From natural wonders springs trailblazing science.
It may be a stretch, but here goes: Everything made possible by modern DNA technology was made possible by Yellowstone National Park.
Specifically, by a particular microorganism—a strain of bacteria that lives in the park’s many thermal pools and geysers. How it went from the water’s edge to scientific ubiquity is not only a story of UC San Diego alumni, but a story told by a Triton, Robert Lindstrom ’73, in his recent book that is also the namesake of this article. It’s the story of bioprospecting, of finding an organism that unlocked one of the most revolutionary scientific advancements of the 20th century—which is a pretty remarkable legacy for what the untrained eye might consider just a bright yellow goo.
Whether yellow, orange, red or green—the spectrum of colors in Yellowstone’s thermal pools and the rest of the the area’s magnificence is nothing new, of course. It’s been known as a natural wonder ever since it was Native American land, made the world’s first National Park in 1872 and now frequented by millions of visitors year after year. But the first person to take a scientific interest in Yellowstone’s pools was Thomas Brock, a microbiologist whose curiosity was sparked during a vacation in the mid-1960s. Brock returned to place microscope slides in a few pools, and soon enough, the slides were coated in bacteria, one of which Brock named Thermus aquaticus, from the Greek for “hot water,” a nod to the 170°-180°F-degree environment that makes a perfect home for these golden mats of microbes.
Dubbed Taq for short, it is just one of many microorganisms known collectively as “thermophiles,” another Greek nod meaning “heat-lovers.” Brock did his due diligence in cataloguing this new bacterial species by culturing Taq in a lab and placing a specimen in the American Type Culture Collection (ATCC), a national nonprofit that serves largely as a library reference desk for such bioresources. And there Taq remained, waiting for its moment.
Meanwhile, at UC San Diego, a counterculture was blossoming in the late ’60s as a new student matriculated from Brandeis University to the graduate program in biology. David Gelfand, PhD ’70, arrived on campus equally as interested in folk music and scuba diving as he was in science. “I knew nothing,” he says, “and I wanted to change the world.”
Studying gene expression under Professor Masaki Hyashi, Gelfand remembers years of intense work and extreme independence. “You had to learn everything on your own, but I did learn science very well,” he says.
By the time Gelfand headed to the San Francisco Bay Area with his degree in the early 1970s, another young student was riding his motorcycle onto campus, fresh from the Army and a recent transfer from community college to Muir College. Robert Lindstrom recalls a campus alive with protest, “a very revolutionary period,” he says. The same description went for his chosen major in biology, where breakthroughs in the understanding and usage of genetics were taking the discipline to exciting new frontiers.
“The more I learned, the more I thought it was beautiful, how it all worked,” says Lindstrom. “I grew up fascinated with the tide pools in Ocean Beach, but professors like Ralph Lewin and Michael Soule opened up the world of biology to such deeper levels. I was learning about enzymes and ribosomes; it was so enlightening.”
After some post-graduation rambling through the Americas, Lindstrom eventually headed to Montana, where he found work in logging and was able to purchase property with friends. The logging experience would be of use in building himself a cabin, as well as in his first job in Yellowstone National Park on a crew cutting trails. Yet his UC San Diego education never left him, especially when proposed trails crossed habitats only a biology major would know about. “One day, my crew wanted to cut through a hot spring overflow with thermophiles in it,” he says. “It just looked like orange slime to them; no one knew what it was. But I said, ‘Not only is that alive, but it may not be found anywhere else on the planet!’”
Needless to say, the trail went around.
Back on the West Coast, Gelfand was a postdoctoral fellow at UC San Francisco when he got a call from Cetus Corporation, an early biotechnology company that wanted him to lead a brand-new genetic engineering division. Gelfand was reluctant to leave academia at first but ultimately took the job, seeing great potential for doing collaborative work, his preferred mode of science.
There were plenty of collaborators to be had at Cetus. While the general life and times at the company are described in detail in Paul Rabinow’s 1996 book, Making PCR, it’s fair to say that relationships within the organization were at times congenial, at times contentious, but above all, exciting. After all, the company was at the forefront of using genetics to develop clinical therapeutics such as interferon and cancer-fighting pharmaceuticals that could benefit society on a large scale.
There was also the particular focus of a particular scientist, Kary Mullis, who would ultimately go on to earn the Nobel Prize for his conception of the polymerase chain reaction, or PCR, a novel method of amplifying DNA. There were a number of factors contributing to Mullis’ creation of the concept, one of which was frustration with the prevailing method of DNA analysis at the time, Southern blotting. It was a process of variable accuracy requiring many steps and substances such as gels, electricity, photosensitive films and—the clincher—radioactivity. Mullis started thinking of another way.
The goal was to take an entire genetic code and detect a target fragment of DNA—one piece of code that might indicate the presence of a certain disease. As for analogy, the endeavor could be likened to listening for a distinct yet barely-audible tone in a cacophonous sea of static. Methods like blotting were analogous to recording the cacophony and sorting out the tones so that a super-sensitive listening device might hear the one being sought. Mullis’ concept was different: Isolate the tone—the DNA fragment—and turn its volume up to a billion (see sidebar).
As early experiments of PCR eventually saw success, its benefits became apparent: PCR promised to be quicker, simpler, more sensitive and convenient—theoretically, the whole process could be done in one test tube, with cycles automated by a machine.
Yet there was one hitch—the rounds of high heat required to split the DNA also degraded the enzyme that catalyzed the chain reaction. They needed something that could take the heat, so to speak—a thermostable enzyme that could withstand the temperature fluctuations. Gelfand had been in PCR meetings at Cetus due to his experience in enzymology, and though making such an enzyme was not quite within his purview, he and colleague Suzanne Stoffel had the tools and the enzymatic know-how. Gelfand also knew where to start, securing thermophilic cultures from the ATCC—including the strain of Taq that Brock had obtained from Yellowstone years prior. After hard work in the lab, Taq’s efficacy ultimately transformed the process. Says Gelfand, “It was amazing. Not only did it enable PCR, but it enabled automation. You put everything in a tube, and that’s it.”
The rest is biotech history, as PCR would come to revolutionize medical diagnostics, support AIDS testing and research, catch criminals, free those wrongly convicted, enable the Human Genome Project (featuring another Triton, J. Craig Venter ’72, PhD ’75), connect us with our ancestry and, of course, become the gold standard in detecting COVID-19 on nasal swabs the world over.
But let’s rewind back to our man in Yellowstone: Lindstrom’s biology education kept bubbling up through further roles at the park, until he eventually became the research permit coordinator—the primary liaison for scientists seeking biological samples from park lands. “Eventually, it was understood that I could talk knowledgeably to these scientists about what they wanted and where it might be found,” he explains. PCR had hit the big time, and with Yellowstone yielding the key that unlocked the process, other bioprospectors were eager to see what else could be found. “Before Taq, nobody really understood the potential of thermophiles,” says Lindstrom. “But afterward, there was a surge of interest in every kind of habitat: pools and mudpots of different temperature, pH, acidity. In such unique chemistry, there were a lot of unknowns.”
Would the next enzyme be the protein-eating protease, thermophilic enough to survive the hot water cycle in a laundry machine? Or something from Thermoanerobacter ethanolicus, which turns sugar into ethanol? Such interest inspired Lindstrom to host the first science conference on Yellowstone microbiology, bringing together key figures such as Brock and Gelfand along with microbiologists, astrobiologists, lawyers, corporate executives and conservationists alike. “We needed to have a conference to straighten out bioprospecting and its attending issues, like who owns the patent rights,” he says. “Brock had put Thermus aquaticus in the ATCC well before anyone thought of things like that, and Gelfand got his from there, so the issue was moot when it came to PCR. But moving forward, it was apparent that the national park system had to consider how to preserve the genetic resources they had, and make policy on allowing for their use by industry for the benefit of society.”
Among the first to engage in these new policies was the San Diego biotech company Diversa, which entered into an intellectual property agreement with the National Park Service to commercially develop products derived from Yellowstone’s genetic resources. Jeff Stein, PhD ’91, led Diversa’s microbial diversity division at the time and was among the researchers Lindstrom brought to the backcountry.
While in graduate school at Scripps Institution of Oceanography, Stein had done similar bioprospecting, albeit underwater in the unique seafloor environments near hydrothermal vents. After graduation, Stein was at the forefront of using the PCR process to capture DNA sequences straight from the environment, without having the extra step of pure-culturing microbes in a lab, like Brock had done with Taq. “Another Scripps graduate, Ed DeLong, PhD ’86, contributed to the discovery that 99% of microbes in environmental samples could not be grown in pure culture,” Stein says. “Yet if a majority of our drugs came from that 1% that could be cultivated, imagine the potential in the vast majority of microbes that cannot be grown.”
Stein’s team took samples from Yellowstone with a loose idea of what they were looking for, mostly enzymes that may have industrial applications. But they were also extracting all kinds of environmental DNA and screening for any enzymatic activity, open to discovering possibilities they didn’t expect. “We found the enzyme phytase, for instance,” he recalls, “which can be used in livestock feed to help break down phytic acid. Normally, that acid sequesters nutrients in grains and makes them inaccessible. But a thermostable enzyme could survive the feed extrusion temperatures and release those nutrients.
“So much of what we found was unexpected,” he continues. “And that can be a common theme when working in these areas—a preconceived notion of what should be there can often be an impediment to understanding what you might actually find.”
As for what might yet be found through bioprospecting, the proverbial toe has only been dipped into that pool—in Yellowstone and beyond. The value of such natural resources is great and well worth protecting, Lindstrom holds: “To think that Taq was inadvertently preserved for so long without knowing its potential, and then it opens up a whole world of discovery.” His book can be read as an homage to such discovery, a salute to the thermophile and an appreciation for being able to serve our natural wonders, be they magnificent lands and animals or microscopic species. “I’m just a regular guy who got an amazing education,” he says. “It’s served me well, and it’s served Yellowstone, too.”
David Gelfand, PhD ’70, still consults on PCR in his retirement in Oakland, Calif., with Ellen Daniell, PhD ’73.
Robert Lindstrom ’73 retired from the park service and wrote Laboratory Yellowstone, available on Amazon. He lives near the park and has restored a log cabin for rentals. He can be reached at: email@example.com
Jeff Stein, PhD ’91, is president and CEO of Cidara Therapeutics, a San Diego biotechnology company.