Microbes offer new ways to monitor coral reef health

Coral reefs are some of the most colorful and diverse ecosystems on Earth. Much of this beauty comes from the tiny algae that live inside coral tissues. But the story doesn’t end there.

The water surrounding coral reefs is filled with invisible life – bacteria, archaea, and other microscopic organisms. These microbes don’t just float around unnoticed; they react to changes in the environment and can tell us a lot about the health of coral reefs.

In a recent study by scientists from the Woods Hole Oceanographic Institution (WHOI) and George Mason University, researchers make the case for using these microbes as a valuable tool in coral reef monitoring and conservation.

The findings offer new hope for helping reefs recover from the increasing threats of climate change, pollution, and habitat destruction.

New insights into coral reef health

Amy Apprill is an associate scientist in Marine Chemistry & Geochemistry at WHOI and lead author of the study.

“Factoring in microbes is very helpful to understand more about overall reef health,” said Apprill. “My team has produced over a dozen detailed datasets that demonstrate these connections.”

“Our goal with this new paper is to make this knowledge accessible to the programs and people interested in using microbes to diagnose reef health and ocean conditions.”

Traditionally, coral reef monitoring depends on what people can see – changes in coral color, signs of bleaching, or physical damage.

However, microbial sampling offers a different kind of insight. It can provide more immediate feedback and a clearer picture of what’s happening beneath the surface.

Improving coral reef conservation

These techniques aren’t just for scientists. The study explains how park managers, conservation groups, restoration teams, and policy makers can all benefit.

Water samples can be collected without harming the reef. Analyzing the samples can be as simple as using a microscope or as complex as genetic sequencing. Costs and technical requirements vary, but that’s part of the appeal – this method can be adapted to many situations.

Study co-author Jennifer L. Salerno is a marine biologist and associate professor in the Department of Environmental Science and Policy at George Mason University.

“The utility of using microbes as meaningful indicators is increasing as our understanding of their roles in maintaining or destabilizing health and ecosystem function is growing,” explained Salemo.

“I think we have the science and accessible technology to take a more nuanced approach to coral reef conservation, management, and policy decisions by deploying diagnostic tools like this.”

What microbes tell us

Microbes respond to all sorts of environmental cues – nutrients, oxygen levels, temperature, pH, and light.

For example, the presence of E. coli in reef water typically signals contamination from human or animal waste, which is bad news for the reef. On the flip side, certain photosynthetic microbes may suggest a healthy ecosystem.

This kind of data is more than just interesting. It can guide decision-making about where and when to intervene, and even how to design better reef restoration projects.

Benefits of microbial monitoring

One strength of this approach is that it doesn’t require a one-size-fits-all solution. Some tools are inexpensive and easy to use, while others offer deeper insights but require more resources.

The authors of the study also urge the coral reef community to develop standard methods and share their findings.

“Because of the decline of coral reefs and the increased attention towards interventions such as restoration or rebuilding of a reef, it is important to bring all the relevant tools to the table to help restore, manage, and conserve reef ecosystems,” noted Aprill.

Protecting reefs from emerging threats

With regular sampling, we can track how a reef’s microbial community changes over time. That opens the door to larger-scale monitoring efforts.

Eventually, scientists hope to build open databases of microbial data from reefs around the world. These databases could be used with machine learning tools to predict reef health and create a kind of microbial health index for coral ecosystems.

“As coral reef scientists, we are very good at monitoring change and sometimes determining the root causes of the changes we are seeing on the reef,” Salerno said.

“We aren’t as well versed in mitigation and coordinated responses to emerging threats, but I would say as a community, we are improving.”

“If we can become better at predicting emerging threats through the use of diagnostic tools, perhaps we can also become better at preventing them from impacting reefs in the first place.”

The coral reef bleaching crisis

Recent years have brought some of the worst coral bleaching events on record. This happens when corals lose their symbiotic algae due to heat stress or pollution.

As oceans keep warming due to climate change, these events are becoming more frequent and severe. The researchers emphasize that we need every tool we can get to help coral reefs survive.

“We need to provide as much practical and accessible information as we can to the people making decisions,” Apprill said. “I think these microbes can enhance our knowledge of the ecosystem and elevate our framework for decision making.”

“I want people to get excited about this idea, and for current coral reef monitoring programs and management agencies to understand how this can make a difference to their programs.”

By listening to the tiniest voices in reef waters, we may be able to protect some of the ocean’s most vital ecosystems before it’s too late.

The full study was published in the journal Cell Reports Sustainability.

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