Researchers Develop a Faster and More Accurate Way to Track Toxic Algae That Threaten Shellfish Industries

Tiny algae may look harmless under a microscope, but some species can have enormous consequences for coastal ecosystems, public health, and the livelihoods that depend on the sea. A new scientific development is now offering hope to shellfish growers and resource managers by making it easier to detect one of the most dangerous toxic algae before it causes widespread damage.

Researchers from the University of Maine and the Bigelow Laboratory for Ocean Sciences have developed a new genetic testing method that allows for faster, more precise detection of a toxic algae species called Pseudo-nitzschia australis. This breakthrough could significantly improve how harmful algal blooms are monitored and managed, especially in regions like the Gulf of Maine, where shellfish farming is a major economic pillar.

Why Pseudo-nitzschia australis Is a Serious Threat

Not all algae are harmful. In fact, many algae play a vital role in marine food webs and oxygen production. However, certain species can produce toxins that disrupt ecosystems and pose serious risks to humans and wildlife.

Pseudo-nitzschia australis is one of the most dangerous species in its group. About half of all Pseudo-nitzschia species are toxic, but P. australis is known for producing exceptionally high levels of domoic acid, a potent neurotoxin.

Domoic acid is responsible for amnesic shellfish poisoning, a condition that can cause nausea, seizures, memory loss, and in severe cases, death in humans. Marine mammals are also affected, sometimes displaying unusual or aggressive behavior after consuming contaminated prey.

The danger became very real on the U.S. East Coast in 2016, when P. australis bloomed there for the first time. The bloom spread rapidly, contaminating shellfish along the coast from the Bay of Fundy to Rhode Island. Shellfish farms were forced to halt harvesting for weeks, and product recalls followed. Although a bloom of that scale has not occurred again in the Gulf of Maine, the species has remained present at low levels, continuing to threaten hatcheries and working waterfronts.

The Limits of Traditional Monitoring Methods

Until now, monitoring for Pseudo-nitzschia has relied largely on light microscopy, where technicians examine seawater samples and count algae cells. While this method can detect the presence of the genus, it has a major flaw: toxic and non-toxic species look almost identical under the microscope.

Even highly trained experts cannot reliably tell whether a sample contains harmless Pseudo-nitzschia or a dangerous toxin-producing species like P. australis. As a result, when cell counts rise above a certain level, shellfish managers often take precautionary measures, including closing harvest areas.

These closures remain in place until shellfish tissue tests confirm whether domoic acid is present. While necessary for public safety, this approach is slow, expensive, and disruptive for the shellfish industry, often leading to economic losses even when toxins are not ultimately detected.

A New Genetic Test Changes the Game

The newly developed test uses a quantitative Polymerase Chain Reaction (qPCR) technique applied to environmental DNA (eDNA) found in seawater. Environmental DNA refers to tiny fragments of genetic material that organisms leave behind as they move, grow, and reproduce.

By targeting a unique genetic marker specific to Pseudo-nitzschia australis, the test can identify the species quickly and accurately, even when cell concentrations are extremely low. Remarkably, the assay can detect the algae from as little as one liter of water.

This approach builds on more than a decade of Pseudo-nitzschia research conducted in the laboratory of Peter Countway at Bigelow Laboratory, where Sydney Greenlee, a Ph.D. candidate at the University of Maine, is based. Greenlee led the development of the assay alongside researchers Robin Sleith and Countway.

The results were published in the peer-reviewed journal Harmful Algae, marking an important step forward in harmful algal bloom monitoring.

Faster Detection Means Better Decision-Making

One of the most important advantages of the new eDNA test is speed. Compared to traditional microscopy and toxin testing, genetic analysis offers a much faster turnaround time. This allows water samples to be tested more frequently and enables resource managers to respond earlier to potential threats.

Because the test provides species-level identification, managers can distinguish between harmless Pseudo-nitzschia and toxin-producing P. australis. This precision could help refine management practices, reduce unnecessary closures, and better protect both public health and the shellfish industry.

Scientists from Maine’s Department of Marine Resources have already been trained to use the assay, signaling that it may soon become part of routine monitoring programs.

Understanding Bloom Dynamics and Long-Term Risks

Beyond immediate monitoring benefits, the new test opens the door to deeper scientific understanding. Pseudo-nitzschia australis has been present in the Gulf of Maine at low levels since 2016, but the reasons behind its sudden bloom and toxin production remain unclear.

With this new detection tool, researchers can study how P. australis behaves alongside other Pseudo-nitzschia species, tracking its seasonal persistence and identifying environmental conditions that may trigger blooms. This knowledge could help scientists anticipate future events rather than reacting after damage has already occurred.

The ultimate goal is to ensure that surprise bloom events like the one in 2016 do not happen again.

Why Environmental DNA Is Gaining Attention

Environmental DNA has become a powerful tool in marine science and conservation. By detecting genetic material in water samples, researchers can monitor species without physically capturing or observing them.

This approach is increasingly used to track invasive species, endangered populations, and pathogens. Its application to harmful algal blooms demonstrates how molecular tools can complement traditional monitoring methods and provide earlier warnings of ecological threats.

In coastal regions facing warming waters and changing ocean conditions, these tools may become essential for protecting both ecosystems and economies.

A Win for Coastal Communities

Shellfish farming is a cornerstone of Maine’s coastal economy, supporting jobs, local food systems, and long-standing maritime traditions. Harmful algal blooms threaten all of this, often with little warning.

By offering earlier detection, greater accuracy, and faster results, the new eDNA assay gives resource managers and shellfish growers a valuable advantage. It also highlights how targeted scientific research can directly support working waterfronts and public health.

As researchers continue refining this and similar tools, the hope is that toxic algae like Pseudo-nitzschia australis can be monitored closely enough to prevent economic and ecological damage before it begins.

Research Reference:
https://doi.org/10.1016/j.hal.2025.103039