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Table of contents
GENERAL INTRODUCTION
1. MARINE MICROORGANISMS
1.1. Marine bacteria : a recent story
1.2. Key role of planktonic bacteria in marine ecosystems
1.2.1. Role in primary production
1.2.2. Role in Organic Matter recycling and the food web: the microbial loop
1.2.3. Role in global biogeochemical cycles
1.2.3.1. Carbon
1.2.3.2. Nitrogen
1.2.3.3. Sulfur
1.3. The revolution of molecular tools in marine microbial ecology
1.3.1. Accessing diversity using 16S sequencing
1.3.1.1. Methods and limits
1.3.1.2. An unsuspected diversity in the ocean
1.3.2. Metagenomics
1.3.2.1. Methods and limits
1.3.2.2. New capacities discovered
1.4. Marine microbial ecology based on DNA data
1.4.1. Bacterial communities characteristics
1.4.1.1. Free-living and particle-attached bacteria
1.4.1.2. Rare biosphere of sea water
1.4.2. Bacterial communities dynamics
1.4.2.1. Temporal dynamic
1.4.2.2. Spatial dynamic
1.4.2.3. Everything is everywhere
1.4.3. Marine bacteria trophic strategies
2. THE IROISE SEA AND THE BAY OF BREST
2.1. Coastal oceans: a crucial but fragile ecosystem
2.2. The Iroise sea and the Ushant Front
2.3. The Bay of Brest and the SOMLIT station
CHAPTER I SPATIO-TEMPORAL DYNAMIC OF BACTERIAL COMMUNITIES IN THE IROISE SEA
1. RESUME EN FRANÇAIS
2. ABSTRACT
3. INTRODUCTION
4. RESULTS
4.1.1. Environmental settings
4.1.2. Bacterial community dynamics in the Iroise Sea
4.1.3. Description of modules with a specific dynamic, diversity and correlation with environmental parameters
5. DISCUSSION
6. CONCLUSION
7. MATERIAL AND METHODS
7.1. Study site and sampling design
7.2. Nutrients, phytoplankton counts and pigments analysis
7.3. Bacterioplankton communities sampling
7.4. DNA extraction and sequencing
7.5. Bioinformatics analysis
7.6. Statistical analysis
7.7. Network analysis
8. SUPPLEMENTARY DATA
CHAPTER II. TEMPORAL DYNAMIC OF BACTERIAL COMMUNITIES IN THE BAY OF BREST
1. RESUME EN FRANÇAIS
2. ABSTRACT
3. INTRODUCTION
4. MATERIAL AND METHODS
4.1. 1. Study site and sampling strategy
4.2. 2. DNA extraction and sequencing for bacterial diversity
4.3. 3. Bioinformatics analysis
4.4. 4. Statistical analysis
4.5. 5. Looking for general patterns of seasonality
5. RESULTS
5.1. Environmental settings
5.2. Bacterioplankton community’s characteristics
5.3. Seasonality of bacterial communities
6. DISCUSSION
6.1. Seasonal dynamics of bacterial communities
6.2. Break of seasonality: spring blooms
6.3. Late summer communities
6.4. Multiple possible drivers in winter.
7. CONCLUSION
8. SUPPLEMENTARY DATA
CHAPTER III. INTO THE GENOME OF AN ABUNDANT RHODOBACTERACEAE
1. RESUME EN FRANÇAIS
2. ABSTRACT
3. INTRODUCTION
4. MATERIAL AND METHODS
4.1. Study site and sampling
4.2. Libraries preparation for metagenomes
4.3. Reconstruction of Metagenome Assembled Genomes (MAGs)
4.3.1. Sequences quality filtering and assembly
4.3.2. Binning and MAG characterization
4.3.3. Phylogenomic
1. RESULTS AND DISCUSSION
1.1. Recovery of MAGs and identification of the dominant MAG affiliated to the Rhodobacteraceae family
1.2. Genomic characteristics of MAG ID03_00003
1.3. Gene content and putative metabolism
1.4. Taxonomic affiliation and Phylogeny
1.5. Importance of MAG ID03_00003 in the Bay of Brest and the Iroise sea.
2. CONCLUSION
3. SUPPLEMENTARY DATA
DISCUSSION AND PERSPECTIVES
1. THE BREST BAY TIMES SERIES IN THE CONTEXT OF COASTAL GENOMIC OBSERVATORIES
1.1. How to bridge the gap between physical and chemical oceanography and microbial ecology in sub-mesoscale structures?
2. FROM ABIOTIC TO BIOTIC DRIVERS
3. A PERSPECTIVE: BETTER UNDERSTANDING OF ANTHROPIC PRESSURES ON COASTAL ECOSYSTEMS
GENERAL CONCLUSION
REFERENCES
