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 on 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 on diverse aspects of diatom biology and evolution. The books 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     

 

Part coordinator : Thomas Mock 

 

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 Töpel    

   

 

Part  2:  GENOMICS   

 

Part coordinator : Thomas Mock 

  

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, Timothée Chaumier and Leila Tirichine   

   

 

Part 3: CELL BIOLOGY  

 

Part coordinators : Nicole Poulsen, Nils Kröger  Wim Vyverman, 

   

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 KroÌger    

   

Chapter 12 : Biomolecules involved in Frustule Biogenesis and Function

Nils Kröger   

   

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    

 

Part coordinators : Yusuke Matsuda & Peter Kroth 

 

  

Chapter 15:  Photosynthetic Light Reactions in Diatoms. I. The Lipids and Light-harvesting Complexes of the Thylakoid Membrane   

Claudia BuÌchel, 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 BuÌchel, 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     

 

Part coordinators : Assaf Vardi & Angela Falciatore 

 

 

Chapter   21 : Sensing and signalling in diatom responses to abiotic cues    

Marianne Jaubert, Carole Duchêne, Peter G. Kroth, Alessandra Rogato, Jean-Pierre Boulyand 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. Shibland 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     

 

Part coordinator : Angela Falciatore 

 

 

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 Research Director of the French National Centre for Scientific Research (CNRS). She received a Master's degree in Biological Sciences (1995) at University Federico II of Naples, Italy, where she studied osmotic stress responses in bacteria. Her interest for marine biology stems from the research performed at the Stazione Zoologica Anton Dohrn of Naples (SZN) in Italy, in Chris Bowler 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 on 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 enlarge 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 from 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 at 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 speciesPhaeodactylum 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 disclose some of the diatom specific photoacclimation properties, by identifying critical regulators of photosynthesis that also influence the natural variability of diatoms 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 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 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.

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 on 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 on diverse aspects of diatom biology and evolution. The books 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.