Bioinformatic Data Analysis:  A powerful tool to unravel microbial diversity

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Table of contents

Chapter 1
1.1. Introduction
1.1. Grapevines
1.2. Plant associated Microbiome
1.2.1 Rhizosphere
1.2.2. Endosphere
1.2.3. Phyllosphere
1.3. Characterisation of plant-associated microbiome
1.3.1. Culturable vs Non-culturable …
1.3.2. Next Generation Sequencing (NGS)
1.3.3. Target genes
1.3.4. Bioinformatic data analysis …
1.3.4.1. Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST)
1.3.4.2. Quantitative Insights into Microbial Ecology (QIIME):
1.3.4.3. MOTHUR
1.3.4.4. UPARSE: highly accurate OTU sequences from microbial amplicon reads
1.3.4.5. Divisive Amplicon Denoising Algorithm (DADA) …
1.4. Scope of the thesis
1.4.1. Objectives
1.4.2. Organization
1.5. References
Chapter 2 Assessing the impact of plant genetic diversity in shaping the microbial community structure of Vitis vinifera phyllosphere in the Mediterranean (Published Manuscript)
2.1 Abstract
2.2 Introduction
2.3 Material and Methods
2.4 Results
2.5 Discussion
2.6 Acknowledgements
2.7 Disclosure Statement
2.8 Funding
2.9 References
Chapter 3 Genotype-Environment Interaction Shapes the Microbial Assemblage in Grapevine’s Phyllosphere and Carposphere: An NGS Approach (Published Manuscript)
3.1 Abstract
3.2 Introduction
3.3 Material and Methods
3.4 Results
3.5 Discussion
3.6 Conclusion
3.7 Author Contribution
3.8 Acknowledgements
3.9 Funding
3.10 References
3.11 Supplementary Informations
Chapter 4 Understanding the phyllosphere microbiome assemblage in grape-species with amplicon sequence data structures (Submitted Manuscript)
4.1 Abstract
4.2 Introduction
4.3 Results
4.4 Discussion
4.5 Material and Method
4.6 References
4.7 Acknowledgements
4.8 Author Contribution
4.9 Tables & Figures
Chapter 5
5.1. Concluding Remarks
5.2 Phyllosphere Microbiome as Biocontrol Agent (BCA)
5.3 Microbiome Engineering
5.4 Phyllosphere microbiome for wine quality improvement
5.5 References