Researchers explore the life cycle of North America’s last Atlantic salmon population

Researchers at the University of Maine at Machias are using a new survey method, environmental RNA, to understand the life cycle of Atlantic salmon.

Maine’s Atlantic salmon population has experienced significant decline due to stressors including dams, overfishing and pollution. The Atlantic salmon teeters on the brink of extinction in the Gulf of Maine, and comprise the wild populations of their species in the United States. 

Atlantic salmon are anadromous fish, meaning they hatch in freshwater, migrate to saltwater where they spend most of their lives and return to freshwater to spawn. These fish have several life stages before they become adults. When they live in freshwater they are called parr; once they are ready to move to saltwater they are called a smolt. Knowing when and where Atlantic salmon smolt swim is vital to conservation efforts. For several decades, efforts worked to restore their population. However, new research at the University of Maine at Machias (UMM) may offer new insights and hope for Maine’s endangered Atlantic salmon population.

Gerard Zegers is an associate research professor of biology at UMM studying Atlantic salmon. He served as a board member and past president of the Downeast Salmon Federation (DSF), as well as a board member and past president of the Maine Council of the Atlantic Salmon Federation (MCASF). Zegers is working on a seed grant alongside Sherrie Sprangers, co-chair of UMM’s Integrative and Marine Sciences Division,  and undergraduate students Ollie Kyllonen and Grace Pine to test environmental RNA (eRNA) as a tool to detect specific life stages of Atlantic salmon. This seed grant project was funded by the NSF EPSCoR RII Track-1 Maine-eDNA project.

Environmental DNA (eDNA) and eRNA are genetic materials shed by organisms in the environment and are useful tools for environmental research. All living organisms have DNA and RNA that carry genetic information but differ in their structure and function. In an environmental context, researchers can extract eDNA from a sample of water and analyze the DNA to discern which organisms live in it. Techniques using eDNA were frequently used over the past decade to detect the presence of certain organisms. Now, eRNA is an emerging tool that offers a finer spatiotemporal resolution. 

Salmon, like any organism, have the same DNA throughout their lives. RNA, meanwhile, changes through that animal’s life cycle as different genes are expressed. Through eRNA techniques, researchers can pinpoint when and where certain life stages occur. “For certain species such as Atlantic salmon, detecting the presence or abundance of a particular life history stage is more relevant than only knowing of their presence,” Zegers said. 

Zegers first read about eRNA research with zebrafish. From there, Zegers explained, “I thought about how salmon do something different. They have to prepare themselves to go from freshwater to saltwater. They turn on different genes and up-regulate genes to do that. That’s the kind of signal you ought to be able to measure.” With eRNA, scientists may be able to detect smoltification in Atlantic salmon. The non-invasive nature of the method is also a benefit. 

“The beauty of this is that Atlantic salmon are an endangered species. We are only collecting a water sample. We’re not looking at their RNA directly, we are looking at RNA from shed cells,” Zegers said.

The ability to detect salmon smoltification offers widespread applications to both aquaculture and conservation efforts. In aquaculture, salmon are typically raised in freshwater facilities, and eventually moved out to sea. If an operation knows when salmon have smoltified, they can reduce the risk of mortality when they are moved to a saltwater environment. 

Different hatcheries produce smolts in different ways. Federal hatcheries produce smolts in just one year. In wild settings, salmon generally spend two years in freshwater before they transform into smolt and leave the river. Unlike many hatcheries, the DSF develops their fish slower, which is helpful for testing eRNA methods. 

“The DSF produces a hatchery product that’s advertised to be more like a wild fish than the fish produced at the federal hatcheries. So if we have access to salmon cells throughout this process, we can compare salmon cells captured from hatchery water at the federal hatcheries and also at the DSF,” Zegers said. 

The eRNA technique, once refined, may offer a boon to salmon conservation. “Knowing when smolts are coming out of a river as well as how many are important metrics for conservation,” Zegers said. 

Understanding which parts of rivers produce smolt can inform land acquisitions or other protections. The Maine Department of Marine Resources (DMR) monitors smolts with small traps to estimate their numbers in a given river. The trapping approach, however, is expensive and limited to the main stem of rivers, which excludes small tributaries. eRNA is free of these constraints. “You can collect samples from anywhere in the watershed if you use a water sample,” Zegers said. 

While the eRNA techniques the UMM team are refining focus on detecting life stages in Atlantic salmon, the approach can be applied to other species. 

“There are all sorts of species that undergo transitions and dramatic changes in their life cycles, and it might be important to measure that,” Zegers said.

Zegers’ team has developed a DNA aptamer that helps isolate the salmon cells so RNA can be extracted. They are now working to turn the DNA aptamer into a tool and operationalize it. In the lab, they are working to determine how many salmon cells need to be captured to detect an organism’s complete RNA record. In coming years, they plan to collect water samples from hatcheries, smolt traps, and river locations with high parr densities to determine if the technique is effective in those settings. 

In time, this eRNA will provide insights into their lifecycle and movement of Atlantic salmon in Maine through non-intrusive methods, ideal for an endangered species. 

“This is sort of the ultimate extension of what I think is possible with this technique. We are not there yet, but I think it’s possible to get there,” Zeger said about the potential for this research to ultimately advance a wider understanding of our environment.