SymbioScope: Assessing the ecological diversity and dynamics of symbiotic interactions in a key phytoplankton by automated high-content 3D microscopy

• Applicant: Dr. Marie Walde
• Subject Area: Ecology and Biodiversity of Plants and Ecosystems ; Image and Language Processing, Computer Graphics and Visualisation, Human Computer Interaction, Ubiquitous and Wearable Computing ; Measurement Systems ; Virology
• Term: from 2021 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 464344344

• Final Report Year: 2025

Final Report Abstract

Photosynthetic plankton (phytoplankton) forms the basis of global biogeochemical processes. High-throughput sequencing of DNA and RNA now makes it possible to comprehensively map the genetic diversity of plankton in the environment. It has shown that the diversity and quantity of microbial eukaryotes in the sea (protists, e.g. diatoms) has long been underestimated and provides no information about their forms, complex cell structures and behavior. At the same time, there is increasing evidence that biotic interactions, including symbioses (in the broad sense) between different plankton taxa, are important drivers of the ecology and evolution of species and ecosystems. The more detailed study of such symbioses in environmental protists remains a challenge due to their high morphological complexity compared to protists. The SymbioScope project addressed this lack of quantitative high-throughput techniques to recognize, describe, enumerate and assess the subcellular structures of eukaryotic phytoplankton sampled from the ocean - a blind spot in plankton ecology. I developed a method based on automated fluorescence microscopy to quantitatively measure the subcellular structure and interaction landscape of microbial plankton. Next, I applied this method to investigate the symbiotic complexity of Guinardia delicatula, (a cosmopolitan eukaryotic phytoplankton species forming large blooms off the coast of Roscoff). First, I investigated the effect of RNA infections on the cell structure and physiology of these diatoms in locally isolated cultures. Then, I collected environmental samples to study their symbiotic interactions on a seasonal scale. To better identify morphologically divergent life cycle stages as well as morphologically undescribed protists, I additionally developed a labelling and imaging method based on fluorescence in situ hybridization for environmental samples. I was also able to transfer the potential of these approaches for marine ecology to other marine protists, whose symbiotic interactions and morphologies I studied in collaboration with colleagues in Roscoff.

Publications

• Image-based Systems Biology (Jena, Germany + hybrid). Insights into the 3D subcellular impact of viral infection in an abundant marine diatom. Selected Talk
  M. Walde, C. Camplong, C. De Vargas, A.-C Baudoux & N. Simon
  
• Marine Imaging Workshop (Brest, France). Insights into the 3D subcellular impact of viral infection in an abundant marine diatom. Selected Talk
  M. Walde, C. Camplong, C. De Vargas, A.-C Baudoux & N. Simon
  
• oligoN-design: First beta version
  M. M. Sandin & M. Walde
  
• 8th European Phycological Congress (Brest, France). Preliminary study on the Role of the allelopathic shuttle in the development of Alexandrium minutum. Poster
  M. Long, M. Walde, L. Guillou & B. Moriceau
  
• 8th European Phycological Congress (Brest, France). The impact of biotic interactions on subcellular structure – an automated 3D imaging approach for marine diatoms. Selected Talk
  M. Walde, C. Camplong, C. De Vargas, A.-C Baudoux & N. Simon
  
• Viral infection impacts the 3D subcellular structure of the abundant marine diatom Guinardia delicatula. Frontiers in Marine Science, 9.
  Walde, Marie; Camplong, Cyprien; de Vargas, Colomban; Baudoux, Anne-Claire & Simon, Nathalie
  
• Conférences Jacques Monod “Evolution des virus” (Roscoff, France). Ecological and biogeochemical implications of diatom infection by viruses
  N. Simon, L. Arsenieff, M. Walde, F. Le Gall, E. Jaouen, P. Nogaret, C. Fiorile, L. Blondel, P. Riera, M. Gachenot, C. Six, E. Bigeard, C. Leroux, S. Le Panse, E. Corre, C. Berthelier, I. Probert, M. Boccara, G. Blanc, S. Monteil Bouchard, B. Moriceau, M. Gallinari & A.-C. Baudoux
  
• Correlative Genomics of Unicellular Eukaryotes (Sant Feliu, Spain). Meet the new stramenopile class: The Massanaxicophyceae. Poster
  A. Boukkheroub, M. M. Sandin, M. Walde, N. Henry, M. Gachenot, P. Gourvil, N. Chomerat, S. Le Panse, C. Six, I. Probert & C. Bachy
  
• Correlative Genomics of Unicellular Eukaryotes (Sant Feliu, Spain). Subcellular imaging of symbiotic interactions in environmental marine protists. Flash Talk
  M. Walde, M. M. Sandin, C. Camplong, C. de Vargas, A.-C. Baudoux & N. Simon
  
• EMBO Lecture Course “Imaging Marine Organisms Across Scales” (Napoli, Italy). Subcellular monitoring of symbiotic interaction in environmental marine microeukaryotes. Selected Talk
  M. Walde, M. M. Sandin, C. Camplong, C. de Vargas, A.-C. Baudoux & N. Simon
  
• EVOLECO (Brest & Paris, France). ROSKO-GO : un observatoire augmenté à la station marine de Roscoff. Poster
  J. Castel, C. Daguin Thiébaut, M. Ballenghien, A. C. Baudoux, C. Berthelier, E. Bigeard, Y. Bozec, C. Broudin, S. Bureau, A. Chambouvet, C. De Vargas, L. Dufour, L. Guillou, N. Henry, C. Houbin, F. Le Gall, S. Loisel, D. Marie, F. Partensky, M. Ratin, F. Rigaut-Jalabert, S. Romac, D. Vaulot, M. Walde, T. Comtet, L. Garczarek, C. Jeanthon, N. Simon, F. Not & E. Thiébaut.
  
• Journée Scientifique sur l'Observation en Milieu Marin, IFREMER (Plouzané, France). Viral infection impacts the 3D subcellular structure of the abundant marine diatom Guinardia delicatula. Talk
  M. Walde, C. Camplong, C. de Vargas, A.-C. Baudoux & N. Simon