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Hardy Bacterium is Target for Genome Sequencing
A bacterium that is completely comfortable living in some of the most hostile environments on Earth will be among more than 40 projects undertaken for genome sequencing by the U.S. Department of Energy (DOE) over the next year.
Chris Mackenzie, Ph.D., is working at the UT Medical School at
Houston to better understand the genetic makeup
of a bacterium
that endures in some of the most hostile environments on Earth.
Photo by David Mendel
At The University of Texas Medical School at Houston, Chris Mackenzie, Ph.D., is eager to learn more about the genetic makeup of this hardy bacterium, Pedomicrobium, which is capable of enduring blazing desert heat and drought, radiation and ultraviolet light. Mackenzie is research assistant professor of microbiology and molecular genetics.
Pedomicrobium lives on the surface of desert rocks. This ecological niche can expose it within minutes or hours to massive fluctuations in temperature, ultraviolet irradiation and states of hydration.
“Consequently, its genome must have evolved to encode the diverse physiological capabilities required for survival in this inhospitable environment,” said Mackenzie, principal investigator on the Pedomicrobium segment of the DOE Joint Genome Institute (JGI) project.
Looking beyond our own planet, this organism has piqued the interest of NASA’s Ames astrobiology group. Its ability to withstand environmental extremes on rock surfaces makes it a model organism for the study of potential life on other bodies in our solar system.
Besides deserts, Pedomicrobium also exists in aquatic and marine environments, within sediments extracted from deep boreholes and soils.
Uranium Sites
Of particular relevance to the DOE is the fact that the microbe makes up a significant part of the soil at sites where uranium was mined during the Cold War for producing energy or nuclear weapons. Residue from many of these mines threatens to contaminate groundwater and, in some cases, has done so already.
The DOE JGI Community Sequencing Program seeks alternative clean energy sources and methods of environmental clean-up.
“Adding credence to Pedomicrobium’s possible role in bioremediation is that it has been used in pilot bioreactor purification plants to assist in the removal of magnesium and radioactive metals from contaminated water,” Mackenzie said. “More recently, it has proven effective in the removal of uranium and radium from a uranium mine retention pond in Australia. The ability to live in sites contaminated with radioactive waste and its tolerance to ultraviolet light make it of interest to groups examining radiation tolerance and DNA repair.”
Pedomicrobium is the only bacterium from those mine sites that has not been examined by genome sequencing. Most bacteria divide by binary fission. However, Pedomicrobium divides by branching and has a complex internal membrane system, two features that endear it to the study of microbial development.
Desert Varnish
On desert rocks it is a component of a biofilm, a blend of various types of bacteria, fungi and lichens that oxidizes manganese metal to manganese oxide, generating a dark patina called desert varnish. This characteristic makes Pedomicrobium intriguing to geologists and biologists alike. However, the scientific community understands very little about the underlying biology of desert varnish formation. “Indigenous peoples have carved this varnish to produce petroglyphs,” Mackenzie said. “Such carvings are visible at sites such as Petroglyph National Monument. The preservation of this important part of our national heritage falls to the Department of the Interior, and its geologists and archaeologists look on this genome project with enthusiasm.”
Other findings suggest that Pedomicrobium may be involved also in the deposition of gold flakes and veins, which could have implications in the fields of biology, bioremediation and commercial mining.
As part of this year’s DOE JGI program, more than 15 billion letters of genetic code – the equivalent of the human genome five times over – will be processed through the DNA sequencers at the DOE JGI Production Genomics Facility in Walnut Creek, Calif. Ultimately, the information will be made freely available to the greater scientific community.
By David Mendel, Institutional Advancement