Coral reefs are renowned for their beauty as well as their diversity. But not many people know that most of the diversity found around coral reefs is completely hidden to the naked eye. Welcome to the world of microbes.
Just like humans need a healthy microbiome, a balanced mix of invisible bacteria, fungi, algae and plankton in seawater are essential to the functioning and health of organisms in coral reef ecosystems.
These microbes are important drivers of nitrogen and carbon cycles on reefs, playing a role in keeping the environment in which a coral lives healthy and balanced.
They are responsible for taking nutrients that would otherwise be unavailable to plants and animals, such as nitrogen and phosphorus, and turning them into forms that the cells of living organisms use for metabolism and growth.
“They are the unsung heroes of life on Earth. And without them, life on coral reefs would grind to a halt,” AIMS research scientist Dr. Patrick Laffy said.
The mystery of what’s out there and what they do
Despite their ubiquitous nature, diversity and importance to reef ecosystems, scientists have only just scratched the surface of microbial communities out in the Great Barrier Reef and their functions.
As well as nutrient recycling, we know that microbes in the seawater form the basis of food webs, providing energy to animals in the ecosystem.
There are other complex interactions underway that AIMS scientists are unpicking.
AIMS research scientist Dr. Yun Kit Yeoh explained, “Just like the diversity of corals on the Great Barrier Reef contribute to unique functions, the individual functions of each microbe provide critical ecosystem services to coral reefs.
“Identifying which microbes are important, how they interact with the environment and other reef organisms including corals will help us understand how microbes contribute to the overall Great Barrier Reef ecosystem.
“This is critical for the future of the system and could help other coral reefs.
“We are well placed at AIMS to examine the diversity and roles of microbes. Through our extensive collections of water samples across our monitoring programs, and long-term data sets on Reef health, we can leverage existing knowledge and see where microbes fit in this complex space.”
Microbial functions in seawater reflect ecosystem status
To understand their functions, the AIMS research team are looking into the DNA of the microbes, setting out initial findings in a paper published in the journal Microbiome.
This work maps the critical microbial genes that underpin the Reef’s productivity, providing a crucial reference for its future health and management.
Lead author and AIMS@JCU Ph.D. student Marko Terzin said the team analyzed seawater samples collected at 48 offshore reefs across the GBR by AIMS’ Long Term Monitoring Program, and found the functional genes within the microbes were a strong predictor of reef condition and health.
“Because these microbes play a critical role on coral reefs, their gene functions are a reflection of what is going on at that moment on a coral reef,” he said.
“Analyzing seawater microbial functions could be expanded to indicate additional stressors like elevated sea temperatures or additional nutrients in the water column because of a flood or pollution event.”
Seeing the unseen with DNA
Dr. Laffy illustrated the complexity of the task: “We’re putting together a jigsaw puzzle of the role of these communities on the reef, where the genetic information in the seawater are the puzzle pieces.
“We’re attempting to put this puzzle together without any guide from a picture and the sizes of the pieces can vary depending on the technologies we use to reveal the pieces.
“For this study we had small, raw pieces of the puzzle and worked out that the role of the genes in the samples we found were more informative of the water quality, or chemistry, than knowing what bacteria they came from.”
A future for reef monitoring?
Microbial communities are the first responders to change on a coral reef. They rapidly react to changing conditions on reefs and can influence outcomes for corals as they experience changes in temperature, shifts in light intensity and chemical variations in the water.
Their sensitivity highlights the potential of seawater microbes to be used as indicators of reef health.
“Previous studies have shown that microbes collected from a sample of seawater are valuable indicators of these changes, even better than microbes in the sand or from inside corals,” said Dr. Laffy.
“As seawater samples are easy to collect, it’s possible that we could use seawater microbial communities as a complementary method when monitoring changes in reef health.”
Dr. Yeoh said the work could help with reef monitoring efforts.
“In the future, understanding microbes could complement our current monitoring efforts, meaning we are able to understand coral reefs in remote or dangerous places for humans, simply by analyzing a water sample,” he said.
“This might be helpful in the future for countries with less resources for in-water monitoring of their coral reefs.”
The team is currently preparing to publish more on their research into microbial communities.
More information:
Marko Terzin et al, Gene content of seawater microbes is a strong predictor of water chemistry across the Great Barrier Reef, Microbiome (2025). DOI: 10.1186/s40168-024-01972-0
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Australian Institute of Marine Science
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