Researchers have developed a set of oil-degrading bacteria and fungi isolated from corals that could offer a less toxic alternative to chemical remediation of oil spills.

Similar to dish detergent on a greasy pan, chemical dispersants break down oil slicks into smaller droplets, but this process mixes toxic compounds into the water, which can harm corals and other marine life. In a study published May 21 in Microbiome, researchers found that a probiotic microbial consortium was more effective than a commonly used dispersant at degrading oil — but unlike the dispersant, the probiotics were not toxic to corals and did not alter their microbiomes.

Corals are marine animals that form reefs — complex ecosystems that provide habitats for thousands of other species. Many corals house food-producing photosynthetic algae symbionts in their tissues and are also teeming with microorganisms that collectively form the microbiome.

"Just like us, corals have many microorganisms: viruses, fungi, yeast, bacteria," said Denise Silva, one of the study's lead authors and the manager of Rebecca Vega Thurber's microbiology lab at Oregon State University, who started this work as a Ph.D student at Federal University of Rio de Janeiro. "Some microorganisms can be opportunistic and cause disease, but in most cases, these microorganisms help the coral, just like we have bacteria in our gut that have important functions." 

Beneficial gut bugs have a hand in many aspects of human health, a finding that has led to development of, for example, fecal microbiota transplants for treating conditions such as obesity and gastrointestinal diseases. A recent study found that, more than ever before, people are downing more probiotics — live microbes — in supplements and in foods such as kombucha and yogurt.

Probiotics could have uses beyond people as well, according to Silva. Previous research from some of the study's authors found that beneficial bacteria from corals can protect the animals from temperature stress and disease, and other bacteria can degrade oil, suggesting that probiotics could be a better alternative to chemical dispersants such as Corexit, a product that is widely used for remediation of oil spills.

Other work with soil microbes found that a mixture of fungi and bacteria broke down oil better than bacteria alone, which led Silva and her colleagues to suspect that a consortium of different microbes could be a good approach to developing coral probiotics for oil bioremediation. 

The researchers collected fragments of two coral species — Millepora alcicornis and Siderastrea stellate — from reefs near Rio de Janeiro. To isolate oil-degrading fungi and bacteria, the team extracted microbes from the corals and grew them in media supplemented with crude-oil fractions. The final probiotic consortium included six strains of bacteria and three strains of fungi that didn't inhibit each other's growth and weren't known to be harmful to corals.  

Next, the researchers set up a seawater tank experiment to test how M. alcicornis fared under different conditions. To mimic remediation after an oil spill, they applied crude oil to seawater tanks, followed by Corexit, probiotics, both or neither. They also tested tanks with just dispersant, just probiotics or both dispersant and probiotics. Finally, they left one set of tanks as plain seawater as a control. 

In agreement with other studies, the team found that Corexit, whether applied alone or with oil or probiotics, caused visible bleaching, which occurs when corals expel symbiotic algae in response to stress. As a result, corals exposed to the dispersant had much lower photosynthesis rates than controls after four days, and many of the corals died.

Corexit was much more harmful to corals than oil alone. Compared with corals in plain seawater, those exposed to oil had only somewhat reduced photosynthesis rates and were slightly paler, evidence of bleaching.

When the probiotic consortium was applied after oil, photosynthesis rates and coral color were similar to that of control corals. 

The researchers suggest that the dispersant could harm corals both directly and by disrupting the microbiome. Corals treated with Corexit had higher levels of bacteria associated with stress and disease and lower levels of beneficial bacteria, while those treated with oil or probiotics had similar microbiomes to control corals. 

"This is the first work that explores how the dispersant can affect the microbiome of corals," Silva told The Academic Times. "The dispersant can really affect the microbiome of the coral and the coral itself very quickly: In just four days, the coral was dead."

The researchers also found that the probiotic consortium was much better at breaking down oil compounds than the chemical dispersant was, supporting the idea that these microbes could be a better way to clean up oil in the environment. 

"Major oil spills, like that which occurred in Brazil in 2019 that affected 2,000 kilometers [1,243 miles] of the coast, are very hard to take out of the environment. It can take decades to take out of the environment, so it's persistent pollution," Silva said.

In addition to major oil spills, smaller spills occur very frequently, but they often go unreported, she added.

According to the researchers, coral probiotics could be used to remediate environmental oil contamination in the future, but more work is needed to scale-up their approach for use in natural systems and assess any potential risks.

The specific probiotic consortium for remediation of oil spills would depend on the coral species in nearby reefs, Silva said. The study lays out methods that could help select appropriate microorganisms from other corals. 

"Each coral has its own microbiome, and each coral reef has different species of corals," she explained. "In Brazil, we have many endemic species of corals. I can't apply the same probiotic, for example, in Australia, because [the species there are] different."

Coral reefs are not only biodiversity hot spots; they are also important for reducing flooding risk in coastal communities. But many corals around the world are threatened by climate change and human development, which puts them at greater risk of being smothered by sediment and bleaching.

But it's not all bad news for corals. A recent study suggested that many coral species are so widespread that extinctions are less likely than some people had feared, and another group of researchers developed coral cell lines, which they say could simplify lab-based research on these animals.

The study, "Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites," published May 21 in Microbiome, was authored by Denise P. Silva and Rebecca L. Vega Thurber, Oregon State University; Helena D.M. Villela, Gustavo A.S. Duarte, José Roberto Ribeiro, Angela M. Ghizelini, Caren L.S. Vilela, Phillipe M. Rosado, Carolline S. Fazolato, Erika P. Santoro, Flavia L. Carmo and Caio T.C.C. Rachid, Federal University of Rio de Janeiro; Henrique F. Santos, Fluminense Federal University; Dalton S. Ximenes and Adriana U. Soriano, Leopoldo Américo Miguez de Mello Research Center; and Raquel S. Peixoto, Federal University of Rio de Janeiro and King Abdullah University of Science and Technology.