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Caldera Chronicles

Caldera Chronicles is a weekly article written by U.S. Geological Survey Yellowstone Volcano Observatory scientists and colleagues.

March 30, 2020 Article Link

How a thermophilic bacterium from a Yellowstone hot spring is helping the fight against the COVID-19 pandemic.

Yellowstone Caldera Chronicles is a weekly column written by scientists and collaborators of the Yellowstone Volcano Observatory. This week's contribution is from Jeff Havig, professor of Earth and Planetary Science, and Trinity Hamilton, professor of Plant and Microbial Biology, both at the University of Minnesota.

Epidemiologists are working around the clock to understand and learn how to best fight the virus named COVID-19 (aka, the coronavirus), while the healthcare system is doing its best to take care of those made sick by the virus. Over the past few months, the world has taken unprecedented measures to stop the spread of the virus; understanding how it spreads is critical as well. And this is where Yellowstone enters the picture. We would not be able to test for the COVID-19 virus without microbes from Yellowstone hot springs!

Bacterium Thermus aquaticus (Click image to view full size.)
Bacterium Thermus aquaticus

While each of us do our part through social distancing, restricting contact with others, and eliminating unnecessary travel, epidemiologists have specialized tools they use in their fight. One of these that you may have heard discussed in the news or via social media releases is the Polymerase Chain Reaction. PCR amplifies the amount of DNA in a sample. So when a sample is collected from a person suspected to be infected by COVID-19, viral RNA is extracted from the sample, converted into DNA, and then replicated with a PCR machine so that even the smallest amount of RNA in the sample can be detected and quantified. Without PCR, the race to count the infected and develop a vaccine would be dramatically hindered.

At the core of PCR is an enzyme called taq polymerase (the P in PCR), which can amplify DNA at high temperatures. This allows a sample with DNA to be heated and cooled, with each cycle of heating and cooling resulting in a doubling of the amount of DNA (and a rapid increase in the amount of DNA to analyze). So where did this seemingly magical enzyme come from, you might wonder? To answer this, we have to take a trip back in time.

In 1966, Professor Thomas Brock of Indiana University was just getting started with his research studying microorganisms in Yellowstone hot springs. He was interested in learning about life that thrived at temperatures that would give a human third degree burns from just moments of exposure.

Mushroom Pool, in the Lower Geyser Basin of Yellowstone National Park. The pool is the source of the sample of Thermus aquaticus strain YT-1 taken by Thoas Brock in 1966. (Click image to view full size.)
Mushroom Pool, in the Lower Geyser Basin of Yellowstone National Park, as it looked in June 23, 1967. The sample that would be the source of Thermus aquaticus strain YT-1 came from this hot spring. Pictured is Thomas Brock standing near the edge of the pool. Image from the self-published "A Scientist in Yellowstone National Park" (Brock, 2017).

At the end of their field work in Yellowstone, Brock and his then-undergraduate student Hudson Freeze collected some microbial mat samples to bring back to the lab to attempt isolating microorganisms, including a sample of a photosynthetic mat thriving at 71.5°C (160 °F) in Mushroom Spring (located in the Lower Geyser Basin). From this sample, Freeze and laboratory technician Sally Murphy worked to isolate the bacterium Thermus aquaticus strain YT-1. This bacterium was then studied through the 1970s and 1980s, with the basis of the patent for PCR founded on the themo-stable enzyme taq polymerase from T. aquaticus YT-1.

From there, amazing innovations including sequencing the human genome, genetic tests, and characterizing entire microbial communities across the globe came to be, with some of this research even garnering the Nobel Prize! Now, as our health care professionals scramble to determine infection and transmission rates and how to combat the new COVID-19 (and any future infectious diseases), we can look back to research describing microbes in Yellowstone hot springs to see how fundamental explorative scientific research is an amazing benefit to humankind. In a place perhaps better known for megafauna, like bison, elk, wolves, and bears, it is the microfauna—the bacteria that live in the hot springs—that are providing some of the most important weapons in our fight against deadly diseases and viruses.