There are many unknowns about how salmon live on the high seas, but new research is helping to understand why these fish can struggle to warm up in the seas.
Pacific Salmon Foundation scientist Christoph Deeg joined the Gulf of Alaska Winter 2019 International Expedition to study the interrelationship between ocean conditions, pathogen loads and genetic expression in salmon, and to test new analytical techniques. A study of his work on this journey, titled Way Over There: Pathogens, Health and Status of Overwintering Salmon in the Gulf of Alaskawas published on February 24 in the journal VENEERS.
Late winter is the perfect time to study factors affecting salmon survival, Deeg said.
“In winter, primary production, meaning the growth of phytoplankton that sustains the whole ecosystem, is very limited,” he said. “The theory is that winter is the cut-off time when salmon struggle, and at that time of year you would be able to see what factors limit their survival.”
The Gulf of Alaska expedition filled knowledge gaps about salmon behavior and distribution during these colder and less productive months.
“We weren’t sure if the salmon were going through the winter, feeding fast, starving, or just curling up,” he said.
Researchers found that instead of being evenly distributed, salmon form large aggregations as they follow food sources; they seem to be attracted to oceanographic features, such as eddies, containing more phytoplankton capable of supporting a food web.
On the research vessel, Deeg dissected captured salmon and took tissue samples. These samples were frozen to preserve the genetic material they contain — not just fish, but dozens of pathogens living inside them.
Those samples were then analyzed in a lab using polymerase chain reaction (PCR) — a technology that gained fame for its use during the COVID-19 pandemic — to identify the pathogens in each. A sophisticated ‘high throughput’ system was used, allowing over a thousand different tests to be performed at once.
“It basically allows us to do a COVID test for 96 fish, but not just for one pathogen, like in the case of COVID, but for 47 different pathogens, all at the same time,” Deeg said.
Salmon on the high seas had fewer pathogens than those found on the coast. That means the salmon either recover from the infection after leaving the coast, or these diseases are so costly that infected fish die before they reach the open sea, he said.
Pathogens found in the open ocean appear to have been transmitted there, from prey or between salmon.
Gene expression patterns of 90 salmon genes associated with their response to stressors were also analyzed.
Rather than having certain genes expressed in relation to certain stressors, salmon showed a tendency to reduce the expression of many “non-essential” genes.
“Basically, these fish are trying to save energy and not do things they don’t need to do,” he said.
But this poses a trade-off, as fish with this expression pattern generally had higher levels of opportunistic pathogens.
“In these fish, when they downregulate genes, like their immune system, these pathogens have an easier time, so there are more of them, which is obviously not necessarily good for the fish,” said said Deeg.
Salmon showing this pattern of expression were often found where prey was less abundant.
“It suggests they are doing this because they weren’t getting enough food there,” he said.
At the time of sampling, there was a marine heat wave, meaning high water temperatures may have affected the food web, reducing food availability. Since salmon are cold blooded, they also expend more energy in warmer waters.
“We’ve seen this pattern where all of these factors combine – it looks like in a warming ocean the salmon are struggling because they’re not getting the food they need and they have to use more energy,” he said.
As the study represents a “snapshot in time”, rather than a measured trend, the researchers cannot be sure that this is why fewer salmon are returning from the ocean.
Better understanding this dynamic is one of the goals of the Pan-Pacific Winter High Seas Expedition 2022, a multi-ship venture of which Deeg will be a member. On this expedition, researchers will try to get more samples from a larger area of the ocean, to help compare trends between ocean areas with normal temperatures and warmer ones.
“If we can get enough samples from these regions, we can really determine how different ocean conditions affect salmon,” he said.