Prepping gene libraries
Hot Water Wildlife
Thermus Aquaticus may be the star of the story, but Yellowstone pools hold many more microbes of interest:
Going from park to pipette, a lab tech at Diversa in La Jolla builds a genetic library of useful genes from dozens of Yellowstone hot springs specimens.
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: blindstrom @ wyellowstone. com Jeff Stein, PhD’ 91, is president and CEO of Cidara Therapeutics, a San Diego biotechnology company.
Photos: Jill Scarson
Thermoanaerobacterium thermosulfurigenes is a producer of amylase, used in the food and beverage industry to break down starch. It has potential in brewing and starch processing.
Thermoanaerobacterium xylanolyticum is named for its growth on xylan, or the cell wall of plants. Its enzymes break that structure down, which could be applied to the pulp and paper industry.
And the newly identified
Marsarchaeota is of great interest to astrobiologists: Found in iron-rich, low-oxygen areas, it may be similar to the kinds of life someday found on Mars. Yellowstone has even become a NASA training ground for identifying fossil evidence of organisms on extraterrestrial volcanoes.
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