- An increasingly common way to keep tabs on coral reef health is by measuring microorganisms in the local seawater.
- Microbial-based coral reef monitoring is excellent at detecting nutrient and health changes on a reef and can draw attention to environmental disturbances; microbes are particularly good at sending such signals because they react quickly to pollution.
- This type of monitoring can help provide a fuller, faster and lower-cost picture of reef health than visual surveys alone, the most common current method.
- Two marine scientists explain the “why” and the “how” of microbial-based reef monitoring in a recent paper.
Prochlorococcus, a genus of bacteria that’s key to oxygen production in the ocean, tends to disappear when faced with marine pollution. It lives throughout the sunlit layer of tropical oceans and, while it doesn’t necessarily play a key role in coral biology, its abundance is a sign of a healthy coral reef ecosystem. A growing number of scientists are studying it and other microorganisms to keep tabs on reef health.
Two marine scientists explain the “why” and the “how” of microbial-based reef monitoring, which is still relatively rare, in a paper published May 23 in the journal Cell Reports Sustainability. Lead author Amy Apprill, an associate scientist at Woods Hole Oceanographic Institution, a nonprofit research center in the United States, said this kind of monitoring is part of a larger effort to protect reefs.
“Coral reefs are in decline worldwide, and I’m one of many scientists trying to do everything we can to help them, and so we were excited to put this article together because we think it’s an important way to examine the health of reefs,” Apprill told Mongabay.
Apprill said the paper is aimed at coral reef conservation practitioners and managers. She’s given talks on the subject for the last two years, and a journal editor commissioned the paper after hearing her speak. She said the message of the talks is, “You all should think about using reef water microbes to understand more about what’s going on at your reef sites.”
The world’s coral reef ecosystems, which are some of the most biodiverse places on Earth, have faced staggering losses in recent decades due to factors such as climate change and marine pollution. Among the most common methods to track changes to reefs is visual survey monitoring, which usually focuses on macroorganisms like corals, sponges and fish.
Apprill, making an analogy to human health, said understanding reef health requires more than just visual assessments.
“If I take my child to the doctor, and the doctor just looks at them and doesn’t take any kind of physical or chemical measurements, then how are they going to know how to treat them, right?” she said.
Microbial-based monitoring is not the only type of reef monitoring to apply chemical measurements — using sensors to assess temperature, oxygen and pH is another, more common method — but it is excellent at detecting nutrient and health changes on a reef, the paper says. The method involves collecting seawater in special bottles or syringes, usually about half a meter (1.6 feet) from the seafloor, and analyzing the microbes in the water.
Systematic monitoring of microbes in the ocean has taken place since at least 1988, when U.S. government funding led to the opening of two deep-sea research sites taking continuous measurements. Much of the groundwork for microbial-based monitoring of coral reefs specifically was then laid in the 2000s and 2010s by researchers such as Forest Rohwer at San Diego State University, whose team helped established a baseline understanding of reef microbiomes. He and his colleagues were among the authors of a seminal 2008 study in the journal PLOS One that compared the microbial makeup of the seawater around coral atolls in the central Pacific Ocean that had been polluted or otherwise affected by human activities with that of atolls that hadn’t. Work in the field has since expanded, including with a number of studies of the Great Barrier Reef’s microbiome.
Apprill herself has studied reef-water microbes for more than a decade and has been an author or co-author of more than a dozen scientific articles on the subject. For the new paper, she put together what she’s learned from her research and that of other scientists around the world.
“The paper makes a strong case for microbial monitoring and draws on published studies as examples of how microorganisms can be indicative of coral health and disease, nutrient levels in seawater, influence of human activity, etc.,” Patrick Laffy, a genomic bioinformaticist at the Australian Institute of Marine Science, which has led much of the microbiome research at the Great Barrier Reef, said in a statement emailed to Mongabay.
The idea of using microbes as a diagnostic health indicator on reefs is not new to microbiologists, but Apprill and her co-author Jennifer Salerno, an environmental microbiologist and coral reef ecologist at George Mason University in Virginia, U.S., seek to bring it to a larger audience.
Apprill and Salerno call for the development of a reef-water microbial health index — a report card that shows a reef’s status based on factors such as the abundance of different cells, microbial diversity and the ratio of photosynthetic to heterotrophic cells. A healthy reef will generally have a higher ratio of photosynthetic cells, which convert sunlight into energy, to heterotrophic cells, which decompose organic matter.
Such report cards could help with, for example, choosing locations for reef restoration by indicating which spots have suitable biomes for coral outplanting. Microbe monitoring could also draw attention to environmental disturbances such as aquaculture effluent entering a coral area, the paper says. Microbes are particularly good at sending such signals because they react quickly to pollution.
Apprill said there was a reef in the U.S. Virgin Islands that lost 30% of its photosynthetic bacteria — a sign of declining health — and there was circumstantial evidence that some form of industrial dumping was taking place in the area.
Andrew Taylor, the director of Blue Corner Marine Research, an Indonesia-based NGO that restores coral reefs, said microbial-based monitoring would be especially helpful for reefs in Southeast Asia because local communities often lack a sophisticated sewage treatment system, raising the possibility of effluent affecting a reef’s biome.
“I think it would be really good to get to use the kind of monitoring that’s outlined in the paper … in some of these reef areas that are close to villages,” Taylor said. “And see if maybe there’s things we can work together with the local villages to show that, OK, maybe there are elevated pollutants in the water and that’s affecting the marine life that they’re fishing.”
Experts say one of the advantages of microbial-based monitoring is that it can be conducted with limited resources, and even citizen-led.
Apprill and Salerno’s paper breaks down the tools needed to collect samples and analyze them, offering inexpensive alternatives for those working on a budget. For example, for teams that can’t afford to send samples off for a full “microbial community composition” analysis, which involves DNA work and can cost $55-$99 per sample, they suggest options such as measuring cell abundance using a microscope, which costs about $7 per sample.
Such options are important for teams working in remote areas or on tight budgets, Taylor said.
“Probably us and most conservation organizations in Southeast Asia and more remote areas would be more able to adopt the cheaper methods that are able to be done on site by our own personnel,” Taylor said.
Though much work remains to be done to establish reference data for coral reef microbes, scientists do have a bit of a head start: A huge amount is known about the DNA sequences of microorganisms in general because of their significance to the health care, agriculture and waste management industries. Microbial-based monitoring is a way of taking advantage of those data, which aren’t nearly as prevalent for, say, fish genomes, Apprill said.
The new paper calls for the establishment of global standards and coordination for microbial-monitoring of reefs, yet the largest barrier to progress in the field may be a familiar one: funding.
“I think that is the biggest roadblock,” Apprill said. “Usually, you have people that are eager to learn and … make these things happen, but you need money to make it happen.”
Banner image: A coral reef around Nukuoro Atoll in the Federated States of Micronesia, where microbial-based monitoring is undertaken to assess reef health. Image courtesy of Alyson Santoro/WHOI.
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Citations:
Apprill, A., & Salerno, J. L. (2025). Reef water microorganisms as diagnostic indicators for coral reef ecosystem management and sustainability. Cell Reports Sustainability, 2(5), 100403. doi:10.1016/j.crsus.2025.100403
Dinsdale, E. A., Pantos, O., Smriga, S., Edwards, R. A., Angly, F., Wegley, L., … Rohwer, F. (2008). Microbial ecology of four coral atolls in the northern Line Islands. PLoS ONE, 3(2), e1584. doi:10.1371/journal.pone.0001584
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