Symbiosis on the Reef: Healthy Relationships Under Stress

It’s no secret that healthy relationships can disintegrate in stressful environments. Like any breakup, the separation between corals and their symbionts can be caused by a multitude of factors, with some relationships proving stronger or more tolerant than others.

A healthy coral reef.Coral reefs are among the world’s most beautiful and biodiverse ecosystems, forged by a series of unlikely partnerships between organisms large and small. Though typically found in nutrient-poor environments, coral reefs are immensely productive and biodiverse, providing habitat for an estimated 25% of marine life. Additionally, reefs serve as nurseries for fish species of commercial value and as hot spots for ecotourism. Yet these ecosystems also face immense pressure on multiple fronts—from climate change and ocean acidification to overfishing and damage by certain sunscreens. In stressful environments, relationships cannot survive, much less thrive. News stories over the last few decades have reported significant losses in coral reefs and described sobering bleaching events associated with corals ejecting their symbionts. This dysbiosis occurs first on a microbial level and, though not initially evident, could result in a deserted, lifeless reef, if not addressed.

Corals And Their Symbionts

Perhaps the best-known relationship on the reef is the one between the tropical stony coral species and Symbiodiniaceae zooxanthellae, photosynthetic algae that provide a source of food for the sessile coral animal. However, corals form relationships with a wide variety of bacteria, algae, fungi, archaea and even viruses, which can be found in the coral’s surface mucus layer, in its tissue and within its calcium carbonate skeleton. For obligate symbionts, like some stony corals (class Hexacorallae) and zooxanthellae, the relationship is essential to survival. In other cases, microbial symbionts provide nonessential, but highly valuable, benefits to the host, like antimicrobial properties or nutrient exchanges. A diverse microbiome can therefore increase a coral’s resilience and provide abundant alternative nutritional sources if symbioses with zooxanthellae break down.

Phylogenetic trees of bacterial strains and coral species.“We know that [bacteria] aid the coral with nutrition and growth, mitigation of toxic compounds or stress, early life development and even pathogen control,” said Dr. Michael Sweet, a microbial ecology professor at the University of Derby’s Environmental Sustainability Research Centre, whose recent paper was the first study to synthesize decentralized data of cultured microbes associated with corals. “Some bacteria increase the bioavailability of iron to the algal symbionts or supply inorganic carbon for the host’s all-important calcification reaction—production of the skeletons which produce the structures that make reefs so important for life in our oceans,” he said.

The strength of the relationship depends on the health of both coral and symbiont. High taxonomic diversity in both partners allows multiple coral-symbiont combinations with unique costs and benefits that influence the overall fitness of the holobiont. Environmental stressors, particularly temperature fluctuations, can quickly disintegrate symbiotic relationships, stressing either the coral or the symbiont to the point that it dies or physically separates from its partner. Some symbionts even have the potential to turn pathogenic if their host becomes vulnerable—endoliths like Ostreobium, a genus of green algae, may begin to break down the internal structure of the coral, eating it from the inside out. Loss of a symbiont can mean loss of a food source, and a weakened immune system that leaves the coral susceptible to disease and death.

A Deeper Dive

Earth contains over 6,000 species of coral, and no 2 relationships are alike, although "closely related species and genera exhibit similar microbiomes," said U.S. Geological Survey research microbiologist Dr. Christina Kellogg, who leads the coral microbial ecology laboratory and has studied both tropical corals and deep-sea corals hundreds of meters below the surface. The work is challenging and cost-prohibitive. Collecting samples from deep-sea corals, which make up the majority of coral species, typically requires submersibles or robotic devices. Kellogg brings the samples to the surface in individual, thermally-insulated containers to minimize contamination and reduce thermal stress responses in the transition.

“All deep-water corals and some mesophotic (middle-light zone) corals lack photosynthetic algal symbionts, so in that sense, they have different microbiomes from tropical reefs,” said Kellogg. “As far as bacteria, there are, in fact, some that are the same across corals, no matter where they are or how they live.” For example, the chemoorganotrophic marine bacterial group Endozoicomonas is commonly associated with tropical coral species and shallow-water Mediterranean gorgonians, but recently Kellogg detected them in deep-water corals. Endozoicomonas exhibits a high amount of genetic and functional diversity and tends to dominate coral microbiomes, suggesting there might be a correlation between symbionts and their coral hosts, similar to the various species of zooxanthellae observed in stony versus soft corals.

Each symbiont likely confers unique benefits on its host species. Kellogg speculates that the non-algal symbionts of deep-sea corals help make carbon and nitrogen cycling as efficient as possible in an environment where nutrient availability is based on unpredictable currents from the surface. “[The corals] don’t know when their next meal is coming, and they don’t know what the quality of it is. How much more important must their microbial companions be?” Kellogg wondered.

A cold-water reef.

Signs of Coral Stress

An obvious sign of stress is coral bleaching—when a coral turns white upon expelling its zooxanthellae, which give the otherwise-clear coral its color. Disease, warming temperatures and cold spells have all been associated with bleaching. Although zooxanthellae can survive in the open ocean, bleaching indicates a very likely death for its coral host, as it enters a starvation period. Establishing what a healthy coral holobiont looks like may help scientists diagnose stress or illness in the early stages, allowing them to intervene before it's too late. However, there are challenges to doing so; each coral species is unique in its baseline measurements, and little data exists thus far. Moreover, as more coral reefs die, there are fewer “healthy reefs” by which to compare findings.

Scientists like biogeochemist Dr. Colleen Hansel are working to identify chemical signatures that serve as early warning indicators of coral stress. Hansel, a senior scientist at Woods Hole Oceanographic Institution, monitors chemicals involved in the physiology and immune systems of corals and the chemical signatures that occur when coral physiology is impaired or stressed.

“For the most part, corals and symbionts have a mutualistic interaction,” Hansel said. “There is evidence that a trigger (can disrupt) that happy situation. One of the members may become pathogenic or initiate antagonistic behavior, such as sequestering nutrients that the coral needs and breaking down that relationship that was critical for keeping the happy ecosystem together. A lot of those interactions are based on chemical exchange.”

One chemical signature that Hansel’s lab focuses on is the reactive oxygen species (ROS) superoxide, a fundamental chemical produced by both corals and their symbionts on a regular basis. Under normal conditions, superoxide plays an important role in cell signaling, reproduction and tissue repair. However, an overabundance of intracellular superoxide, produced in response to sudden stress, leads to the breakdown of DNA and other biomolecules, and ultimately results in death. It has been historically assumed that a disruption in ROS homeostasis by triggering algae to overproduce superoxide causes corals to eject their symbionts. "Since superoxide does not pass biological membranes, the link between superoxide and bleaching is unresolved," said Hansel.

Superoxide has a half-life outside of the cell of only a few seconds, posing a challenge for making in-situ measurements. "By the time water samples are collected and brought to the surface," Hansel said, "the superoxide is long gone." She and her team at Woods Hole, with funding from Schmidt Marine Technology Partners, developed a unique submersible sensor, DISCO, to allow for superoxide monitoring underwater at the source. Using this sensor, the team recently showed that healthy corals make superoxide outside of their cells, which they predict is providing essential physiological roles for the coral and symbionts. A deep-sea version of the technology, SOLARIS, accomplished the first superoxide measurements associated with deep-sea corals and sponges (a paper on this is forthcoming).

“Each coral has a basal level of ROS always present that is part of their normal physiological function," said Hansel. “We need to quantify these baseline values so that when we have measurements over the healthy level, we will know the organism is stressed internally, it is fighting off a pathogen or it’s struggling with tissue degradation.” As ROS are part of the immune system response, elevated ROS production can precede more obvious visual symptoms of stress or disease. “Identifying these signatures and developing low-cost deployable sensors will allow us to implement a global early warning system for coral reef health,” Hansel said. “Let’s do some bloodwork. Let’s take its pulse.”

Developing Solutions to Coral Die-offs

Scientists are still far from understanding the causes of most coral diseases, like the rapidly moving, highly virulent stony coral tissue loss disease (SCTLD) currently decimating Caribbean corals. According to University of North Carolina Wilmington professor Dr. Blake Ushijima, the cause of SCTLD is likely complex, but probiotic treatments composed of microbial cultures from resistant corals may be the solution.

Ushijima found that corals less susceptible to SCTLD are colonized by beneficial bacteria, some of which produce broad-spectrum antibacterial compounds. “At least some of these very specific isolates, if put onto the coral, will actually protect them from disease and sometimes treat the disease directly," he said. “Right now, we are at the stage where [probiotic applications] seem to work in lab and aquarium trials, and we need to see if they can work in the field.” His lab is also currently studying opportunistic infections by the bacterium Vibrio coralliilyticus, a pathogen implicated in a large number of diseases of corals and shellfish. "Though V. coralliilyticus is likely not the cause of SCTLD, it may play a role in coinfections that exacerbate existing SCTLD lesions," he explained.

Map of stony coral tissue loss in Florida.

Kellogg said that the Caribbean/U.S. coral community has responded en masse to the topical pastes impregnated with chlorine or antibiotics and culling diseased colonies. Another effort has involved rescuing unaffected corals from the reefs, then housing them in zoos or aquaria for safekeeping until the disease passes and the reefs can be restored.

Lab settings allow for controlled experiments, although there is no way to replicate the complete holobiont and its dynamics as one could in an ocean environment. A lab does, however, provide a safe area in which to test proposed probiotic treatments before deploying them in the field as tools for reef restoration or conservation. Sweet is now exploring ways to enrich the media with host tissue or mucus, which may unlock more of these symbiotic microbes in culture collections.

Astrangia poculata colonies during the course of treatment.Is recovery possible? Research has shown that the Astrangia poculata microbiome can recover from antibiotic disturbance, and that individuals with algal symbionts reestablish their microbiomes in a more consistent manner compared to corals lacking symbionts. New studies are examining whether symbionts from more heat-resistant corals could transfer heat resistance to more vulnerable individuals, inviting the concept of “microbiome transplantation” treatments using inoculations of homogenized coral tissues. However, these studies are still in the beginning stages.

“There is a cost to inaction,” Sweet said. “Reefs are dying all over the world, and our ‘tool’ can and does help (a little). I always describe our probiotics as a sticky plaster—they can stem the bleeding to some degree (reefs or individual coral colonies dying from bleaching or disease), but it won’t really help unless we deal with the cause of the bleed (climate change). We have shown it works, now it is time to deploy and save a few corals—[those] which may be key to repopulating reefs in the not-too-distant future.”



To protect coral communities, support for microbiome research, data sharing and a collaborative approach that includes residents who depend on the ecosystem are critical. Learn about community approaches to coral conservation and what is needed to:

Save the Coral


Author: Ashley Jones Robbins, MELP

Ashley Jones Robbins, MELP
Ashley Jones Robbins, MELP is the advocacy communications coordinator at the American Society for Microbiology.

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