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Table of contents
INTRODUCTION GENERALE
General context of the thesis
I. Scientific context
II. Structure of the PhD thesis
L iterature review
1. Microbiota composition
1.1 Plants and microorganisms, an ubiquitous alliance
1.2 Plant-microorganisms symbiosis
1.3 The root microbiota: Diversity and composition
2. Endophytes induced functions and phenotypic modifications
2.1 Resources acquisition
2.2 Resistance to environmental constraints
2.2.1 A biotic stresses
2.2.2 Biotic stresses
2.3 Growth and reproductive strategy
3. Plant microbiota assembly
3.1 Microbiota recruitment
3.1.1 The soil as a microbial reservoir
3.1.2 Rhizosphere
3.1.3 Endosphere
3.2 Controls of the plant over its microbiota
3.2.1 Microorganisms recruitment through compounds secretion
3.2.2 The immune system
3.2.3 Regulation of symbiotic interactions
3.2.4 The host plant effect: genetics and biogeography
3.3 Biotic interactions
3.3.1 Microbe-microbe interactions
3.3.2 The plant community context
3.4 Microbiota transmission
3.4.1 Horizontal or pseudo-vertical transmission
3.4.2 Vertical transmission or heritability
4. The plant is a “holobiont”
5. Objectives of the thesis
C hapter I: C onsequences of mutualist-induced plasticity
I.1. Introduction
Scientific context
Objectives of the chapter
Methods
Main results
I.2 A rticle I: Epigenetic mechanisms and microbiota as a toolbox for plant phenotypic adjustment to environment
I.3 A rticle II: A M fungi patchiness and the clonal growth of Glechoma hederacea in heterogeneous environments
Chapter II: T he heritability of the plant microbiota, toward the meta-holobiont
II.1 Introduction
Scientific context
Objectives of the chapter
Methods
Main results
II.2 Article III: A microorganisms journey between plant generations
II.3 Article IV: Introduction of the metaholobiont concept for clonal plants.
Chapter III:Importance of the plant community context for the individual plant microbiota assembly
III.1 Introduction
Scientific Context
Objectives of the chapter
Methods
Main results
III.2 A rticle V: Plant-plant interactions mediated by fungi impact plant fitness
GENERAL DISCUSSION AND PERSPECTIVES
I. Plants and microorganism: a tight association
II. Redefining the individual plant : from holobiont to meta-holobiont
III. From individuals to community
IV. Microbiota assembly and agricultural practices
Bibliography
