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Abstract Tropical corals construct the three-dimensional framework for one of the most diverse ecosystems on the planet, providing habitat to a plethora of species across taxa. However, these ecosystem engineers are facing unprecedented challenges, such as increasing disease prevalence and marine heatwaves associated with anthropogenic global change. As a result, major declines in coral cover and health are being observed across the world's oceans, often due to the breakdown of coral-associated symbioses. Here, we review the interactions between the major symbiotic partners of the coral holobiont—the cnidarian host, algae in the family Symbiodiniaceae, and the microbiome—that influence trait variation, including the molecular mechanisms that underlie symbiosis and the resulting physiological benefits of different microbial partnerships. In doing so, we highlight the current framework for the formation and maintenance of cnidarian–Symbiodiniaceae symbiosis, and the role that immunity pathways play in this relationship. We emphasize that understanding these complex interactions is challenging when you consider the vast genetic variation of the cnidarian host and algal symbiont, as well as their highly diverse microbiome, which is also an important player in coral holobiont health. Given the complex interactions between and among symbiotic partners, we propose several research directions and approaches focused on symbiosis model systems and emerging technologies that will broaden our understanding of how these partner interactions may facilitate the prediction of coral holobiont phenotype, especially under rapid environmental change.
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This content will become publicly available on June 1, 2026
Leveraging Functional Genomics and Engineering Approaches to Uncover the Molecular Mechanisms of Cnidarian–Dinoflagellate Symbiosis and Broaden Biotechnological Applications
Functional genomics is a powerful approach for uncovering molecular mechanisms underlying complex biological processes by linking genetic changes to observable phenotypes. In the context of algal symbiosis, this framework offers significant potential for advancing our understanding of the molecular interactions between marine dinoflagellates and their cnidarian hosts, such as corals—organisms that are foundational to marine ecosystems and biodiversity. As coral bleaching and reef degradation intensify due to environmental stressors, novel strategies are urgently needed to enhance the resilience of these symbiotic partnerships. This opinion piece explores emerging directions in functional genomics as applied to coral–algal symbiosis, with a focus on uncovering the molecular pathways that govern photosynthesis and stress tolerance. We discuss the challenges and opportunities in applying functional genomics to support coral health, improve ecosystem resilience, and inform biotechnological applications in agriculture and medicine. Together, these insights posit the potential for engineered symbioses as a needed focus in mitigating biodiversity loss and supporting sustainable ecosystem management in the face of accelerating environmental change.
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- Award ID(s):
- 2308644
- PAR ID:
- 10634406
- Publisher / Repository:
- Multidisciplinary Digital Publishing Institute
- Date Published:
- Journal Name:
- Phycology
- Volume:
- 5
- Issue:
- 2
- ISSN:
- 2673-9410
- Page Range / eLocation ID:
- 14
- Subject(s) / Keyword(s):
- functional genomics marine symbiosis cnidarian dinoflagellate photosynthesis biotechnological applications
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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