Saving Sal

New technology could keep one incredibly popular pet from going extinct

Environmental DNA can diagnose pathogens before they end up in your pet's tank.


They are some of nature's raddest creatures. Some species can regrow limbs, glow in the dark, and live at least 50 years. For these qualities, they are incredibly popular for many who prefer a "hands-off" pet.

Unfortunately, the amphibian, a freakishly cool amphibian, is under threat of a deadly fungus that effectively eats them alive. Researchers have developed a new way to detect the dangerous pathogen in one of its most common avenues into the United States: the pet trade.

The new method of identifying the salamander pathogen Batrachochytrium salamandrivorans, or Bsal, relies on what's called environmental DNA — eDNA for short. That essentially involves taking samples from an animal's habitat (water, soil, poop), and it's often used to detect animals in an ecosystem: Animals shed bits of skin, for instance, which is traceable in the eDNA.

When an animal is infected with something like Bsal, it will also shed bits of that pathogen. So taking samples of the water from salamanders' tanks can help to detect Bsal, new research shows — and keep it from contaminating millions of animals shipped around the globe as pets. In turn, that may help stop some species from going extinct.

This process — scanning water's eDNA to look for Bsal — is far more efficient than taking samples from individual animals, reports biologist Jesse Brunner in a paper published on Wednesday in the journal Scientific Reports.

In the study, Brunner describes the statistical formulas that would underlie this kind of salamander surveillance and explains how scientists would need to scale up the process. Brunner and others are in the process of testing the framework described in the study.

Fire salamanders are common in Europe, where Bsal has already been detected. Jasius/Getty

Keeping the US fungus-free — Each year, more than 225 million live animals are imported into the US — the vast majority of which are pets.

A 2017 analysis showed that Bsal is not present in pets in the US. But that doesn't guarantee the safety of future aquatic animals. In Europe, the pathogen has made the jump from pets, imported from Southeast Asia, into wild salamander populations.

The US is home to the world's greatest salamander diversity. To protect wild species from becoming infected, the US Fish and Wildlife Service has already banned 201 salamanders species from entering the country.

"The best way to prevent the emergence of these pathogens, and the diseases that come from them, is to keep them from getting here in the first place," Brunner said. A researcher at Washington State University, Brunner is also part of a Bsal Task Force aimed at keeping the fungus under control.

The sleek Northern two-lined salamander lives in forests, shrublands, and rivers of the US and Canada.Paul Starosta

Fending off Bsal saves salamanders from a particularly nasty death. The full name of the fungus literally means "salamander-eating," referring to "extensive skin destruction and rapid death in infected salamanders."

Being able to accurately and efficiently test for Bsal can be a matter of life or individual salamanders. It might also stave off the extinction of some species. We've seen a pathogen-related demise of amphibians before: A related pathogen, called Batrachocytrium dendrobatidis, was responsible for decimating more than 500 amphibian species and driving 90 species to extinction. Most of that damage happened in the 1980s, marking the "greatest recorded loss of biodiversity attributable to a disease," according to a 2019 study.

While keeping the fungus away from the US is key, it's difficult to scale-up screening for the pathogen when dealing with animals on the order of millions.

"With the eDNA method you are theoretically sampling an entire population at once," Brunner said, "so you are more likely to detect whatever is there, and you can do that much more efficiently than with traditional approaches."

Abstract: The regional and international trade of live animals facilitates the movement, spillover, and emergence of zoonotic and epizootic pathogens around the world. Detecting pathogens in trade is critical for preventing their continued movement and introduction, but screening a sufficient fraction to ensure rare infections are detected is simply infeasible for many taxa and settings because of the vast numbers of animals involved—hundreds of millions of live animals are imported into the U.S.A. alone every year. Batch processing pools of individual samples or using environmental DNA (eDNA)—the genetic material shed into an organism’s environment—collected from whole consignments of animals may substantially reduce the time and cost associated with pathogen surveillance. Both approaches, however, lack a framework with which to determine sampling requirements and interpret results. Here I present formulae for pooled individual samples (e.g,. swabs) and eDNA samples collected from finite populations and discuss key assumptions and considerations for their use with a focus on detecting Batrachochytrium salamandrivorans, an emerging pathogen that threatens global salamander diversity. While empirical validation is key, these formulae illustrate the potential for eDNA-based detection in particular to reduce sample sizes and help bring clean trade into reach for a greater number of taxa, places, and contexts.
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