The challenge of environmental microbiology

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Table of contents

CHAPITRE 1 : Introduction
Background and objective of the thesis
Thesis content and structure
The challenge of environmental microbiology
Microbial ecology history
Bacteria
Bacterial genetic diversity
Bacterial roles in nature
Bacterial Diversity
Importance of bacterial diversity in ecosystem
Factors important on bacterial diversity
Abiotic factors
Biotic factors
Measurement of bacterial diversity
Measurements of taxonomic distinctness
The species equal to OUT
How to assess microbial diversity?
Traditional methods
Culture-independent method
Importance of soil
The spatial distribution patterns of micro-organisms
The temporal distribution patterns of micro-organisms
Alpine ecosystem
Definition
Heterogeny of the alpine stage
The history of bacterial characterization in artico-alpine
Phenotypic characterization and adaptation to cold condition
Bacterial diversity in cold environment
Bacterial diversity and structure based on culture
Bacterial diversity and structure based on method molecular
CHAPITR 2: Effet des régimes d’enneigement sur la diversité et relative abondance de la communauté bactérienne des sols alpins 
Contexte général
Objectifs de l’étude
Article I: Microbial diversity in alpine tundra soils correlates with snow cover dynamics
Principaux résultats et discussion
CHAPITRE 3: Effet des régimes d’enneigement sur la structure phylogénétique des communautés bactériennes des sols alpins 
Contexte général
Objectifs de l’étude
Article II: Snow cover dynamics and phylogenetic structure of bacterial communities in alpine tundra soils
Abstract
Introduction
Material and Methods
Study site, sample collection and bacterial ssu sequences
Sequence data treatment
Statistical Analysis
Results
Comparison of bacterial communities using taxonomic information
Comparison of bacterial communities using phylogenetic information
Distribution of bacterial groups at finer taxonomic scale
Discussion
Conclusion
Acknowledgements
References
Principaux résultats et discussion
CHAPITRE 4 : Effet des régimes d’enneigement sur la richesse des espèces bactériennes cultivables des sols alpins
Contexte général
Objectifs de l’étude
Article III: Phylogenetic diversity of cultivable bacteria in soils of temperate alpine tundra
Abstract
Introduction
Material and Method
Site sampling description and sample collection
Culture media
Isolation of bacterial strains
PCR amplification and sequencing of 16S rRNA
Phylogenetic analysis and sequence comparison
Results
Counts and phenotypic characterization of the isolates
Phylogenetic analysis of isolated strains
Comparison with ESM and LSM ssu libraries
Seasonal and spatial distribution
Discussion
Conclusion
Acknowledgements
References
Principaux résultats et discussion
L’effet le enneigement sur la richesse, abondance et composition des bactéries cultivable
Comparaison des résultats obtenus par approches classiques et moléculaires
CHAPITRE 5: Synthèse et perspectives
The limits of molecular approaches
DNA extraction and PCR
Molecular profiling method: CE-SSCP
Random sequencing of ssu libraries
Importance of traditional and cultural methods
Link between bacterial phylogenetic and function
Bacterial assemblage and filtering factors
Link between snow cover and bacterial activity
Bacteriobio geography
Conclusion
Bibliographie
Annexe