"Shedding" Light on the Microbiome

“Shedding” light on the Microbiome

By Lauren Quinn Photos by James F. Quinn

Visitors to Chicago’s Shedd Aquarium are naturally drawn to the dolphins and smiley white beluga whales that make the 3-milliongallon Abbott Oceanarium their home. People crowd against the railings, waving and grinning at the chirping belugas, or go below to watch dolphins plummet and glide through the blue depths.

When the visitors are ready to say goodbye to their new cetacean friends, many head up the steps toward a gift shop and the dramatic floor-to-ceiling Caribbean Reef exhibit. Few notice the doors to the left, through which something equally dramatic—if less visually stunning—is happening.

Through those doors, scientists are discovering microscopic creatures that live inside, on, and around every animal in the aquarium and in aquatic habitats in the wild. The first-of-its-kind project is designed to improve the health of aquatic animals at Shedd and around the world.

MARINE MAMMAL MICROBES

The microbiome—the unique collection of bacteria, fungi, and viruses that lives in and on every animal body, including yours—is having a moment. In recent years, scientists have made discoveries linking the human microbiome to everything from inflammation to cancer to brain function. But far fewer researchers are investigating the role of the microbiome in animal health.

Angela Kent, a microbial ecologist and professor in the Department of Natural Resources and Environmental Sciences, might argue that aquatic animals make ideal subjects for microbiome research. After all, they swim in a literal sea of microbes, some of which have formed intimate partnerships with the animals for their mutual benefit. The finely tuned and complex system is difficult to study, much less replicate in highly managed, artificial environments like public aquariums, but Kent and her Shedd collaborators are trying to do both.

Take the cetaceans. About a decade ago, Kent got involved in a project to investigate how the Abbott Oceanarium compares to the true ocean habitat of belugas and dolphins. In terms of the microbiome of the water, the oceanarium was less diverse.

“Shedd follows federal regulations to keep the habitats clean with frequent water changes, but that means the microbes never had a chance to establish. The dolphins and belugas were healthy, but we know from human studies that being ‘too clean’ can keep our immune systems from receiving beneficial stimulation,” Kent says.

Aquarium staff decided to replace some of the water going into the oceanarium with nitrogen-rich water that would typically have been discarded from marine fish tanks throughout the aquarium.

Kent explains that because cetaceans breathe air, not water, they aren’t bothered by a little extra nitrogen in the water. Instead, the nitrogen allows certain beneficial microbes to flourish.

“Now the microbial diversity in the cetacean habitat is similar to what you’d see in the ocean, so everyone wins! And we’re conserving water as well,” she says.

To follow up on this move, Kent suggested cycling the water temperature in the oceanarium to mimic natural seasonal variations in the ocean.

“Temperature is a primary ecological driver of the microbial community, so we see annual cycles of microbial communities in the oceanarium now, too. Using ecological drivers to optimize the microbiome for these animals was a really creative use of microbial ecology,” she says.

“Now the microbial diversity in the cetacean habitat is similar to what you’d see in the ocean, so everyone wins! And we’re conserving water as well.”

INTO THE WILD

The Shedd Aquarium Microbiome Project optimizes animal health by working to understand and manipulate the aquatic microbiome, but the project isn’t confined to Shedd Aquarium. Participating scientists are working on projects at zoos and aquariums, as well as in wild habitats, around the country.

During a seven-month sabbatical at Shedd last year, Kent learned about an ongoing project in the Pacific Northwest that she thought could use some help from a microbial ecologist. Zoos in Washington, Oregon, and California were working together to save the Western pond turtle from extinction.

The little turtle, once common in rivers and ponds along the west coast of North America, began to decline dramatically starting in the 1980s due to habitat destruction, disease, and predation by nonnative bullfrogs and sport fish. Several area zoos started bringing turtle eggs to “head start” habitats in their facilities, where babies could hatch and grow large enough to avoid being gobbled up when returned to the wild. The program was successful for over 20 years, but then it hit a snag.

“The population had been recovering very well, but recently the turtles have been coming down with a shell fungal disease that decomposes the keratin of their shells and causes ulcers,” Kent explains. “We thought, what if we could manipulate the head-start environment to give the animals some protection from this disease?”

The first step is to understand whether the microbiomes of healthy and diseased, wild and human-reared turtles differ. NRES master’s student Monique Hazemi is heading up a study to answer that question. She spent the summer swabbing wild and head-start turtles in Oregon and Washington and analyzing their microbial makeup through DNA sequencing in the Shedd Aquarium Microbiome Project’s laboratory.

Hazemi suspects that, as was once true of Shedd’s oceanarium habitat, the turtles’ head-start environments might be too clean.

“Because of the disinfecting and frequent water changes, microbial communities that might have a protective effect against pathogens can’t sustain themselves,” she says. “But Seattle’s Woodland Park Zoo is trying a new biofilter system. If we find that it allows beneficial microbes to sustain themselves, then other head-start programs can implement similar systems and give those turtles the edge they need.”

Back at Shedd, Kent says the aquarium's microbiome project is really highlighting the importance of the microbiome and its management in maintaining animal health. “We’re showing it’s a critical part of the care we provide these animals.”

As the belugas frolic and dive in their finely tuned microbial sea, it would seem they couldn’t agree more.

Several area zoos started bringing turtle eggs to “head start” habitats in their facilities, where babies could hatch and grow large enough to avoid being gobbled up when returned to the wild.