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Table of contents
Chapitre I : Etat de l’art sur les BALOs et objectifs de la thèse
Bactéries prédatrices : zoom sur les Bdellovibrio et organismes apparentés
1. Introduction
2. Caractéristiques générales des BALOs
3. Aspects phylogénétiques
4. Cycle de vie
4.1. Phase d’attaque
4.2. Mode endobiontique
4.3. Mode épibiontique
5. Prédation
5.1. Hôte indépendant, BALOs saprophytique ou axénique
5.2. Prédateur à Gram positif
5.3. Les autres caractéristiques de la prédation des BALOs
6. Rôle écologique
7. Applications (biotechnologie et médecine)
8. Conclusion
9. Encadrés
Bdellovibrio and like organisms: The smallest cellular hunters of the microbial world
1. Introduction
2. What makes BALOs so special to be in the spotlight?
3. BALOs phylogeny
4. Life cycle of BALOs
Box 1: Predators, micropredators, parasitoids or parasites?
4.1. Attack phase (AP)
4.2. Transition phase
4.3. Periplasmic life cycle
4.4. Epibiotic life cycle
5. BALOs predation strategies
5.1. Predation spectrum and preference
Box 2: A preference for Gram-negative prey?
5.2. Factors acting on predation
5.3. Obligate predation and host independence
6. Ecological features of BALOs
6.1. Habitats, abundance and distribution of BALOs
Box 3: Statistical methods to identify co-occurring taxa
6.2. BALOs as “population balancer” ?
6.3. The hunter hunted
7. Biotechnological applications of BALOs
7.1. Why use BALOs to fight pathogens?
7.2. Understanding pathogen predation of BALOs in vivo
8. Conclusions
Box 4 Examples of successful applications
9. Acknowledgements
Objectifs de la thèse
Chapitre 2 : Les BALOs sont-ils présents et diversifiés dans les grands lacs péri-alpins ?
Diversity, dynamics and distribution of Bdellovibrio and like organisms in perialpine lakes
1. Introduction
2. Results
2.1. Primer selection
2.2. Abundances and distribution of the BALOs
2.3. Relationships between BALOs, total bacteria, and other environmental data
2.4. Genetic structure
2.5. Diversity
3. Discussion
3.1. BALOs’ probable role and diversity in peri-alpine lakes
3.2. Peredibacteraceae are the most abundant BALOs family in peri-alpine lakes
3.3. Low abundance of BALOs may not be indicative of a weak functional role
3.4. BALOs and environmental factors
3.5. BALOs’ provenance and form
4. Conclusions and perspectives.
5. Materials and Methods
5.1. Study sites and sampling strategy
5.2. DNA extraction and PCR primers
5.3. FCM
5.4. DGGE
5.5. DNA purification, cloning and sequencing
5.6. Sequences processing, alignment and phylogenetic analysis
5.7. Accession number(s)
5.8. Data analysis of abundance in relation to environmental data
6. Supplementary data
Bdellovibrio and like organisms in Lake Geneva: An unseen elephant in the room?
1. Introduction
2. Materials and methods
2.1. Study site
2.2. Sampling strategy
2.3. DNA extraction
2.4. PCR and sequencing
2.5. Bioinformatics pipeline
2.6. Statistical analysis
2.7. Phylogeny
3. Results
3.1. Diversity
3.2. Phylogeny
3.3. Distribution and dynamics
3.4. Relationships between BALOs and other bacteria
4. Discussion
5. Data Availability Statement
6. Supplementary data
Chapitre III : Quelle est la diversité réelle des BALOs et leurs abondances dans divers environnements ?
New 16S rRNA primers to uncover Bdellovibrio and like organisms diversity and abundance
1. Introduction
2. Materials and Methods
2.1. BALOs primer design workflow for Illumina sequencing technology
2.2. BALOs primer design workflow for quantitative PCR
2.3. Bdellovibrio and like organisms (positive control) strains and culture
2.4. Negative control of bacteria strain and culture
2.5. Environmental samples for PCR and qPCR tests
2.6. DNA extraction
2.7. PCR amplification (primers optimization and Nano MiSeq run preparation)
2.8. qPCR amplification, cloning-sequencing and taxonomic assignation
2.9. Bioinformatics pipeline
2.10. Phylogeny
3. Results
3.1 qPCR primers specificity check and Sanger sequencing results
3.2 PCR primers specificity check and 2×250 NanoV2 MiSeq results
4. Discussion
5. Conclusion
6. Data accessibility
7. Supplementary data
Constats
Exploring the diversity, abundance and structure of Bdellovibrio and like organisms in four contrasted ecosystems over a year
1. Introduction
2. Materials and Methods
2.1. Study sites, sampling and environmental descriptors
2.2. Molecular analyses
3. Results
3.1. BALOs abundance, distribution and dynamics
3.2. Relationships between BALOs and environmental variables
3.3. OTUs diversity and structure
4. Discussion
5. Conclusion
6. Data availability
7. Supplementary data
7.1. DNA extraction
7.2. qPCR standard curves
7.3. PCR and Next-generation sequencing
7.4. Bioinformatic pipeline
7.5. Statistics
7.6. Phylogeny
Chapitre IV : Un écosystème modèle, le Léman ?
Bdellovibrio sp: An important bacterial predator in Lake Geneva?
1. Introduction
2. Material and Method
2.1. Prey isolation, selection, and culturing from different origins
2.2. Sampling and enrichment of BALOs
2.3. Predator isolation and growth on double-layered agar plates
2.4. DNA extraction
2.5. PCR amplification
2.6. Cloning, Sanger sequencing and taxonomic assignment
2.7. Phylogeny
2.8. Data accession numbers
2.9. Predatory spectrum experiment
3. Results
3.1. Characterization of the prey and predators
3.2. Predation spectrum (host-range experiment)
4. Discussion
5. Conclusion
6. Supplementary data
Short-term dynamics of Bdellovibrio and like organisms in Lake Geneva in response to a simulated climatic extreme event
1. Introduction
2. Materials and Methods
2.1 Experimental set up
2.2. Sampling strategy and analyzed parameters
2.3. DNA extraction
2.4. Quantification of BALOs by qPCR
2.5. Flow cytometry analysis
2.6. Statistics
3. Results
3.1. BALOs abundance and dynamics
3.2. Relationships with abiotic factors
3.3. Relationships between biotic variables
4. Discussion
5. Conclusions
6. Acknowledgements
7. Supplementary data
Chapitre V : Discussion et perspectives
La présence des BALOs
Références
