Diatom classification

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Table of contents

1. Diatom Biodiversity Assessment: General Introduction
1.1. Diatoms: life in glass houses
1.1.1. Diatom ultrastructure
1.1.2. Habitats and adaptations
1.1.3. Life history
1.1.4. Secondary endosymbiosis
1.1.5. Evolutionary and geological history
1.1.6. Diatom classification
1.1.7. Global importance
1.2. Marine biodiversity and biogeography
1.2.1. General introduction
1.2.2. Characterizing biodiversity
1.2.3. Microbial biogeography: processes and patterns in microbial diversity
1.2.4. Future directions in the study of microbial biogeography
1.3. Metabarcoding: a new paradigm for biodiversity assessment
1.4. Tara Oceans: a comprehensive sampling of marine planktonic biota
1.4.1. Background
1.4.2. Sampling strategy and methodology
1.4.3. Tara Oceans integrated pipeline
1.5. Aim of the thesis
1.6. Thesis outline
2. Insights into the Biogeographical Patterns of Planktonic Diatom Diversity – an Assessment Using Metabarcoding
Abstract
2.1. Introduction
2.2. Results
2.2.1. Evaluation of V9 region of 18S rDNA as a diversity marker for diatoms
2.2.2. Global dataset of diatom V9 metabarcodes
2.2.3. Diatom community composition
2.2.4. Unassigned sequences/ Novelty
2.2.5. Comparison between light microscopy and V9 ribotype counts
2.2.6. Global diversity patterns
2.2.7. Community similarity
2.3. Discussion
2.4. Materials and methods
2.4.1. Distance based Analysis
2.3.2. Metabarcoding dataset
2.3.3. Morphological analyses
2.3.4. Taxonomy-based clustering
2.3.5. Global distribution analysis
Figure legends
Supplementary Material
References
3. Niche-based and Spatial Processes Shaping Diatom Community Structure
Abstract
3.1. Introduction
3.2. Materials and methods
3.2.1. Dataset
3.2.2. Statistical analyses
3.3. Results
3.3.1. Distance-decay relationships (DDR)
3.3.2. Mantel analysis
3.3.3. Multiple regression analyses on individual environmental variables
3.3.4. Relative role of niche-based and spatial processes
3.4. Discussion
4. A Metabarcoding-based Assessment of Diatom Assemblages
Abstract
4.1. Introduction
4.2. Materials and methods
4.2.1. Study area and dataset
4.2.2. Statistical analyses
4.3. Results
4.3.1. Ordination of environmental variables
4.3.2. Correlation of individual variables to each ribotype
4.3.3. Taxonomic and environmental characterization
4.3.4. Spatial characterization at local scale
4.3.5. Spatial characterization at regional scale
4.3.6. Environmental determinants of the global distribution of clusters
4.4. Discussion
5. Discerning and Quantifying Power-law Behavior of Protistan Communities
Abstract
5.1. Introduction
5.1.1. Marine community structure: evident structuring processes
5.1.2. Overview on rank-abundance distribution (RAD) curve
5.1.3. Commonness and rarity
5.1.4. Power-law distribution
5.1.5. Structure of the study
5.2. Materials and methods
5.2.1. Protist dataset
5.2.2. Delineating rare ribotypes in the world’s ocean
5.2.3. Fitting power-laws to the community data
5.3. Results
5.3.1. Potential insights into commonness and rarity patterns of protists
5.3.2. Discerning, quantifying and comparing power-law behavior
5.4. Discussion
5.4.1. Potential insights into commonness and rarity patterns in the world’s ocean
5.4.2. How plankton gets dispersed in random environment
5.4.3. Power laws in ecology
5.4.4. Explanations of power-laws
6. General Conclusion and Future Perspectives
References
Annexes
A. Glossary
B. Diversity and similarity Indices
C. Multivariate statistical methods
D. Resolution of V9 18S rDNA tags in diatom phylogeny
E. Supplementary Information to Chapter 2
F. Supplementary Information to Chapter 3
G. Supplementary Information to Chapter 4
H. Supplementary Information to Chapter 5
I. Co-authored manuscripts