SIU researcher discovers new bacterium living deep beneath former atomic test site

Those hilariously serious nuclear age monster movies from the 1950s haven’t got anything on the latest discovery by a researcher at Southern Illinois University Carbondale. Only his science is for real, and it could lead to important breakthroughs in understanding how life makes its way beneath the Earth’s surface, and possibly on other planets.

The SIU team, led by Scott Hamilton-Brehm, assistant professor in the microbiology degree program, isolated a bacterial genus that is anaerobic and thrives at hot temperatures. But maybe the most interesting thing is where it was found: Deep beneath the area formerly known as the Nevada Test Site, where the United States conducted hundreds of nuclear tests between 1951 and 1992.

Scott Hamilton-Brehm picture
Scott Hamilton-Brehm, assistant professor in the microbiology degree program at Southern Illinois University Carbondale, works in his laboratory. Hamilton-Brehm led a team of researchers that recently isolated a bacterial genus found deep beneath the area formerly known as the Nevada Test Site, where the United States conducted hundreds of nuclear tests between 1951 and 1992

The team of researchers, including those from the University of Nevada Las Vegas and the Desert Research Institute (DRI), have proposed the name of the new life form Thermoanaerosceptrum fracticalcis, strain DRI-13, and recently published their findings in the open source journal Frontiers in Microbiology.

Digging deep

Life in the deep fractured rock ecosystems across North America remains mostly a mystery. But the Great Basin, which in particular includes the Nevada National Security Site (formerly the Nevada Test Site), has played host to several influential subsurface investigations.

Hamilton-Brehm said he got interested in investigating life forms pulled from deep mines and wells in that area during his post-doctoral studies at the DRI in Las Vegas.

Duane Moser, a senior staff scientist at DRI and former mentor of Hamilton-Brehm, received grants to study how subsurface microorganisms affect radionuclide movement in underground water systems. The deep groundwater samples in which the organism was extracted were collected during routine monitoring of a well associated with the Bilby underground nuclear test, which took place on Sept. 13, 1963. The well is 923 meters deep, or more than half a mile underground.

Gaining access a challenge in itself

It’s not easy to find a hole that deep. Anywhere. Period. Access to the life this deep underground is a constant challenge for researchers based on that logistical challenge alone. Because of that, mines and wells created for other purposes – in this case studying the effects of a nuclear blast – are about the only opportunities that exist.

“That means access is at the pleasure of site owners and managers, in this case the federal government,” Hamilton-Brehm said. “The entire Nevada National Security Site is subject to controlled access and the samples needed to be collected not only with permission, but also considerable logistical support from the Department of Energy and its contractors. Without this support, the project would not have been possible.”

As it was, the DOE does allow visits to such sites through tour reservations. And the Bilby shot, which was part of group of 41 nuclear tests under the umbrella name of Operation Niblick, is a popular feature of the tour, Hamilton-Brehm said. Security is tight, with items such as cameras, camcorders, tape recorders, cell phones, binoculars, computers and other items, prohibited.

“Visitors may not pick up or remove soil, rocks, plant samples or metal objects from the NNSS,” the tour website states.

Samples date back to 2011

But back in 2011, some of Hamilton-Brehm’s post-doctoral colleagues at the DRI managed to gain access to the site where water from a deep zone of fractured carbonate rock is was being pumped during routine monitoring. Researchers Moser and Jenny C. Fisher collected water samples in airtight, stoppered bottles. The DOE in this case allowed the researchers to take the samples with them, to Moser’s lab in Las Vegas, where there were continually stored at 4 degrees Celsius – about 39 degrees Fahrenheit.

Hamilton-Brehm, who started working there in 2012, began enriching and analyzing the samples, eventually isolating the new genus of bacterium. His research on the microorganism spanned into his time at SIU, where he was able to publish the findings using startup funds and publishing open-source support from Morris Library.

Finding, characterizing a new life

During his research, Hamilton-Brehm enriched the water samples with protein, teasing out and characterizing the single microbial strain.  Eventually, researchers discovered the novel bacterial genus and species, known as DRI-13, had very limited ability to use carbon and instead subsisted primarily on the abundant intracellular metabolite, fumarate.

“The subsurface here had very limited carbon and energy resources to sustain the metabolic activities needed for life,” Hamilton-Brehm said.

With such a narrow menu to “eat” from, the researchers hypothesized that the microorganism might somehow live off products given off by other subsurface microorganisms, Hamilton-Brehm said. But genome analysis revealed an important secret: The organism was carrying so-called TRAP transporters, which allow an organism to transport molecules without expending energy to do so.

The fact that the organism was found in a largely nutrient-starved environment give scientists clues about how life can exist there.

Where else might such environments exist?

Well, places like other planets, for instance.

“The TRAP transporters might help DRI-13 balance the checkbook of life,” he said. “In this case, it able to keep a low overhead of metabolic bills to pay in order to sustain life in this extreme environment. Understanding how this model microorganism lives can enhance our interpretations of where life can survive in other similar subsurface environments, such as Mars.”

Samples continue teaching at SIU

As he started his first year as an assistant professor at SIU, Hamilton-Brehm used the anaerobic culturing and harvesting of the DRI-13 cells as a teaching tool for undergraduate students (Brittany Jones and Mitchel Peal both graduated in 2017 from the Department of Microbiology).The cell pellets were used to determine the membrane lipid profile, a signature of a microorganism, much like your own finger print.

Trevor Murphy, a current graduate student of Hamilton-Behm’s, is using high performance computers to stitch together the DNA of DRI-13 into a complete genome. The genome is a DNA library of genes that make up a particular life form. Analyzing the genome of DRI-13 may provide further hints as to how subsurface ecologies operate.

“Trevor has made several more discoveries through analyzing the genome, even some surprises like imbedded subsurface viruses that may lead to a better understanding what the subsurface life for a microbe is like,” Hamilton-Brehm said. “His findings are expected to be published in a follow up manuscript to this one.”

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