Hurricanes and waterspouts. Bone-chilling rain and 100 degree Fahrenheit temperatures. Jellyfish and fire coral stings. Broken toes, shoulders, knees and fingers. Entanglements in fishing gear and stranded boats. Cockroaches, mosquitoes and sandflies. Hundreds of SCUBA dives and thousands of hours underwater. And to end it all, mountains of very different kinds of data to integrate.

These are just a few of the challenges we ran up against on our four-year endeavor to ask the the not-so-simple question: “How do three human factors – overfishing, pollution and climate change – intersect to cause the decline of coral reefs?”

By looking at the microbial communities that live on corals, our research uncovered a crucial role that fishes play in protecting coral reefs. We also discovered that these fishes together with clean water may be a vital buffer against the coral disease and decline caused by climate change-induced warming ocean waters.

Coral reef decline and human impacts

You may have seen that the plight of the world’s coral reefs, pinnacles of marine biodiversity, has been in the news a lot lately.

Currently, El Niño-driven increases in ocean temperatures are causing a third worldwide coral bleaching event. Australia’s Great Barrier Reef, one of most protected and largest coral reefs in the world, may lose a third of all its corals. Jarvis, a remote U.S.-protected island, is suffering an unimaginable 90 percent coral mortality.

While this recent bad news for reefs is eye-catching, coral reefs have been in trouble for a long time. Many reefs around the world have seen gradual declines in corals over the past two to three decades.

Becky Vega Thurber , Author provided

The decline in corals has many culprits, but they can be classified as two major kinds, local and global stressors. Local stressors involve aspects of human activity that impact reefs on a small regional scale, while global stressors can impact reefs over the entire planet. Local stressors are things like overfishing, pollution and sedimentation from coastal development; they may kill corals all by themselves.

But these local factors never occur in a vacuum. It is likely these local human impacts combine with the ubiquitous ongoing global stressors such as warming oceans and ocean acidification that drive the huge bleaching events we are witnessing today. Yet although we know they occur simultaneously, scientists have rarely investigated the effects of these combined local and global stressors on coral reefs, outside of simplified and unrealistic lab-based experiments that are generally short in duration.

Also, most coral reef research has emphasized the effects of these human stressors on the conspicuous animals and plants that live on a coral reef. In our study, we chose to focus on the microscopic marine life and its role in coral health.

Over the last two decades, scientists have come to understand that all multicellular organisms have evolved with a variety of microorganisms. Much like the microbes that live on and in healthy humans, this “microbiome” of corals helps gather important nutrients and minerals and fight off infection from pathogens. Major changes in the microbiome, in humans, corals, or other organisms, are thought to be detrimental because they can switch a system from a healthy “stable” state to a diseased one.

Thus, we (a coral microbiologist and marine community ecologist) sought to combine the expertise and field work experience of our labs to test the effects of both local and global stressors on corals as well as their microbiomes.

Our reasoning was that by physically changing conditions on areas of reef over the long term, we could monitor what would occur naturally in the system across seasons, and also see how effects at one level of complexity (macroorganisms – that is, the corals) transcended down to another level of complexity (microorganisms).

Vital role of herbivorous fishes

We tackled these questions by running a three-year field experiment that mimicked overfishing (using fish-exclusion cages) and nutrient pollution (via the addition of common garden fertilizer) on a coral reef in the Florida Keys, U.S. To do this we had to build and maintain the experiment underwater for three years, which required continuous upkeep of our cages and resupply of the nutrients every few weeks. We closely monitored the health and growth of corals and seaweeds in our experiment four times a year and evaluated the microbiomes of about 80 corals monthly.

Using this experimental design, we wanted to examine how two of the most common stressors on reefs – overexploitation of important species like herbivorous fishes (i.e., fishes that eat seaweeds) and nutrient pollution – affect the microbes that live on corals and, ultimately, the health of corals.

Rebecca Vega Thurber , Author provided

Lots of previous work shows that herbivorous fishes, especially parrotfishes, are important for helping corals reproduce, grow and survive because they consume seaweeds that can outcompete, smother or even poison corals.

Our work reinforced that these herbivorous fishes protect reefs by preventing coral-seaweed competition. But we also showed that the loss of these fishes ultimately led to the subsequent disruption of the coral microbiome.

When we removed herbivorous fishes from reefs, coral-seaweed competition increased, which led to declines of some of the beneficial bacteria on corals, including bacteria that produce antibiotics to keep harmful pathogenic bacteria at bay.

Importantly, the presence of herbivorous fishes appeared to buffer some of the negative effects of ocean warming on corals. We knew this because thermal stress led to the disruption of coral microbiomes and coral death only after herbivorous fishes had already been removed. In other words, during the warmest summer and fall months of the year, 95 percent of corals in areas with abundant fishes survived and in fact grew. But if we removed fishes, almost 40 percent of corals succumbed to seaweed competition and thermal stress and died.

Nutrient pollution turns fishes into coral killers

Although parrotfishes are important herbivores that help keep reefs clean of seaweeds, many of them periodically supplement their diets by biting corals. In our experiment 100 percent of the corals survived these periodic bites just fine under low nutrient conditions, demonstrating that parrotfishes are an overwhelmingly positive force for helping corals persist on reefs.

One of the most surprising and perhaps worrisome elements uncovered by our study was how nutrient pollution – such as from agricultural runoff or sewage discharge – changed the impact of parrotfish bites on corals.

Rebecca Vega Thurber , Author provided

In the presence of nutrient pollution, 66 percent of corals died after being bitten by parrotfishes. These corals also showed an increase in pathogenic bacteria at the expense of beneficial bacteria following parrotfish bites, possibly leading to coral mortality. The parrotfish wounds likely allowed a space for colonization by new bacteria and then the excess nutrients allowed unregulated growth of these new pathogens.

It is important to note that the parrotfishes here are not the problem. The nutrient pollution is the problem as it changes the nature of a normally beneficial interaction between species on these reefs. This finding is especially concerning as it suggests that even on reefs where parrotfishes are protected from fishing, a common management practice to protect reefs, corals may still be in peril if pollution is not also kept in check.

What do we do to save reefs?

Our work suggests that managing reefs at the local level by protecting important fish species and minimizing pollution can help prevent coral death. Even during the most warmest periods of the year, when temperatures were most stressful, we saw little coral mortality in places where there were abundant fishes and low levels of nutrients.

Becky Vega Thurber , Author provided

Possibly, protecting fishes and minimizing pollution will help protect corals from pathogenic bacteria that kill corals during stressful thermal events. This is especially important in an era of global climate change where ocean temperatures are gradually rising. Our work suggests there is hope for the future of coral reefs.

There is little we can do about the impacts of massive El Niños on coral reefs. These are global anomalies out of our control. But, abundant fishes and clean water may be key to helping coral reefs survive increasingly stressful normal ocean temperatures – at least in the near term. In the long term, to ensure the persistence of coral reefs, curbing carbon emissions and slowing down the rapidly changing climate is essential.