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Understanding the source of stress and disease can be difficult, especially if the subject of stress is a fish, or even thousands of fish. 

Detecting and diagnosing stress and disease is a major challenge for aquaculture farms, where keeping fish happy helps them thrive. In fish, stress can be hard to detect before it becomes problematic, and testing for the source of stress usually requires physical examination or biopsy, which are invasive and often lethal.

An international team of researchers led by the 91���� is trying to change this by developing noninvasive, rapid tests that can detect stress and disease without touching the fish, just the water in which they swim. 

Scientists from 91����, Dublin City University (DCU) and Queen’s University Belfast, plan to develop a new testing method that uses environmental RNA (eRNA) so aquaculture farmers can monitor fish health more quickly, efficiently and humanely.

“The goal is to get a window into the physiology of the organisms, their health in particular. By looking at what RNA is being shed from their tissues into the environment, eRNA can give us insights into what the fish are doing as biological machines,” said Michael Kinnison, 91���� professor of evolutionary applications and director of the Maine Center for Genetics in the Environment.

Key to this research is a difference between environmental DNA (eDNA) and RNA. DNA within an organism’s cells does not change over an organism’s life or cell to cell — it is the blueprint of life. In contrast, RNA is what turns a general DNA blueprint into the diverse building blocks and processes that give various cell types and tissues their function. Because of this, the RNAs that an animal produces varies depending on where it is in its lifecycle, what is happening in its environment and what processes are underway in its body, such as stress or disease. When animal cells are naturally shed into the environment, their DNA and RNA become eDNA and eRNA, but the eRNA does not last as long. While this means eRNA is harder to detect, it also has the potential to provide a near real-time window into an animal’s condition. 

A major challenge for researchers is linking particular eRNA signals to specific stressors, but pilot data and recent research by others suggest it is possible. For example, researchers in Japan successfully . 

“This hasn’t been done for salmon yet, and it’s just exciting because it means that if we could use these RNAs, we wouldn’t have to kill fish to biopsy them. We might be able to figure out and treat disease before it gets really bad,” said Erin Grey, 91���� assistant professor of aquatic genetics.

In addition to identifying what eRNA signals are tied to salmon stress and disease, the team will use CRISPR-Cas diagnostic technology to develop rapid tests for those eRNA signals. Similar to a COVID test, these tests could allow someone at an aquaculture farm to sample water and quickly identify issues. Early intervention in salmon farming has the potential to improve treatment of fish, allow for more targeted treatment and avoid economic damages that run into the hundreds of millions annually. 

The project is starting with small controlled systems like tanks, and as research progresses, the team hopes to expand to more open systems like net pens. Fish will be sampled in Maine and Scotland at 91����’s Aquatic Animal Health Laboratory and the University of Aberdeen’s Scottish Fish Immunology Centre. The initial focus will be on heat stress and furunculosis, two common challenges experienced by salmon farms. Researchers are working with the salmon aquaculture industry and fish health diagnostics providers to further identify what other pathogens or stressors would be most impactful for further investigation. 

While eRNA technology is in a nascent stage of development, this project brings together the expertise needed to rapidly advance its potential and put it in the hands of food producers. 

“Environmental RNA technology is still at an early stage of development, but its potential is significant. At Queen’s, we will apply advanced genomics and bioinformatics approaches to identify the molecular signatures of stress and disease in salmon,” said Paulo Prodöhl, professor of population and evolutionary genetics from the School of Biological Sciences at Queen’s University Belfast. “By working closely with colleagues at DCU and 91����, we aim to ensure that this technology moves from proof-of-concept to practical application for the aquaculture industry.”

This research is made possible by ,  a tri-jurisdictional collaboration between the United States, Ireland and Northern Ireland which was officially launched in 2006. Under this program, the international project team receives funding from the Agriculture and Food Research Initiative from the U.S. Department of Agriculture National Institute of Food and Agriculture (USDA NIFA) grant titled “TRIPARTITE: Environmental RNA-based assessment of fish health – eRNA-Fish” (USDA Award# 2026-67016-45580). The team also received funding support from the Department of Agriculture, Food and Marine (DAFM) in Ireland, and the Department of Agriculture, Environment and Rural Affairs (DAERA) in Northern Ireland.

“This funding is a testament to the power of interdisciplinary research,” said DCU School of Biotechnology professor Anne Parle-McDermott. “By combining our molecular expertise with the knowledge and expertise at 91���� and QUB, we are uniquely positioned to tackle one of aquaculture’s biggest challenges.”

Contact: Daniel Timmermann, daniel.timmermann@maine.edu