Article image

Microbes reveal the health of coral reefs in real time

Coral reefs are like the bustling cities of the ocean that house a quarter of all marine species, including countless microbes. These reefs boost economies by supporting tourism and fisheries that adds billions to global economies.

However, these vital ecosystems are currently facing unparalleled threats. The combined pressures of climate change, disease, and various stressors have contributed to their consistent decline.

In response to this crisis, researchers from the Woods Hole Oceanographic Institution (WHOI) have embarked on a remarkable study. The experts have turned their attention to an unexpected ally for real-time monitoring of reef health: the microbes inhabiting these aquatic environments.

Microbes role in coral reef survival

Cynthia Becker, a recent graduate of the MIT-WHOI Joint Program, led the research, which uncovers the critical role microbes play within coral reef ecosystems.

Microbes are essentially minuscule life forms that are invisible to the naked eye. They inhabit virtually every corner of our planet. This includes the air we breathe, the soil beneath our feet, the bodies of water that surround us, and even the internal recesses of our own bodies.

Within the intricate ecosystems of coral reefs, these microscopic organisms undertake the vital task of recycling organic substances and nutrients. The recycling process carried out by microbes goes beyond merely breaking down materials; it acts as a lifeline for the corals. This process provides corals with the essential nourishment they need to thrive.

Moreover, microbes lay the foundation for a diverse web of life that thrives on coral reefs. They support a vast array of species that depend on these vibrant underwater cities for survival.

Microbial shifts in coral reefs

For seven years, the researchers closely studied microbial communities around eight reefs in the U.S. Virgin Islands. Their findings showed major changes in these communities due to hurricanes and disease outbreaks.

“Coral reefs have been declining for decades… It is important for us to monitor changes in coral reefs as they are happening, and the microbes in their environment can really help us do that,” said Becker.

The study documents the effects of major events, including hurricanes Irma and Maria in 2017. It also covers the onset of the stony coral tissue loss disease outbreak in 2020.

Furthermore, the research details the significant changes within the microbial community resulting from these disturbances. This includes a notable 34% decline in Prochlorococcus, a critical photosynthetic bacteria, illustrating the profound impact these events have on the ecosystem’s microbial balance.

Microscopic monitoring with eDNA

The research highlights a shift from traditional macro-level studies of coral reefs to a focus on the microscopic level.

“A lot of how we study coral reefs is done on a macroorganismal level. This makes it difficult to track the health of these vulnerable reefs in real time,” explained study co-author Amy Apprill, a microbial ecologist at WHOI.

To bridge the gap, the team utilized environmental DNA (eDNA) techniques to examine microbial DNA, providing a noninvasive method for assessing reef health. This approach allows for almost instantaneous health evaluations of the reefs, offering a crucial advantage in conservation efforts.

Stages in eDNA

The technique starts with collecting water samples from the coral reefs, each containing approximately 1 million microbes per milliliter.

After collection, the microbial DNA within these samples is sequenced to analyze the present microbial communities.

Subsequently, this method provides a snapshot of the microbial community’s composition, offering an insight into the reef’s health in near real-time.

“Microbes are the hidden engines of coral reefs. By sampling the water, we can see the immediate impacts of disturbances and intervene to support the reefs before the situation potentially worsens,” noted Apprill.

Towards a future of healthy reefs

Understanding the composition of a healthy reef microbial community is crucial for assessing the overall health of the ecosystem.

Consequently, this knowledge can complement visual assessments, providing a fuller picture of a reef’s condition and informing conservation strategies.

As the challenges facing these ecosystems intensify, the study offers a beacon of hope, leveraging the power of modern genomics to safeguard the future of our planet’s coral reefs.

The study is published in the journal Environmental Microbiology.


Like what you read? Subscribe to our newsletter for engaging articles, exclusive content, and the latest updates. 

Check us out on EarthSnap, a free app brought to you by Eric Ralls and


News coming your way
The biggest news about our planet delivered to you each day