Note: Front Cover -- Advances in Phytoplankton Ecology -- Copyright -- Dedication -- Contents -- List of contributors -- Acknowledgment -- Introduction -- Part 1 Phytoplankton taxonomy -- 1 Cyanobacterial diversity and taxonomic uncertainty: polyphasic pathways to improved resolution -- Introduction -- Background -- Nomenclature -- Species concepts -- Pathways from morphology to molecules -- Polyphasic approach -- Morphology and ecology -- Molecular evidence of monophyly -- Formal designation of taxa according to the nomenclatural system -- Opportunities through whole genome sequencing -- WGS applications -- Conclusions and future challenges -- References -- 2 Uses of molecular taxonomy in identifying phytoplankton communities from the Continuous Plankton Recorder Survey -- 2.1 The Continuous Plankton Recorder Survey across large time- and space scales -- 2.2 The challenge of using formalin-preserved CPR phytoplankton samples in molecular work -- 2.3 Case studies -- 2.4 The future of CPR sample archive repository as a tool for global ecological and taxonomic research -- References -- 3 Impact of molecular approaches on dinoflagellate taxonomy and systematics -- 3.1 Molecular systematics and diversity of dinoflagellates: a historical perspective -- 3.1.1 Dinoflagellates: rich morphological and functional diversity -- 3.1.2 Growth of dinoflagellate molecular systematics -- 3.2 Phase I: challenging existing evolutionary theories -- 3.2.1 Establishing the phylogenetic position of the dinoflagellates -- 3.2.2 Evolution and phylogeny of the dinoflagellates -- 3.3 Phase II: discovering widespread cryptic diversity -- 3.3.1 The rise of reverse taxonomy: sequence first, identify later -- 3.4 Phase III: increasing taxon and gene sampling -- 3.4.1 Solving the culture bias problem -- 3.4.2 Increasing gene targets and multigene phylogenies. , 3.5 Phase IV: technology-accelerated diversity discovery -- 3.5.1 DNA barcoding and meta-barcoding in taxonomy -- 3.5.2 Transcriptomics in dinoflagellate taxonomy -- 3.5.3 Ancient DNA and palaeomics -- 3.6 Future perspectives: where to from here? -- 3.6.1 Data quality control -- 3.6.2 Taxon coverage and species assignment -- 3.6.3 Filling in the blanks: the taxon coverage problem -- 3.7 Conclusions -- Acknowledgments -- References -- 4 From molecules to ecosystem functioning: insight into new approaches to taxonomy to monitor harmful algae diversity in Chile -- 4.1 Introduction -- 4.2 Classical taxonomy approach -- 4.3 Molecular approach -- 4.4 Chemotaxonomy -- 4.5 RTgill-W1 fish gill bioassay for ichthyotoxins detection -- 4.6 Imaging flow cytometry for detection of Harmful Algae -- 4.7 MicroToxMap: citizen science for the identification and monitoring of harmful algal blooms -- 4.8 Outlook/overview -- References -- Part 2 Monitoring and sensing systems -- 5 Integrating imaging and molecular approaches to assess phytoplankton diversity -- Introduction -- Continuous automated live imaging: Imaging Flow Cytobot -- Molecular approaches -- Metabarcoding -- Metatranscriptomics -- Conclusion -- References -- 6 Advances in in situ molecular systems for phytoplankton research and monitoring -- Introduction -- Current state of the art -- In situ sampling -- Molecular assays: point-of-use -- Lateral flow assays -- Nucleic acid analysis -- In situ sample preparation -- In situ nucleic acid amplification testing -- Automated in situ molecular detection of phytoplankton -- Miniaturized sequencing technologies -- Unmet needs and recommendations -- Affordability -- Real-time reporting and operational control -- References -- 7 Applications of satellite remote sensing technology to the analysis of phytoplankton community structure on large scales. , 7.1 Challenges of sensors and methods -- 7.1.1 Sensor characteristics -- 7.1.2 Satellite algorithms -- 7.2 Application of satellite-derived phytoplankton diversity for fulfilling user needs -- 7.2.1 Tracing global phytoplankton diversity -- 7.2.2 Satellite products on phytoplankton composition for tackling scientific objectives -- 7.2.2.1 Food web dynamics -- 7.2.2.1.1 Case study on energy content and transfer -- 7.2.2.1.2 Satellite products for studying phytoplankton phenology -- 7.2.2.2 Impact of phytoplankton size on export flux in the global ocean: a case study -- 7.2.2.3 Other applications -- 7.3 Societal benefits of satellite PG and PSC products: integrating into services -- References -- 8 Modeling phytoplankton processes in multiple functional types -- 8.1 Introduction -- 8.2 Photosynthesis and chlorophyll synthesis -- 8.3 Impact of phytoplankton on ocean optics -- 8.4 Macronutrient uptake and stoichiometry -- 8.5 Micronutrients and silica -- 8.6 Nitrogen fixation, calcification, mixotrophy -- 8.7 Phytoplankton mortality -- 8.8 Summary of process descriptions -- 8.9 Marine applications -- 8.10 Summary -- References -- 9 Managing the societal uses of phytoplankton: technology applications and needs -- 9.1 Introduction -- 9.2 Societal uses of phytoplankton and their management -- 9.3 Emerging technologies for management applications -- 9.4 Management applications and technology needs -- 9.5 Conclusions -- References -- Part 3 Omics in aquatic ecology -- 10 Current applications and technological advances in quantitative real-time PCR (qPCR): a versatile tool for the study of phytoplankton ecology -- Introduction -- Method overview -- Quantitative PCR applications in phytoplankton ecology -- Reverse transcriptase qPCR (RT-qPCR) -- Recent advances in qPCR technology -- Detection of harmful algal blooms via portable PCR. , Field collections and extraction of environmental DNA -- Droplet digital PCR -- Building qPCR into community-based monitoring programs -- Acknowledgments -- References -- 11 Phytoplankton diversity and ecology through the lens of high throughput sequencing technologies -- 11.1 Introduction -- 11.1.1 The concept of molecular markers -- 11.1.2 The advent of environmental sequencing -- 11.1.3 The transition to high throughput sequencing (HTS) -- 11.2 The different steps of metabarcoding -- 11.2.1 Sampling and DNA extraction -- 11.2.2 Marker gene selection -- 11.2.3 PCR and sequencing -- 11.2.4 Data processing -- 11.3 Protist metabarcoding studies in aquatic environments -- 11.3.1 Arctic and Antarctic communities -- 11.3.1.1 The risk of habitat loss for ice-associated communities -- 11.3.1.2 Impact of protist diversity on ocean cycles and novel biogeographic patterns -- 11.3.1.3 Bipolarity studies as a proof of concept for microbial dispersal theories -- 11.3.1.4 Metabarcoding as a way to measure vulnerability of polar environments -- 11.3.2 The biological carbon pump -- 11.3.2.1 Molecular approaches applied to biological communities associated with sinking particles -- 11.3.2.2 Phytoplankton and vertical export -- 11.3.3 Predator-prey interactions and trophic connectivity -- 11.4 Marine picocyanobacteria -- 11.4.1 Use of the universal marker gene, the 16S rRNA -- 11.4.2 More resolutive markers -- 11.4.3 mitags as an alternative to picocyanobacteria metabarcoding -- 11.5 Future directions -- Acknowledgments -- 11.6 Supplementary material -- References -- 12 Comparative genomics for understanding intraspecific diversity: a case study of the cyanobacterium Raphidiopsis raciborskii -- Glossary -- Introduction -- Comparative genomics -- Core and pangenome -- Variable shell genome and unique genes -- Genome evolution -- Horizontal gene transfer. , Intraspecific diversity -- Cyanobacteria -- Conclusion -- References -- 13 Transcriptomic and metatranscriptomic approaches in phytoplankton: insights and advances -- Introduction -- How has transcriptomics changed our understanding of phytoplankton ecology? -- Algal diversity -- Endosymbiosis -- Light sensing and transcriptional response -- Ecological interactions -- Virus/host dynamics -- Secondary metabolite production -- Harmful algal blooms (HABs) -- Life stages and trophic strategy -- Nutrient response -- Contaminants -- Transcriptomics limitations and how to avoid them -- Collection -- Processing and preservation -- Extraction -- Library preparation -- Sequencing -- Assembly -- Annotation -- Analysis -- Future prospects -- Single-cell transcriptomics -- Environmental monitoring -- Conclusions -- Acknowledgments -- References -- 14 From genes to ecosystems: using molecular information from diatoms to understand ecological processes -- Introduction -- Case study: silicon metabolism -- Physiological basis of silicon cycling in the ocean -- Silicon metabolism in diatoms and the molecular basis of silicification -- The promise and problems of using omics to understand silicon biogeochemistry -- Case study: cell death -- Cell death: an enigmatic process with profound ecological implications -- The cell death process in phytoplankton and diatoms: specific molecular markers -- Cell death in diatoms: experimental studies -- From cell death genes to cell death ecology: prospects and problems -- Case study: environmental sensing and community-level interactions -- Sensory biology of diatoms: the importance of timescales -- Diatom stress and defense signaling: the challenge of deciphering redox cross-talk -- Communication and microbial dynamics in the diatom phycosphere -- Conclusion: challenges and prospects -- References. , 15 Global marine phytoplankton revealed by the Tara Oceans expedition.