 4. Discussion 9 CHAPTER 3 103 Traceability of ectomycorrhizal fungi in plantations: persistence and quantification of Rhizopogon roseolus and Tuber melanosporum extraradical soil mycelium in de novo and old plantations 1.
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