A new study led by scientists at NOAA’s Atlantic Oceanographic and Meteorological Laboratory (AOML) and the Cooperative Institute for Marine and Atmospheric Studies (CIMAS) indicates that stony coral tissue loss disease (SCTLD) has long-lasting impacts not only on corals, but also on their bacteria.
Just as humans have bacteria and other microbes essential to our gut health, corals also depend on a diverse array of microbes within their tissue, which make up their microbiome.
Studies have shown how these bacteria, fungi, and other microscopic organisms can aid a coral’s resistance to greater temperatures, support metabolic activities and cycling of key nutrients in times of increased stress, and enhance their immune response to diseases. However, changes in the diversity and abundance of certain bacteria within a coral’s microbiome can be a key indicator of extreme stress due to a bleaching event – or a rapidly-spreading coral disease.
Regions impacted by Stony Coral Tissue Loss Disease (SCTLD) since initial observations in Miami. Learn more here about the rapid spread of the disease
First observed off Miami, Florida, in 2014, SCTLD quickly devastated up to 22 species of corals. Today, the disease has impacted Florida’s Coral Reef and spread across the Caribbean at an alarming rate, with high mortality (up to 90% in some cases). While SCTLD is transmitted through the water column, scientists at AOML suggest that a ship’s ballast water may be a reason for the spread of the disease from Florida to the Caribbean.
Massive lesion on a colony of brain coral (Orbicella faveolata) in the Florida Keys caused by stony coral tissue loss disease.
While SCTLD spread rapidly north from Miami across Florida’s Coral Reef, its spread south to the Florida Keys proved more gradual, allowing scientists to more effectively monitor its progression across reefs. This study, led by CIMAS Associate Scientist Stephanie Rosales, Ph.D., was therefore able to capture changes to the microbiome of corals at designated sites within the Lower Keys before, during, and after SCTLD’s impact.
The study sites of the Lower Florida Keys, where samples of healthy corals, seawater, and sediment were collected. Lindsay’s Path, Cliff Green, and Xesto Patch were the three key sites of the Lower Florida Keys. See Rosales et al. (2026) to learn more.
Rosales and collaborators were interested in capturing how the coral reef microbiome changes over time when an ecosystem is impacted by a devastating disease like SCTLD. To understand this, the team sampled the microbiomes of healthy corals and the surrounding seawater and sediment during three disease stages: before the disease was detected (vulnerable), during the disease outbreak (epidemic), and after the wake of the initial exposure (endemic).
Sampling for the vulnerable time point began in 2018, a year before SCTLD spread to these three sites, and sampling continued in 2020 when the disease arrived at these same reefs. Finally, the scientists returned to these reefs in 2021 when the disease was endemic. Ultimately, the researchers observed a significant decline in bacterial diversity and in the number of bacterial interactions within healthy corals once disease reached the endemic stage. Because of this breakdown of essential bacterial interactions, the study found that the disease significantly impacted the potential of key metabolic functions of the microbiome, which could aid corals.
The specific pathogen causing the outbreak of SCTLD remains a mystery, but bacteria commonly have been linked to the disease, including Rhodobacterales, Rhizobiales, Clostridia, and Vibrio. Using these bacteria as biomarkers of SCTLD, the scientists tracked the bacteria through time. They found that even among healthy corals and in the greater reef environment, SCTLD-affiliated bacteria were detected at significantly high levels in the epidemic and endemic disease stages, compared to the vulnerable stage (before the arrival of disease), demonstrating the lasting impacts of the disease once it affects a region.
“This study really demonstrates how SCTLD changes the microbial foundation of the reef in ways we’re only beginning to understand and need to understand to help with reef recovery,” explains Stephanie Rosales, Ph.D.
SCTLD doesn’t just affect visibly diseased corals. This study shows that the disease leaves a lasting microbial footprint, reshaping the microbiomes of corals that appear healthy and altering the surrounding microbial environment long after an outbreak ends.
As SCTLD’s transmission continues into the Caribbean and beyond, the need to monitor and assess the long-term impacts on entire reef frameworks only becomes more pivotal.
Learn more about Stony Coral Tissue Loss Disease here.
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This research was supported by the Environmental Protection Agency (EPA) South Florida Initiative grant (X7-01D00820-0) and carried out in part under the auspices of the Cooperative Institute for Marine and Atmospheric Studies, a cooperative institute of the University of Miami and the National Oceanic and Atmospheric Administration (NOAA), cooperative agreement NA 20OAR4320472.