Every day, coral reefs subtly change the microscopic world drifting right above them. As daylight fades and returns, tiny ocean organisms – bacteria, algae and single-celled predators – come and go in a steady cycle that repeats every 24 hours.
New research published in Achievements of scienceshows that coral reefs are more than just habitats for marine life; they actively organize nearby microbial communities over time. By allowing predictable daily shifts in which microbes dominate the water, reefs influence nutrient cycling and how energy moves through the surrounding ecosystem.
“We found that the reef is not just passively surrounded by microbes,” study co-author Miguel J. Frada said in the paper. press release. “It actively structures microbial life over time, creating daily patterns that repeat seasonally and influence how energy and nutrients move through the ecosystem.”
Read more: The Great Barrier Reef is experiencing its biggest annual decline in nearly 40 years.
Finding out how coral reefs shape nearby waters
To capture these rhythms, the researchers focused on the waters above a coral reef in the northern Gulf of Aqaba in the Red Sea. They compared the microbial communities on the reef with those in nearby open waters, taking samples every six hours in both winter and summer.
The team combined genetic analysis, flow cytometry, imaging tools and environmental measurements to trace microbial populations on unusually precise time scales. This approach revealed rapid, repeatable changes in bacteria, microalgae and microscopic predators—fluctuations that would likely have gone undetected with less frequent sampling.
The same daily patterns continued to emerge across seasons, highlighting that when samples are collected can be as important as where they are taken when studying reef-associated microbes.
Why do bacteria disappear during the day, but predatory microbes appear at night?
One of the most consistent signals was the sharp contrast between the reef waters and the nearby open ocean. There were fewer bacteria and microalgae above the reef, suggesting that the reef organisms actively remove microbes through grazing, filtration and other biological interactions.
After sunset the balance shifted again. The number of heterotrophic protists – microscopic organisms that feed on bacteria – increased dramatically at night, in some cases by almost 80 percent. Time suggests that predation is a key force driving the daily turnover of microorganisms around reefs.
These opposing trends show that reefs shape microbial communities not only depending on who lives nearby, but also depending on when different groups thrive or decline.
Microbes associated with corals follow a circadian rhythm
Microbes closely associated with the corals also showed different daily patterns. Signals associated with Symbiodiniaceae, microorganisms best known for their close partnership with corals, waxed and waned daily in reef waters.
Rather than remaining fixed within corals, these patterns involve constant daily exchange or circulation between corals and surrounding water, which is likely due to changing light conditions and changes in coral activity throughout the day.
“These daily microbial rhythms were as strong as the seasonal differences, and sometimes stronger,” said lead study author Herdís G. R. Steinsdóttir. “This shows that time of day is a critical factor when studying reef-associated microbial communities.”
By revealing how coral reefs regulate daily microscopic life, the study reveals an almost invisible level of reef functioning. Because microbial communities respond quickly to environmental changes, tracking their daily rhythms could be a sensitive way to monitor how reefs are functioning—and how they may be changing—under a warming ocean.
Read more: Seismic activity shakes microbes deep beneath Yellowstone Lake
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