Can corals be saved? The key may be in their microbes

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Can corals be saved? The key may be in their microbes

Biologists are studying corals with techniques designed for humans

Until the 1880s, people thought disease came from noxious air in homes, sewers, or haunted fields. Luckily, a German scientist, Robert Koch, introduced the germ theory and assigned bacteria to specific diseases such as cholera. Since then, we have learned that not all bacteria are harmful. As sequencing technology becomes more accessible, scientists are finding microbes everywhere: on our skin, in our guts, on plant leaves, on dog spit, even inside your coffeemaker. The microbes that we find are both good guys and bad guys – I’d say a majority are actually good guys. Bacteria function in our gut to break down our food and produce vitamins. Bacteria in plant roots protect the plant from disease.

Bacteria are also found in the oceans, both free-floating and living inside marine organisms. That includes coral reefs, where bacteria play equally diverse roles in the health and sickness of corals.

You can tell a coral is sick through visual signs such as black bands, dark spots, and white poxes that differ from the coral’s typically homogenous tissue. Inside this tissue, there are several thousand kinds of bacteria interacting with the coral. I began my PhD career studying diseased corals by measuring the abundance of the bacteria Vibrio, rod-shaped bacteria that are sometimes disease-causing. However, it was frustrating when not all sick corals had a high abundance of Vibrio in their system, or when I found a healthy coral that in fact did have Vibrio living inside of it.

Maite Ghazaleh Bucher

Other coral biologists have similar frustrations. Several bacteria or viruses have been isolated from diseased corals, and only a very small percentage have proven to directly cause a particular disease. I quickly learned that searching for one bacteria that causes a specific disease is close to impossible, especially since there are many bacteria present in both healthy and diseased corals.

So that is exactly what I set out to study for my PhD: the difference in the groups of bacteria that are present in healthy versus sick corals. The questions I try to answer are similar questions that human gut scientists answer: what microbes are present in healthy individuals, what microbes are present in diseased individuals, and what roles do these microbes play in disease development?

Gut microbiologists have discovered that some ailments, like irritable bowel syndrome (IBS), are not caused by a bacterial infection, but by a decrease in the number of good bacteria in the gut. General stress and unhealthy diets can also alter your gut microbiome and potentially cause IBS. 

Maite Ghazaleh Bucher

The bacteria in your mouth, too, maintain a healthy balance between many different types of bacteria that work together toward your oral health. Not flossing and intaking lots of sugar or fast food increases your chances of periodontal disease because you don’t remove the bad guys that thrive in anoxic pockets way down in between your teeth and gums.

There is a good possibility that corals that are getting sick are experiencing a change in their microbiome in a similar way that fast-food eaters experience a change in their gut microbiome: an outside stressor (bad lifestyle habit) shifts the microbiome to an unhealthy state. What if corals are getting sick because the healthy balance of microbes is thrown off by certain environmental stresses? Instead of looking at the presence or absence of a potentially pathogenic bacteria such as Vibrio, I started looking at the entire community of bacteria that live inside healthy and diseased corals.

By applying human microbiome research to coral disease research, I’ve found three patterns of microbiome-related disease that are similar between humans and corals:

  1. Gum disease can be studied by creating a ratio of bacteria correlated with healthy mouths to other bacteria correlated with diseased mouths. Scientists even found that an “in-between” ratio exists in healthy gum tissue of diseased mouths. This means periodontal disease is characterized by a succession in the types of bacteria. This is a promising way to study coral disease, because several papers have compared the entire microbial community between healthy, almost diseased, and diseased corals and have found that all three health statuses of coral have different microbial communities.
  2. Proteobacteria has been observed to abnormally expand in humans with metabolic disorders, inflammation, and cancer. This bloom of Proteobacteria compromises the ability to maintain a balanced gut microbial community. Attempting to describe coral bacteria in this way is also promising – my lab has observed that Vibrio bacteria bloom in Florida Keys water after Saharan dust storms. The Vibrio that rapidly increase in abundance may out-compete the beneficial bacteria from colonizing the coral, and make the coral more prone to getting sick.
  3. People with inflamed sinuses could be missing key bacteria that maintain the peace inside your nose. This causes the microbial network to become fragmented, meaning the microbes don’t function well together anymore. Some coral laboratories have observed Endozoicomonas is abundant in healthy corals but not in diseased corals that might be missing this key member of its healthy microbiome.

Fifty percent of the world’s corals have been lost in the last 30 years, and a shocking 80 to 90 percent of Florida's reefs alone are already devastated due to environmental stress such as warmer waters and nutrient pollution. To save our coral reefs from further destruction, we coral biologists are getting creative with the research connections we make. By using examples in human microbiome research, I hope that we’ll more quickly understand coral disease development and protect our global reefs from future harm.

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Melanie Silvis

Molecular Microbiology

UC San Francisco

I love the comparison you’re making between the human-microbiome health axis and that of another large organism like coral and its associated microbiome! It underlines in a nice way that basically every large living thing is a host to microbial life; or conversely, microbes live anywhere and everywhere they can. 

This piece brought up a few basic questions for me about coral science: 

  1. Are there equivalent tissue/organ distinctions in coral (akin to the human skin vs. gut microbiome) where different species of bacteria are found? 
  2. Do you know of any coral model systems where people can grow and manipulate them in the lab? I would love to know if some/any corals can grow without any bacteria (like germ-free mice which have no microbiome). This could be one approach to testing some of your hypotheses about the causes of coral health/disease because you could manipulate their bacterial contents directly. 
  3. Do you think that the imbalance in some coral systems’ microbiomes is driven by phages depleting “good” bacteria, or environmental changes depleting them, or random spread of “bad” bacteria (like infection)? Probably a mixture of reasons, but what is the current thinking in the field or in your lab on this?

Maite Ghazaleh Bucher responds:

  1. Yes! Corals have different microbial communities that live in/on different parts of the coral. You can find microbes on the surface mucus layer of the coral that is in contact with seawater, inside the corals, on endodermal cells, and on the calcium carbonate skeleton that corals secrete.
  2. The sea anemone Aiptasia is currently the model organism for corals, mainly because they house the same symbiotic algae that are also coral symbionts. Scientists have used it to study the symbiosis between corals and these symbiotic algae since you can make an “algae-free” Aiptasia. I imagine you can dose the anemones with antibiotics and get a close-to-sterile anemone.
  3. It could be all the above! We first need to know how the healthy and unhealthy coral microbiomes differ. Then we need to investigate how the coral microbiome changes when the coral is stressed. This way, we can determine the sequence of events that yields coral disease. My hypothesis is: a coral gets stressed, the microbiome is altered, and pathogens take advantage of the compromised coral.

Cassie Freund


Wake Forest University

I am going to play devil’s advocate here, and I am not doing this to be mean, I promise! But…

Microbiome research is a huge fad in science right now, to the point where I see it as an economic bubble of sorts. The conclusions that can be drawn from microbiome research are correlational at best, without any real connection to conservation action. And the biggest threat to coral reefs right now is climate change, specifically coral bleaching (which is essentially polyp death, right?) in response to high water temperatures. So how will microbiome research help save the corals? Is there some bacteria-temperature interaction that needs to be investigated? 

Temperature seems to be such a strong driver of coral death that I don’t see how a specific microbiome would be able to protect corals from harm, although it may be a factor in susceptibility or in lowering the temperature threshold at which bleaching happens. 

But then, what should we do about it? I say this because I think that a lot of researchers – myself included – occasionally make these grand-but-vague statements about how our work will connect to conservation but that rarely come to fruition, and meanwhile species are rapidly disappearing from this planet.

Maite Ghazaleh Bucher responds:

Great points, Cassie - thanks! First, I wouldn’t be so quick to doubt the relationship between microbiome research and conservation. How can we protect an endangered species if we don’t understand it? The microbiome of animals, such as the coral, is vitally related to its well-being. For example, without microbes in our gut, humans don’t have a way to breakdown certain carbohydrates or make certain vital proteins. To effectively protect corals, we need to understand how they function and what they need to be healthy, especially when they rely heavily on symbiotic microorganisms.

Secondly, you’re right that climate change is the main threat to coral reefs – and it’s a threat that influences coral bleaching and disease. When water temperatures get too hot, the corals get so stressed out that its relationship with its symbiotic algae essentially backfires, and the corals expel their symbiotic algae. They continue to live, but mortality rates of bleached corals are higher, and once they reacquire symbionts, they are more susceptible to disease. Not only that, but climate change via increased water temperatures increases disease prevalence, which relates to the resilience of a healthy microbiome. So as you can see, it’s all connected to the microbiome of the coral that includes all of its symbionts and any intruders that cause disease.

Lastly, I echo your concern that it’s hard to apply microbiome research to directly saving coral reefs. The short answer is that coral microbiome research may not directly help immediate conservation efforts. The long answer is that effective/applicable science is a process that builds upon prior work. Microbiome research helps us understand how and why an organism reacts to environmental stress – which is the first step toward being able to do something about it. 

The threats to corals happen at a massive scale (i.e. reef waters are getting warmer at a global scale). But all this doesn’t mean that there’s nothing we can do! We can build more coral nurseries, decrease CO2 emissions to keep oceans from getting warmer, and mitigate localized pollution. John Bruno, a coral biologist from UNC Chapel Hill, does a great job summarizing what can actually be done right now to prevent coral species from disappearing from this planet.

Jennifer Tsang


Once we identify what constitutes a healthy coral microbiome, would introducing those microbes help diseased coral, or are the microbial community more of an indicator for the state of the coral? If the idea is to introduce microbes to diseased coral, how would colonization be established? There’s been some research on coral transplants for the past few decades that is starting to take off. Would a coral transplant be the way to introduce new microbes?

Maite Ghazaleh Bucher responds:

Yes - I think the microbial community could be used as an indicator for the state of the coral. In fact, it’s what I’m hoping to support in my dissertation. Introducing microbes to help a diseased coral is harder than it sounds, since it’s hard to get a permit to introduce microbes from a lab to the environment, and we have no way of controlling where released microbes go.

Coral transplants are a great way to increase coral cover on a reef, and presumably the coral could interact with the water column and exchange some bacteria with seawater that a nearby coral might pick up. But this is very hard to track since there are lots of microbes, and it’s almost impossible to tell where they are sourced from. But great ideas all around, I hope that the future of coral research heads this direction.