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Diatoms are the most species-rich group of algae, and they contribute about 20% of annual global carbon fixation. They play major roles in ocean food webs and global biogeochemical cycles. They are also a target of the biotechnology industry because of their nano-patterned silica cell wall and high lipid content. Diatoms have received increasing attention as more genomes became available and because of the development of genome editing tools such as the CRISPR/Cas9 technology, which has made diatoms as genetically tractable as well-established biological model species.
This book provides an overview of diatom molecular biology. It brings together international leading experts in the field to discuss the latest data and developments from genes to ecosystems. As the understanding of diatoms is currently experiencing a step change, it is critical to allow for synergistic approaches to diverse aspects of diatom biology and evolution. The book offers fundamental insights into the molecular life of diatoms; at the same time, new scientific concepts are developed based on the application of the latest molecular tools and genomic information to explore the fascinating lifestyle of diatoms.
Part 1. ECOLOGY AND EVOLUTION
Chapter 1. Trait-based ecology with diatoms / Elena Litchman
Chapter 2. The population genetics and evolutionary potential of diatoms / Tatiana A. Rynearson, Ian W. Bishop, Sinead Collins
Chapter 3. An integrated view of diatom interactions / Flora Vincent & Chris Bowler
Chapter 4. Ancient diatom DNA / Matthew I. M. Pinder and Mats Toepel
Part 2. GENOMICS
Chapter 5. Structure and evolution of diatom nuclear genes and genomes / Thomas Mock, Kat Hodgkinson, Taoyang Wu, Vincent Moulton, Anthony Duncan, Cock van Oosterhout, Monica Pichler
Chapter 6. Reconstructing dynamic evolutionary events in diatom nuclear and organelle genomes / Richard G. Dorrell, Fuhai Liu, Chris Bowler
Chapter 7. Epigenetic control of diatom genomes: An overview from in silico characterisation to functional studies / Xue Zhao, Antoine Hoguin, Timothee Chaumier and Leila Tirichine
Part 3. CELL BIOLOGY
Chapter 8. Life-cycle regulation / Gust Bilcke, Maria Immacolata Ferrante, Marina Montresor, Sam De Decker, Lieven De Veylder and Wim Vyverman
Chapter 9. Cellular hallmarks and regulation of the diatom cell cycle / Petra Bulankova, Gust Bilcke, Wim Vyverman and Lieven De Veylder
Chapter 10. Cell Biology of organelles / Uwe G. Maier, Daniel Moog, Serena Flori, Pierre-Henri Jouneau, Denis Falconet, Thomas Heimerl, Peter G. Kroth, Giovanni Finazzi
Chapter 11. Structure and Morphogenesis of the Frustule / Iaroslav Babenko, Benjamin M. Friedrich, Nils Kro ger
Chapter 12. Biomolecules involved in Frustule Biogenesis and Function / Nils Kroeger
Chapter 13. Silicic Acid Uptake and Storage by Diatoms / Felicitas Kolbe, Eike Brunner
Chapter 14. Adhesion and Motility / Nicole Poulsen, Metin Gabriel Davutoglu and Jirina Zackova Suchanova
Part 4. PRIMARY METABOLISM
Chapter 15. Photosynthetic Light Reactions in Diatoms. I. The Lipids and Light-harvesting Complexes of the Thylakoid Membrane / Claudia Bu chel, Reimund Goss, Benjamin Bailleul, Douglas A. Campbell, Johann Lavaud and Bernard Lepetit
Chapter 16. Photosynthetic Light Reactions in Diatoms. II. The Dynamic Regulation of the Various Light Reactions / Bernard Lepetit, Douglas A. Campbell, Johann Lavaud, Claudia Bu chel, Reimund Goss and Benjamin Bailleul
Chapter 17. Carbohydrate Metabolism / Peter G. Kroth and Yusuke Matsuda
Chapter 18. Lipid Metabolism in Diatoms / Tsuyoshi Tanaka, Kohei Yoneda and Yoshiaki Maeda
Chapter 19. Comparative and Functional Genomics of Macronutrient Utilization in Marine Diatoms / Sarah R. Smith and Andrew E. Allen
Chapter 20. Molecular Mechanisms Underlying Micronutrient Utilization in Marine Diatoms / Tyler H. Coale, Erin M. Bertrand2, Robert H. Lampe3 and Andrew E. Allen
Part 5. CELL SIGNALLING and INTERACTIONS
Chapter 21. Sensing and signalling in diatom responses to abiotic cues / Marianne Jaubert, Carole Duchene, Peter G. Kroth, Alessandra Rogato, Jean-Pierre Bouly and Angela Falciatore
Chapter 22. An Ocean of Signals: Intracellular and Extracellular Signalling / Shiri Graff van Creveld, Avia Mizrachi and Assaf Vardi
Chapter 23. The Diatom Microbiome: New Perspectives for Diatom-Bacteria Symbioses / Katherine E. Helliwell, Ahmed A. Shibl and Shady A. Amin
Chapter 24. Diatom Viruses / Laure Arsenieff, Kei Kimura, Chana F. Kranzler, Anne-Claire Baudoux and Kimberlee Thamatrakoln
Part 6. GENETIC AND METABOLIC ENGINEERING
Chapter 25. Genetic Engineering in Marine Diatoms: Current Practices and Emerging Technologies / Mark Moosburner, Andrew E. Allen and Fayza Daboussi
Chapter 26. Constraint-based Modelling of Diatoms Metabolism and Quantitative Biology Approaches / Manish Kumar, Cristal Zuniga, Juan D. Tibocha-Bonilla, Sarah R. Smith, Joanna Coker, Andrew E. Allen, Karsten Zengler
Angela Falciatore is the Research Director of the French National Centre for Scientific Research (CNRS). She received a Master’s degree in Biological Sciences (1995) at the University Federico II of Naples, Italy, where she studied osmotic stress responses in bacteria. Her interest in marine biology stems from the research performed at the Stazione Zoologica Anton Dohrn of Naples (SZN) in Italy, in Chris Bowler's laboratory (1995-2001) where she got a PhD in 2002 on the “Molecular studies of environmental signal perception and transduction in marine diatoms”. Particularly interested in the dynamic responses of photosynthetic organisms to light, she joined Jean-David Rochaix's laboratory at the University of Geneva, Switzerland for her post-doc (2002-2005), devoted to the chloroplast-to-nucleus retrograde signalling in the green alga Chlamydomonas reinhardtii. Complementary activities at the Okazaki National Institute for Basic Biology, Japan (1997) and at the Carnegie Institution of Washington, Stanford University, USA (2003) contributed to enlarging her expertise in photobiology. In 2005, with a tenure-track position, she started an independent research activity at the SZN, Italy. At the end of 2009, she got a permanent position at CNRS and moved from Italy to France. She established and led the team “Diatom Functional Genomics” in the Laboratory of Computational and Quantitative Biology directed by Alessandra Carbone at Université Pierre et Marie Curie in Paris. Since 2019, she is the Head of the Laboratory of “Chloroplast Biology and Light Sensing in Microalgae”, affiliated with the CNRS and Sorbonne Université at the Institut de Biologie Physico-Chimique (IBPC) in Paris.
A major focus of her research has been to establish diatoms as new model systems for marine biology and photobiology by developing genomic resources and genetic tools. Combining physiological, biophysical, biochemical and genome-wide molecular approaches in the diatom model species Phaeodactylum tricornutum, her team has characterized diversified photoreceptors, fostering novel hypotheses on the role of these sensors in controlling growth and adaptive responses in a marine context. She also uncovered the existence of a long-foreseen diatom circadian clock, which controls essential rhythmic processes in these algae. Her team also contributed to disclosing some of the diatom-specific photoacclimation properties, by identifying critical regulators of photosynthesis that also influence the natural variability of diatom photoresponses.
Thomas Mock is a Professor of Marine Microbiology in the School of Environmental Sciences at the University of East Anglia (UEA), Norwich Research Park, Norwich, United Kingdom. He obtained his MSc (1998) in Biology with an emphasis on Biological Oceanography at the Christian-Albrechts University in Kiel (GEOMAR) and his PhD (2003) at Bremen University (Alfred-Wegener Institute for Polar and Marine Research), Germany. Before joining UEA in 2007, most of his PostDoc research was conducted with a fellowship from the German Academic Exchange Service (DAAD) in the School of Oceanography, University of Washington (E.V. Armbrust lab) in cooperation with the Biotechnology Centre, University of Wisconsin (M.R. Sussman lab), USA. Before he was promoted to Professor (Personal Chair) at UEA in 2014, he was Reader (2012-2014) and had a Research Councils UK Academic Fellowship (2007-2012). The overarching aim of his research is to identify fundamental biological processes that govern the adaptation and evolution of marine microalgae (Phytoplankton) in the oceans with an emphasis on diatoms. His group uses genomics (e.g., metatranscriptomics, metagenomics) and reverse genetics tools (e.g., CRISPR/Cas) for selected phytoplankton groups (e.g., diatoms) and natural assemblages from the global upper ocean to understand their evolution, diversity, and adaptation. This work leads to the identification of genes that shape their phenotypes and are therefore responsible for their unique biology and evolutionary adaptation to different environments of the upper ocean from pole to pole.
