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Why Are Coral Reefs Dying?

Corals are integral to the health of the entire ocean ecosystem and beyond. But a host of threats have put coral reefs at risk of worldwide collapse within the next decade. Coral probiotics are being explored to restore our planet’s reefs.

5 minutes
13 Citations
Coral Reef HealthWhy Are Coral Reefs Important?What is Coral Bleaching?How Can We Restore Coral Habitats?Probiotics for CoralsCitations

Coral reefs are home to a bustling ecosystem of colorful corals, sea sponges, crustaceans, mollusks, fish, sea turtles, and dolphins. Supporting nearly 25% of all marine life, they are one of the most biodiverse ecosystems on our planet. These otherworldly structures are a sprawling metropolis of vivid colors and species many of us only get to encounter through pictures. But invisible to the naked eye, reefs are also thriving with microscopic life—a collection of bacteria, algae, viruses, and single-celled protists that play a role in everything from providing energy to protecting against pathogenic invaders. 

The health of the coral reef ecosystem is directly linked to the health and diversity of the organisms (both visible and invisible) that live there.1 Unfortunately, a host of threats are lessening the biodiversity and balance of the entire system as a whole. Rising ocean temperatures, ocean acidification, overfishing, and pollution are disrupting this delicate balance, putting reefs at risk of worldwide collapse within the next decade2—a domino effect that begins on the microscopic level, with symbiotic algae, and ripples outward to each member of the reef community.

While corals only cover ~0.1% of the ocean floor, their impact extends past their individual reefs and well beyond the ocean’s shores…to us.3 

Our ocean’s coral reefs are more than just an essential ecosystem for marine life. Coral reefs are important for human health too, as they are instrumental to global economies as a source of employment and income, food, and even medical therapeutics.4 They also help protect coasts (and coastal communities) from harsh waves and tumultuous hurricanes.5

The disappearance of reefs has a vast economical, medical, and humanitarian impact on the world and the species existing at the edges of the ocean.


But, why are coral reefs dying?

The decay of coral reef ecosystems is heavily induced by global-scale climate change that is altering their environment and making it difficult to thrive.6 

One of the many problems: ocean acidification as a result of absorbing CO2 from the atmosphere.

Let’s break it down: One of the ocean’s many roles is absorbing carbon dioxide from the atmosphere. In recent years, following an increase in anthropogenic greenhouse gas emissions, this absorption has increased significantly, changing the chemical compositions of oceanic waters and making them much more acidic. This pH imbalance happens when carbon dioxide mixes with water to create carbonic acid, a compound that impacts certain species’ ability to form structural skeletons and shells (think oysters, mussels, clams, and corals). 

Ocean acidification is just one of the myriad symptoms of climate change impacting the world’s oceanic ecosystems like coral reefs and the actual animal itself, coral polyps. Coupled with rising water temperatures, pollution, and disease, many of the world’s reefs are suffering from coral bleaching events that threaten to collapse entire reef systems and the organisms that live within, around, and beyond them.

As humans, we rely heavily on the microorganisms that thrive inside us to support our health, protect us from pathogens, and even generate important metabolites for our bodies. This symbiotic relationship is very similar to the partnership coral reefs have with their own resident microorganisms. But in the case of coral reefs, they are particularly connected to a type of photosynthetic algae called zooxanthellae that live inside their tissues.7 Coral reef structures provide excellent housing for these microscopic algae that in return, support corals with upwards of 95% of their nutrients and oxygen.8 Much like our own microorganisms, this beneficial relationship serves the best interest of both parties, and the success and livelihood of coral reefs are entirely dependent on this delicate partnership.


comparison of coral when healthy, stressed and bleached


When changes to their environment do occur, corals can become stressed, and expel their symbiotic algae. Without these vital symbionts, corals are left with just their translucent polyps and bright white skeletons. This is known as coral bleaching. When corals bleach, they are not dead (yet), but bleaching disturbs the delicately balanced symbiosis between corals and the assemblage of microorganisms that live on and in them. This dysbiosis makes corals more vulnerable to threats like disease and starvation9, and increases their risk of death.

Just as probiotics are studied to improve human health, probiotics are being explored as a solution to support and improve the health of coral reefs.

Leading the forefront of this new area of research is Dr. Raquel Peixoto—coral microbiologist, Associate Professor at King Abdullah University of Science and Technology (KAUST), and Seed Scientific Advisor. Dr. Peixoto and her team are uncovering the role of the microbiome in coral health and disease, and developing new microbial approaches (such as coral probiotics) to counter the threats corals are facing and rehabilitate these essential systems.

A looping gif of Dr. Peixoto waving under water

At the core of Dr. Peixoto’s research: Beneficial Microorganisms for Corals (or BMCs).

Just like you, coral has a microbiome. And some of its microbes are known to aid in their ability to adapt to changing environments. These health-promoting microbes can be applied to corals as probiotics (also referred to as Beneficial Microorganisms for Corals). Also like humans, the coral microbiome is diverse and dynamic. It can change dramatically across locations, species, age, and stress levels. This makes it difficult to identify which microbes are doing what, and which could be harnessed to create BMCs. Furthermore, the actual effect BMCs have on corals, and whether they can increase coral survival, was previously unknown. That’s where Dr. Peixoto comes in. 

Using controlled experimental setups, Dr. Peixoto and her team have closely investigated the effects of thermal stress on corals, and pinpointed key microbial players involved in making corals more tolerant to oceanic temperature change.10

More recently, Dr. Peixoto has been administering these key live microbes (that were shown to support corals’ ability to fight pathogens, recycle nutrients, clear waste, and protect against UV rays.11,12) to coral reefs in the Red Sea. This research, as well as the development of technology to successfully deliver these coral probiotics, is still underway. 

Much of this work, in addition to other reef-related experiments, is being conducted in KAUST’s newly inaugurated Coral Probiotics Village—a permanent underwater lab also located in the Red Sea. The coral village can be closely monitored, and offers all the natural conditions necessary for experimentation (as opposed to simulated reefs in an above-shore lab), making it an ideal place for this kind of research to take place.

looping gif of the underwater probiotic village

Dr. Peixoto and her team are also using this uniquely biodiverse space to build a repository of microbes. This microbial collection will serve as a biobank of diverse marine microbes—a bank that will hold vast potential for mining microbes that could mitigate the effects of environmental stress and promote restoration and rehabilitation for marine ecosystems.

As climate change continues to impact the far reaches of the world, coral reefs are just one in the growing list of concerns. Dr. Peixoto’s research shows yet another example of how microbial solutions could now be used to recover ecosystems impacted by human-induced activity. And as we continue to expand our knowledge of these complex symbiotic partnerships, we can begin to rebuild for a more resilient tomorrow.


  1. Komyakova, V., Jones, G. P., & Munday, P. L. (2018). Strong effects of coral species on the diversity and structure of reef fish communities: A multi-scale analysis. PloS one, 13(8), e0202206.
  2. Knowlton, N., Grottoli, A.G., Kleypas, J., Obura, D., Corcoran, E., de Goeij, J., Felis, T., Harding, S., Mayfield, A., Miller, M., Osuka, K., Peixoto, R., Randall, C.J., Voolstra, C.R., Wells, S., Wild, C., & Ferse, S. (2021). Rebuilding Coral Reefs: A Decadal Grand Challenge. International Coral Reef Society and Future Earth Coasts, 56 pp.
  3. Hoegh-Guldberg, O., Mumby, P. J., Hooten, A. J., Steneck, R. S., Greenfield, P., Gomez, E., et al. (2007). Coral reefs under rapid climate change and ocean acidification. Science (New York, N.Y.), 318(5857), 1737–1742. 
  4. Osinga, R., Schutter, M., Griffioen, B., Wijffels, R. H., Verreth, J. A., Shafir, S., Henard, S., Taruffi, M., Gili, C., & Lavorano, S. (2011). The biology and economics of coral growth. Marine biotechnology (New York, N.Y.), 13(4), 658–671.
  5. Harris, D. L., Rovere, A., Casella, E., Power, H., Canavesio, R., Collin, A., Pomeroy, A., Webster, J. M., & Parravicini, V. (2018). Coral reef structural complexity provides important coastal protection from waves under rising sea levels. Science advances, 4(2), eaao4350.
  6. Heron, S. F., Maynard, J. A., van Hooidonk, R., & Eakin, C. M. (2016). Warming trends and bleaching stress of the world’s coral reefs 1985-2012. Scientific reports, 6, 38402.
  7. Mieog, J. C., Olsen, J. L., Berkelmans, R., Bleuler-Martinez, S. A., Willis, B. L., & van Oppen, M. J. (2009). The roles and interactions of symbiont, host and environment in defining coral fitness. PloS one, 4(7), e6364.
  8. Muscatine L. The role of symbiotic algae in carbon and energy flux in reef corals. In: Dubinsky Z, editor. Ecosystems of the World 25, Coral Reefs. Amsterdam: Elsevier; 1990. pp. 75–87.
  9. Nielsen, D. A., Petrou, K., & Gates, R. D. (2018). Coral bleaching from a single cell perspective. The ISME journal, 12(6), 1558–1567.
  10. Peixoto, R. S., Rosado, P. M., Leite, D. C., Rosado, A. S., & Bourne, D. G. (2017). Beneficial Microorganisms for Corals (BMC): proposed mechanisms for coral health and resilience. Frontiers in microbiology, 8, 341.
  11. Thompson, J. R., Rivera, H. E., Closek, C. J., & Medina, M. (2015). Microbes in the coral holobiont: partners through evolution, development, and ecological interactions. Frontiers in cellular and infection microbiology, 4, 176.
  12. Peixoto, R. S., Rosado, P. M., Leite, D. C., Rosado, A. S., & Bourne, D. G. (2017). Beneficial Microorganisms for Corals (BMC): proposed mechanisms for coral health and resilience. Frontiers in microbiology, 8, 341.