FY2021 Annual Report

Abstract

The Evolution, Cell Biology, and Symbiosis Unit studies the effects of symbiotic interactions on the evolution and cell biology of the involved symbiotic partners. We are especially interested in the role symbioses played in major evolutionary transitions such as the origin of the eukaryotic cell and its symbiotic organelles, mitochondria and plastids. However, we also study much younger symbioses such as those found in microbial eukaryotes and animals. Currently, our research projects mostly focus on symbiotic microorganisms and organelles found in single-celled eukaryotes (foraminifera, dinoflagellates, ciliates, and a few other lineages), plants (parasites and mycoheterotrophs), and animals (corals and insects).

1. Staff

• Dr. Dewi Langlet, Staff Scientist
• Dr. Courtney M. Dunphy, JSPS Postdoctoral Research Fellow
• Dr. Maria Eduarda Alves dos Santos, JSPS Postdoctoral Research Fellow
• Dr. Jinyeong Choi, NRF Korea Postdoctoral Research Fellow
• Dr. Yumiko Masukagami, Research Technician
• Dr. Iines Salonen, Visiting Researcher
• Kimberlie Ward, Technician
• Machiko Shiomi, Research Unit Administrator
• Javier Tejeda Moja, Ph.D. Student
• Pradeep Palanichamy, Ph.D. Student
• Yong Heng Phua, Research Intern, Rotation Student
• Mariia Naumova, Research Intern
• Zhuli Cheng, Rotation Student (Jan-Apr 2022)
• Rahel Ruppli, Rotation Student (Sep-Dec 2021)
• Daitian Xu, Research Intern (Dec 2021-March 2022)
• Olivia Millar, Research Intern (Oct 2021-March 2022)
• Mei Shimizu, Research Intern (Oct 2021-March 2022)

2. Collaborations

2.1 Endosymbioses of diverse microbial eukaryotes

• Researchers:
  • Dr. Hidetaka Nomaki, JAMSTEC
  • Dr. Iines Salonen, JAMSTEC
  • Prof. Kazuhiko Fujita, University of Ryukyus
  • Assoc. Prof. Naoya Shinzato, University of Ryukyus
  • Assist. Prof. Kevin Wakeman, Hokkaido University
  • Dr. Emma George, University of British Columbia
  • Dr. Vittorio Boscaro, University of British Columbia
  • Prof. Patrick Keeling, University of British Columbia
  • Prof. Marek Elias, University of Ostrava
  • Dr. Dovile Barcyte, University of Ostrava

2.2 Biology of coral symbioses

• Researchers:
  • Dr. Masaru Mizuyama, AIST
  • Dr. Akira Iguchi, AIST
  • Assoc. Prof. James D. Reimer, University of Ryukyus
  • Dr. 'Ale'a Dudoit, University of Hawaiʻi
  • Assoc. Prof. Rob Toonen, University of Hawaiʻi

3. Activities and Findings

3.1 Research Projects

3.1.1 Endosymbioses of diverse microbial eukaryotes

In this collection of smaller projects, we study endosymbioses of many diverse single-celled eukaryotes (reviewed in Husnik et al., Current Biology 2021; Figure 1) and develop tools for analyzing their genome evolution (Figure 2). During FY2021, in the projects led by unit members, we focused mostly on bacterial and algal symbioses of benthic dinoflagellates and foraminifera. Both of these protist groups are very rich in symbioses, yet extremely understudied. From benthic dinoflagellates, we selected toxin-producing lineages (Coolia, Amphidinium, Ostreopsis) as our model group where bacterial symbionts are sometimes hypothesized to be involved in toxin production. As a first step, we untangled their diversity, phylogeny, and in some cases microbial composition (Phua et al., Harmful Algae 2021; Phua et al., Phycologia 2022; Phua et al., submitted). Among foraminifera, we analyzed the algal symbiont diversity of large benthic foraminifera from coral reef flats and uncovered their extreme diversity and in most cases co-evolution with the foraminiferal hosts (Langlet et al., In prep.).

3.1.2 Coral symbioses

In this project, we investigate the diversity and functions of microbial symbionts associated with coral animals. During FY2021, we created a global data set of coral DNA samples and used amplicon and shotgun metagenome sequencing to reveal the distribution of their associated bacteria and eukaryotes across regions with different seawater conditions. Our results show that Palythoa corals are associated with dinoflagellate species of the genera Cladocopium, Durusdinium and Symbiodinium (Santos et al., In prep; Figure 5). Coral samples from the Atlantic and Indo-Pacific differ in their dinoflagellate composition. Stress-tolerant symbionts (e.g., Durusdium) were found associated with corals from the Red Sea and Iotorishima Island, Japan (warmest seawater temperature and low pH seawater conditions, respectively). Among bacterial genera, the most common was the likely mutualistic Endozoicomonas (Figure 6). Interestingly, some coral species also hosted likely pathogenic bacteria from the Vibrio genus.

3.1.3 Cell biology and genomics of scale insect symbioses

During this FY, we sequenced and analyzed metagenomes from over 40 scale insect species and reconstructed the evolution of symbioses in this insect group (Choi and Lee, Systematic Entomology 2022; Choi et al., In prep.). For selected species maintained in our unit as laboratory colonies, we used electron microscopy, confocal microscopy, microCT, and metabolomics to understand the functional role of the symbioses in detail.

3.1.5 Genomics of parasitic and mycoheterotrophic plants

In this collaborative project with prof. Kenji Suetsugu (Kobe University), we provide our expertise in eukaryotic genomics and plastid evolution. For example, Balanophora species (B. fungosa; Figure 10) are parasitic plants with extremely reduced plastid genomes which are also the most AT-rich plastid genomes reported so far (Figure 9). During this FY, we sequenced and analyzed plastid genomes of 14 parasitic and mycoheterotrophic plants from Okinawa and mainland Japan (Svetlikova et al., In prep.).

4. Publications

4.1 Journals

4.2 Books and other one-time publications

Nothing to report.

4.3 Oral and Poster Presentations

5. Intellectual Property Rights and Other Specific Achievements

6. Meetings and Events

6.1 Seminar: Biology of apicomplexans and dinoflagellates

7. Other