eDNA methods provide insight into coral reef health in real time

The human gut is full of microbes. Some microbes can make people sick, while others are responsible for balancing gut health. But humans are not the only species whose health depends on these microorganisms. Coral reef ecosystems rely on microorganisms to recycle organic matter and nutrients. These cells also help feed corals and other reef-dependent life.

WHOI researchers studied microbes in coral reef water by examining eight reefs in the US Virgin Islands over a seven-year period that included periods of disturbance from hurricanes and coral disease.

“Coral reefs have been declining for decades. Climate change, hurricanes, disease and other stressors have played a major role in this,” said Cynthia Becker, first author of the study and a recent graduate of the joint MIT-WHOI program.

“Reefs provide habitat for around 25% of all marine species, but also support billions in tourism and fishing. It’s important for us to monitor changes in coral reefs as they happen, and the microbes in their environment can really help us do that.”

The study, Microorganisms Uniquely Capture and Predict Stony Coral Tissue Wasting Disease and Hurricane Impacts on US Virgin Islands Reefs, published in Environmental microbiologyexplains the impact of coral reef disturbances on microbes.

During the two major events studied, Hurricanes Irma and Maria in 2017 and the stony coral tissue loss epidemic that began in 2020, there were increases in ammonium concentration in the water, which led to a 34% decline in Prochlorococcus bacteria . Prochlorococcus is a small photosynthetic bacterium that brings new carbon into the coral ecosystem, keeping them healthy but also producing oxygen for our atmosphere.

“Much of the way we study coral reefs is done at the level of macro-organisms. However, changes in coral and fish communities may remain invisible for months or years. This makes it difficult to track the health of these vulnerable reefs in real time,” said Amy April, a microbial ecologist at WHOI and corresponding author of the study.

“Microbes are the hidden engines of coral reefs, and they grow rapidly and respond to nutrients, temperature, pH and other conditions. By sampling the water, we can see the immediate impacts of disturbances and intervene to support reefs before the situation potentially worsens.”

The researchers used eDNA to analyze the reef’s microbial community. This genomic technique involves collecting samples of reef water, where there are about 1 million microbial cells in each milliliter, and sequencing the microbial DNA in the samples to identify microorganisms. This provides scientists with a non-invasive way to gather near-real-time information about the condition of the reef.

“Understanding the composition of a healthy reef microbial community is important. “Without the balance of micro- and macro-organism health, you cannot have a healthy functioning ecosystem,” Becker said.

“Another benefit of this progress is coral reef restoration efforts. Microorganisms can provide an assessment of ecosystem health. This can complement visual assessments to determine if reef health has been restored.”