New research from the Hebrew University of Jerusalem shows coral reefs orchestrate daily microbial cycles that shape surrounding ocean ecosystems

Coral reefs don’t just shape marine life over years or seasons—they organize the ocean hour by hour. New research reveals that reefs impose a hidden daily rhythm on microscopic life in surrounding waters, orchestrating predictable rises and falls in microbial populations that could offer powerful new insights into reef health.

The study, published in Science Advances and led by researchers from the Hebrew University of Jerusalem and the University of Haifa, shows that microbial communities above coral reefs change dramatically over the course of a single day. Some microbes peak during daylight hours, while others surge at night, driven by feeding, predation, and coral-related biological processes.

“These reefs are not passive structures,” said Dr. Miguel J. Frada of the Hebrew University of Jerusalem. “They actively shape microbial life in time, creating daily cycles that influence how energy and nutrients move through the ecosystem.”

A Microscopic Timetable

To capture these rapid changes, scientists conducted intensive sampling every six hours above a coral reef in the northern Gulf of Aqaba in the Red Sea, comparing results with nearby open waters during both winter and summer. Using a combination of genetic sequencing, ecological analysis, advanced imaging, and flow cytometry, the team uncovered daily microbial cycles that were previously invisible.

The results show that waters above reefs consistently contained far fewer bacteria and microalgae than surrounding open waters—evidence that reef organisms actively remove microbes from the water column. At the same time, populations of heterotrophic protists—microscopic predators that feed on bacteria—rose sharply at night, in some cases by as much as 80 percent.

“These daily rhythms were as strong as, and sometimes stronger than, seasonal differences,” said lead author Dr. Herdís G. R. Steinsdóttir. “That tells us time of day is a critical dimension we’ve been missing when studying reef ecosystems.”

Corals, Light, and Microbial Turnover

One striking pattern involved Symbiodiniaceae, the family of dinoflagellates best known for their symbiotic relationship with corals. Genetic signals from these organisms regularly peaked around midday, suggesting daily cycles tied to light, coral metabolism, and microbial turnover.

Together, the findings position coral reefs as active ecosystem engineers, regulating not only fish and visible marine life but also the invisible microbial systems that underpin ocean productivity.

A New Indicator of Reef Health

Beyond expanding scientific understanding, the research points to a practical application: daily microbial rhythms could become sensitive indicators of reef condition in a rapidly changing ocean.

“As reefs face increasing stress from warming, pollution, and acidification, these microbial cycles may offer an early-warning system,” the researchers note. Because microbes respond quickly to environmental change, disruptions in daily patterns could signal declining reef function before visible damage appears.

The discovery adds a new layer to how scientists understand coral reefs—not just as static biodiversity hotspots, but as dynamic systems that pulse with life on a daily clock.