Coral Reef Microbiome

About this book

Microorganisms, the catalysts of all biogeochemical cycles on Earth, are the origin and essence of life – an invisible yet powerful force sustaining all living organisms. The health of both individual organisms and ecosystems critically depends on functional microbiomes that drive essential processes such as nutrient cycling, pathogen control, detoxification, and resilience. However, like their macroorganism counterparts, these beneficial microbes are vulnerable to environmental changes, and their decline often accelerates ecosystem degradation.

Anthropogenic impacts have profoundly altered and often degraded most ecosystems and their microbiomes, with coral reefs being no exception. Stony corals, the foundation of these vibrant ecosystems, are among the most threatened marine organisms. Shifts in coral microbiomes toward dysbiotic (harmful) assemblages are increasingly recognised as both a cause and consequence of coral mortality. In response, active intervention strategies are being developed to restore and rehabilitate degraded microbiomes, aiming to restore and re-establish the beneficial microbial communities that sustain the health of both their host organisms and ecosystems.

The success of these approaches depends on our understanding of the distribution, ecological roles, and interactions between corals and their associated microbiomes, as well as how environmental factors influence them and their potential to either amplify or mitigate anthropogenic impacts. This book delves into these topics, examining how they shape coral holobiont assemblages and offer pathways for active intervention. In addition, this book provides a practical, tailored, and adaptable roadmap for stakeholders to integrate the latest insights into a broader One Health framework and ecosystem perspective.

Contents

Part I. Introduction
Chapter 1. Introduction to Coral Reef Microbiome

Part II. Microbial Compartments in the Reef and Coral Holobiont
Chapter 2. Microbial Compartments in the Reef and Coral Holobiont - Symbiodiniaceae
Chapter 3. Bacteria and Archaea within Coral Reef Ecosystems
Chapter 4. Coral Skeleton Dwelling Endolithic Algae: Ostreobium and Its Biology
Chapter 5. Microbial Compartments in the Reef and Coral Holobiont - Viruses
Chapter 6. Microbial Compartments in the Reef and Coral Holobiont - Fungi and Fungi-like Entities

Part III. Emergent Complexity
Chapter 7. The Coral Holobiont
Chapter 8. Complexity of the Coral Microbiome Assembly

Part IV. Ecosystem-Scale Microbiology
Chapter 9. Microbial Processes and Nutrient Uptake in the Coral Holobiont and Reef Ecosystems
Chapter 10. Ecosystem Microbiology of Coral Reefs
Chapter 11. Coral Reef Microbialization and Viralization Shape Ecosystem Health, Stability, and Resilience

Part V. Host-Microbial Interactions as Culprit and Remedy
Chapter 12. When Microbial Interactions Go Wrong: Coral Bleaching, Disease, and Dysbiosis
Chapter 13. Microbial-based Therapies to Restore and Rehabilitate Disrupted Coral Health
Chapter 14. Considerations, Ethics and Risk Assessment for the Development and Application of Microbial-based Therapies; Introducing a Rights-based Framework for Reef Communities

Part VI. Microbiome Biotechnology and Future Outlook
Chapter 15. Beyond Restoration: Coral Microbiome Biotechnology
Chapter 16. Building Coral Reef Resilience through Assisted Restoration

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Biography

Prof. Raquel S. Peixoto is a microbial ecologist investigating the diversity, ecological role, and biotechnological potential of microorganisms associated with marine organisms. Her pioneering work has outlined the protocols and proven the concept that the use of microbial therapies and coral probiotics is possible and can increase a host's resilience and resistance against environmental threats. She is currently the President of the International Society for Microbial Ecology (ISME) and focuses on highlighting the importance of microbes to promote organism and ecosystem health and fight climate change and their impacts, as well as the key role of microbiologists in planetary health discussions.

Prof. Christian R. Voolstra holds the Professorial Chair of Genetics of Adaptation in Aquatic Systems at the University of Konstanz. His most recent research particularly advanced knowledge of how the microbiome contributes to coral acclimation/adaptation and the delineation of standardised analytical methods (SymPortal, CBASS short-term acute thermal assays, Coracle, etc.) to hasten the development of approaches to mitigate climate change. He is an advocate of open science, open access, and free data sharing. He is currently the President of the International Coral Reef Society (ICRS), stressing the urgency of developing and applying science-based solutions to coral reef restoration following a rigorous, evidence-based decision framework.