Contemporaneous Functional Ecology

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Table of contents

INTRODUCTION
1) Preamble: Ecology
2) Marine Protistan Diversity
3) Marine Protistan Ecology: State of the Art
a) Everything is everywhere but the environment selects
b) Redfield Ratio
c) Trophic Ecology
d) Competitive Exclusion and the Paradox of the Plankton
e) Plankton species successions and ecosystem maturity
f) The microbial loop
g) Transitions in pelagic ecosystems
h) Neutral theory and dispersal
i) Conclusion
4) Methodological developments in the sampling of marine protists
5) A perspective for marine protists: functional ecology
a) Strategies of marine protists in aquatic ecosystems
b) Lifeforms and successions
c) Patterns of succession and functional groups
d) Beyond phytoplankton: heterotrophic protists
e) Contemporaneous Functional Ecology
6) Marine Coastal Ecosystems
OVERVIEW AND OBJECTIVES
CHAPTER I: COUPLING BETWEEN TAXONOMIC AND FUNCTIONAL DIVERSITY IN PROTISTAN COASTAL
1) Introduction
2) Results
a) Environmental characteristic of the sampled ecosystems
b) Genetic diversity
c) Functional diversity
d) Functional vs. taxonomical diversity of marine protists
3) Discussion
a) Patterns of genetic diversity of coastal protist communities
b) From a genetic to a functional diversity approach in protists: limits and potential development .
c) Patterns of functional diversity of coastal protist communities
d) Coupling between functional roles and taxonomy among marine protistan communities
4) Conclusions
5) Experimental Procedures
a) Sampling strategy
b) Genetic procedures
c) Sequence data cleaning, filtering and clustering into OTUs and taxa
d) Functional approach
e) Statistical Analyses
6) Supplementary Material
CHAPTER II: PATTERNS OF PROTISTAN DIVERSITY OVER A COASTAL TIDAL FRONT
A. PATTERNS OF PHYTOPLANKTON DIVERSITY OVER A COASTAL TIDAL FRONT 
1) Introduction
2) Material and methods
a) Oceanographic context and sampling strategy
b) Genetic procedures
c) Bioinformatics analyses
d) Phytoplankton Diversity analyses
e) Functional diversity analyses
3) Results
a) Oceanographic Context
b) Metabarcoding of the Protistan Community
c) Phytoplankton Diversity Patterns
d) Functional Diversity
4) Discussion
a) Phytoplankton community composition
b) Phytoplankton diversity and environmental drivers
c) Phytoplankton ecological strategies and environmental drivers
5) Conclusion
6) Supplementary Material
B. HETEROTROPHIC PROTISTS: DYNAMIC AND DIVERSITY OVER A COASTAL TIDAL FRONT
1) Introduction
2) Material and methods
3) Results
a) The heterotrophs/phototrophs ratio
b) Heterotrophic protists diversity
c) Abundant heterotrophic protists and their traits
4) Discussion
a) Trophic ratio of marine protists
b) Heterotrophic protisan community
c) Heterotrophic protistan diversity
5) Conclusions
6) Perspective
CHAPTER III: THE FUNCTIONAL ROLE OF PARASITISM IN A COASTAL ECOSYSTEM
1) Introduction
2) Material and Methods
a) Sampling strategy
b) Genetic procedures
c) Bioinformatics analyses
d) Detection of A. minutum
e) Parasites of A. minutum
f) Ecological analysis
3) Results
a) Protist community diversity across the A. minutum blooms
b) Identification and dynamic of Alexandrium minutum
c) Identification and dynamics of known parasitic interactions
d) Other potential host-parasite interactions
4) Discussion
a) Metabarcoding approach for the study of the dynamic of Alexandrium minutum
b) Known parasites of A. minutum and their dynamic
c) Other potential parasitic interactions
5) Conclusion
6) Supplementary Material
CONCLUSION AND PERSPECTIVES
REFERENCES