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- A new DNA sequencing tool rapidly detected 11 harmful algal bloom species — including those responsible for red and brown tides — across 20 sites in Florida's Indian River Lagoon.
- The study found HAB species frequently co-occur, suggesting shared environmental triggers or interactions that could help explain how blooms develop.
- Real-time, higher-resolution monitoring could improve scientists' ability to detect emerging bloom risks before they become widespread, with implications for coastal waters beyond Florida.
TAMPA, Fla. (Oct. 14, 2026) – A new study by researchers at the University of South Florida and Florida Atlantic University has demonstrated that a promising DNA sequencing tool can rapidly identify harmful algae in coastal waters, offering a new approach for monitoring species that could lead to improved methods for detecting potentially dangerous species before blooms become widespread.
The findings, "Near real-time long-read eDNA sequencing reveals harmful algal bloom dynamics in the Indian River Lagoon," are scheduled to publish on Wednesday, Oct. 14, at 2 p.m. ET in PLOS Water and are embargoed until that time.
The research team utilized a specialized tool called the Oxford Nanopore MinION to identify harmful agal bloom (HAB) species at 20 sites across Florida's Indian River Lagoon. Using the technology, they found 11 harmful algal bloom species, including species responsible for brown and red tides, with some at very low concentrations.
Researchers also found that harmful algal blooms don't exist in a silo: their impact is a cooperative effort.
Their findings could enhance the understanding of how environmental drivers shape bloom risk across brackish coastal systems, particularly in Florida.
The team included Justin Gibbons, a computational biologist in the Department of Global, Environmental, and Genomic Health Sciences in the USF College of Public Health ; and Rays H.Y. Jiang, an associate professor in the genomics program in the college. They collaborated with faculty at FAU's Harbor Branch Oceanographic Institute in Boca Raton, including Greg O'Corry-Crowe, research professor; Heidi Pagáan, research associate; and Tatiana Ferrer, coordinator of research programs.
"The result that stood out to me the most was the frequent co-occurrence of the harmful algal bloom species," Gibbons said. "This suggests that there's either shared ecological drivers for them or that they somehow interact and promote the growth of each other."
The study focused on the Indian River Lagoon, a 156-mile-long brackish estuary system on Florida's east coast. One of North America's most biologically diverse bodies of water, it supports more than 4,300 species of plants and animals. But HABs threaten the harmony of the ecosystem.
To understand how HABs develop and spread, the team analyzed environmental DNA in lagoon water.
Rather than looking at the bacterial marker commonly used in microbial studies, they targeted a specific eukaryotic ribosomal RNA gene, which provides a window into algae that cause blooms. A eukaryotic organism has a distinct, membrane-bound nucleus that holds its genetic material.
Using the Oxford Nanopore MinION, the team performed real-time, full-length sequencing of microbial communities across 20 sites in the lagoon. They detected nearly a dozen HAB species, including those responsible for brown and red tides. Their pattens were linked to such environmental factors as temperature, salinity and nutrients, which can change algae blooms from dormant to destructive. Having a technology that predicts a bloom is similar to how a meteorologist relies on radar to forecast the weather.
"The key is scale and synergy," Jiang said. "Harmful species can sit at low abundance, then expand quickly when conditions change, and several HAB species often co-occur. Nanopore offers near-real-time, higher-resolution monitoring that could catch shared triggers and community shifts before a bloom is obvious.''
Blooms that cause red tide are of special concern because they not only kill fish, birds and marine mammals, but harm people by producing breathable aerosols. They also affect businesses that depend on beaches and tourism. The prolonged red tide bloom that descended on Florida in 2017 caused $2.7 billion in lost income, according to the National Centers for Coastal Ocean Science.
But the research has potential beyond the Sunshine State. The Pacific Ocean, for example, is seeing a massive new heatwave that likely will be compounded by a developing El Niño. The earth's polar regions are experiencing record warming and ice loss, and Europe is suffering from record droughts and wildfires.
"The urgency to understand the drivers and track the development of HABs highlights an even bigger challenge: the race to understand how entire aquatic systems work in an era of climate change and growing (human) impacts," O'Corry-Crowe said. "From bacteria to whales, entire food-webs are witnessing dramatic environmental shifts, and this study provides an incredibly powerful tool to track and understand the processes driving these changes − as well as the impacts."
