Coral reefs around the world have been deteriorating dramatically for at least 20 years. Janelle R. Thompson hopes that a better understanding of the microbes that live in and around coral will help rescue the reefs.

Reefs — besides being popular diving and snorkeling destinations — are part of “nature’s coastal infrastructure,” says Thompson, Gilbert W. Winslow Assistant Professor of Civil and Environmental Engineering. “They provide a nursery for young fish, they protect coastlines from erosion and are extremely important for sustainable fisheries that bolster economic stability.”

Although coral looks like a plant, it’s an animal. Like humans, coral is home to microbiomes — diverse communities of eukaryotes, bacteria, and archea. Researchers estimate that as many as 2,000 different types of microbes co-exist with coral. Separate coral species — there are hundreds — are most likely home to different microbial communities.

Some of the microbes benefit the creature by helping it develop and providing it with food. Some perform photosynthesis, fix nitrogen, or convert carbon dioxide from seawater into sugars the coral needs. Others sicken and kill it.

There are potential benefits to humans and other living things by “linking the identities of microbes to their activities in complex systems,” she says. “This is a critical step toward manipulating microbial systems for pollution degradation, protection against pathogens, and ultimately, preservation of our ecosystems.”


Pollution, massive algae growth, disease, cloudy water caused by increased sedimentation, and higher global temperatures have contributed to coral reef decline from the Caribbean to Thompson’s native Hawaii.

In the turquoise waters off Oahu as a child, coral was sometimes the enemy. “Coral scraped you up when you slipped off your boogie board riding the waves,” she says.

She focused on environmental microbiology (and took up scuba diving) at Stanford University’s Hopkins Marine Station near Monterey. There, she examined marine microbes that inhabit the egg cases of Pacific squid. Joining the MIT laboratory of Martin F. Polz, professor of civil and environmental engineering, in 1999 as a graduate student, she expanded the scope and depth of her research.

Now, in addition to studying water-dwelling microbes, Thompson looks at those that live underground. She explores how subsurface microbes interact with CO2 that has been captured from industrial processes and coal-fired power plants and sequestered underground.

To help investigate the cause of tissue death in coral, Thompson recently visited reefs four miles off Bahia in Brazil’s underwater Abrolhos National Park. She saw coral turning white, the exterior skeleton deteriorating, and the soft tissue underneath eaten away, the victim of a confounding disease that has been attacking coral around the world for the past decade.

Because it can take a year to grow a thumb-sized fragment of coral, Thompson uses as a model the sea anemone Nematostella vectensis. A relative of coral, this organism is plentiful in New England and far easier to grow in the lab. To gather it, Thompson and colleagues wade into the marshes off Sippewissett on Cape Cod. Using a device made from window screens, they scoop up hundreds of the translucent, tentacled, worm-like creatures.

Thompson is one of a handful of researchers employing molecular biological, genomic, and genetic tools to study the expression of genes within the microbes that live in and around anemone and coral. She is seeking a better understanding of what the microbes do for their undersea hosts. Among other things, researchers hope to determine whether the organisms are so closely intertwined because natural selection has defined their relationship or if they are random travelers who go bump in the night.

Researchers are asking the same questions about the human microbiome, which includes our gut-dwelling E. coli bacteria, beneficial in some forms and poisonous in others.


Thompson’s long-range goal is to use the information she uncovers about the coral microbiome as a bellwether for coral reef health. “We want to understand how changes in the surrounding environment shift the balance in the microbiome between one that supports coral life and one that contributes to coral death. We could then use this information to create biomarkers that gauge coral health and its stress or disease susceptibility,” she says.

“Once we know which genes are expressed, we can start to figure out which functions the microbes are mediating in the coral,” Thompson says. “If we knew everything these microbes could do — all the activities they could mediate — that would be completely revolutionary.” Ultimately, the knowledge could save coral reefs.