UNIVERSITY PARK — Brook trout may have a genetic trick up their scales when it comes to adapting, with limitations, to heatwaves that threaten their existence.

Scientists have known for years that brook trout — an iconic coldwater fish species native to streams and lakes in the eastern United States and Canada — are extremely vulnerable to warming temperatures, with more than half of their habitats characterized as highly sensitive and highly vulnerable to such changes by U.S. Forest Service researchers in 2010.

Now, a novel study led by researchers at Penn State suggests that brook trout are capable of mounting a protective genetic response to thermal stress that can be passed on from one generation to the next.

“The responses to heat stress had a high degree of plasticity, with brook trout exhibiting the ability to acclimate and increase tolerance to higher temperatures,” said team leader Jason Keagy, assistant research professor of wildlife behavioral ecology. “Our study covered two heatwaves, and the overall change in expression patterns was more intense during the second heatwave. We think the first heatwave ‘primed’ the response for the second.”

In findings recently published in Science of the Total Environment, the researchers reported that groups of genes involved in immune response and oxygen-conveying activity were upregulated and downregulated, respectively, at higher water temperatures in two successive heat waves in July and August 2022 in four small central Pennsylvania mountain streams.

“Detecting these gene-expression fingerprints of thermal stress allows us to directly ‘ask’ the fish how they are feeling, whether they are stressed out,” Keagy said.

The team closely monitored air and water temperatures and sampled 116 brook trout at eight time points during the heatwaves in each of the four streams. Keagy and his collaborators extracted the fish’s RNA — the genetic material used to build proteins and help regulate biological functions — from their gills without injuring the fish.

They sequenced the RNA, a technique that reveals the number of molecules and in what order they appear, and quantified the expression levels of 32,670 unique genetic transcripts, which carry the instructions for proteins essential for cell and tissue function. The team found that overall gene-expression patterns in response to water temperature change were similar among fish in all four streams studied.

The researchers also detected 43 genes that were differentially expressed at different time points and followed the same expression pattern during the two heatwaves. Of these genes, 42 related to water temperature. Some of these differentially expressed genes — including those producing heat-shock proteins and cold-metabolism proteins — have been linked to temperature responses in other studies, the researchers said.

Keagy noted that brook trout begin to experience declines in growth rate in water above 61 degrees Fahrenheit and acute heat stress above 68 degrees Fahrenheit, with critical thermal maximum temperatures reached near 84 degrees Fahrenheit.

He explained that the frequency and intensity of extreme weather events is increasing, which is predicted to reduce suitable thermal habitats for brook trout, especially when combined with other environmental changes like land-use that removes forests along streams and the introduction of non-native competitors like brown trout.

“Critically, extreme weather events can be more important drivers of extirpation (state or regional disappearance of a species) and selection than changes in annual or seasonal averages, and they pose a particularly large threat to cold-blooded organisms with body temperatures that fluctuate with their environment,” Keagy said.

Studying the gene response of fish to temperature in nature where conditions are “messy,” rather than in the controlled conditions of a lab was a complicated and challenging endeavor, Keagy pointed out.

“This study was a massive undertaking,” he said. “We identified heatwaves using local weather predictions of air temperature and then tried to capture fish at the beginning, peak, ending and one week after each heatwave. We had no way of predicting how the stream water temperatures would be responding. And yet — led by our talented graduate student Sarah Batchelor, co-author on the paper — we pulled it off quite well. Then, the data analysis was not straightforward — gene-expression studies tend to be much simpler when based in the laboratory — but our lab’s postdoctoral scholar, first author Justin Waraniak, came up with novel and creative ways to analyze the data.”

This study was the one of the firsts test of the emerging field of landscape transcriptomics, recently envisioned by an interdisciplinary team led by scientists in Penn State’s College of Agricultural Sciences.

The team, which Keagy leads, hypothesized that it would be possible to collect animals and plants from the wild and determine which stressors they experienced based on specific patterns or signatures in their gene-expression profiles. This is the second landscape transcriptomics paper published this year, with another research group in the college recently publishing on stressors in bumble bees.

“This study shows the utility of landscape transcriptomic approaches to identify important biological processes governing wild organisms’ responses to short-term stressors,” Keagy said. “The results of this study can guide future investigations to identify phenotypic and genetic diversity that contribute to adaptive responses to heatwaves and improve predictions of how brook trout populations will respond to future climate change.”

This research was supported by grants from the Penn State College of Agricultural Sciences Strategic Networks and Initiatives Program and the U.S. Department of Agriculture’s National Institute of Food and Agriculture.