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Gold Mine Metagenomics Project Uncovers Lone Microbe

NEW YORK (GenomeWeb News) – Researchers reported today that they have discovered a bacterial community containing just one species deep within a South African gold mine.
Using metagenomics, an international team of researchers probed the microbial community in gold mine water nearly two miles beneath the Earth’s surface. The researchers found just one microbe in the sample — a bacterial species that they dubbed Candidatus Desulforudis audaxviator. In a paper appearing online today in Science, the researchers describe their find, as well as their subsequent sequencing and characterization of the bug’s genome — a chance afforded them by the species’ solitude.
“It presented us with an opportunity,” senior author Tullis Onstott, a geoscientist at Princeton University, told GenomeWeb Daily News, “because we had not been able to grow this organism.”
Onstott has been studying deep mines in South Africa for roughly a decade. For the latest paper, he and his team sampled water from deep within a gold mine — about 1.74 miles below the Earth’s surface — near Johannesburg, South Africa. By filtering 5,600 liters of water, the researchers were able to pull bacterial DNA from that environment.
But it turned out that the fault site was home to single bacterial species: D. audaxviator, a previously unnamed organism that has also been detected by its 16S rRNA in gold mines in South Africa’s Witwatersrand basin.
“We expected we’d have a good chance of assembling one entire genome of the most dominant species, or perhaps 70 to 80 percent of several species,” lead author Dylan Chivian, a post-doctoral resaercher at the Lawrence Berkeley National Laboratory, said in a statement. “What we instead discovered was that there was only one organism present in the sample. More than 99.9 percent of the DNA came from that single organism, and the tiny remainder appeared to be trace contamination from the mine and the laboratory.”
By filtering large volumes of water, the team got enough D. audaxviator to sequence the genome. Onstott and his team collected the samples and passed them on to the Pacific Northwest National Laboratory, where collaborators extracted the bug’s DNA. The sequencing and analysis were subsequently done by researchers at the Lawrence Berkeley National Laboratory and the US Department of Energy’s Joint Genome Institute, who used a combination of Sanger and Roche 454 sequencing to sequence the 2.35 megabase genome of the new organism.
The D. audaxviator genome was both predictable and surprising, Onstott explained. Based on their analysis, the researchers predicted that it contains 2,157 protein-coding genes. Some of these genes would have been obvious based on the organism’s geochemistry, Onstott said. For instance, the D. audaxviator genome housed genes involved in sulfate reduction and hydrogen gas use — genes that are consistent with pathways that are expected to be energetically favorable in the deep crack environment.
But others were unexpected. For example, the researchers found a gene coding for a nitrogenase enzyme that converts dinitrogen to ammonia. “That was a bit of a shocker,” Onstott noted, given that the dinitrogen to ammonia conversion is a high-cost process, energetically speaking. The team also found genes coding for chemotaxis and flagella, suggesting the bug is actually mobile.
In addition, the researchers found clustered regularly interspaced short palindromic repeat, or CRISPR, sequences — regions used as defense mechanisms against viral infections. That hints at viral life in this region, Onstott said, although the filters used for this study would be too large to pick up viruses, if present. In the future, Onstott noted, he is interested in going back and looking specifically for viruses in this environment.
Overall, the genome suggests that D. audaxviator is self-sufficient and capable of producing everything it needs to survive using inorganic carbon and other resources from deep within the Earth. “This bold traveler (audaxviator) has revealed a mode of life isolated from the photosphere,” the authors wrote, “capturing all of the roles necessary for an independent lifestyle and showing that it is possible to encode the entire biological component of a simple ecosystem within a single genome.”
And that has the researchers excited. “It’s sort of philosophically exciting to know that everything necessary for life can be packed into a single genome,” Chivian said.
Even so, Onstott said, it’s still unclear which genes are actually functional. He said the team eventually plans to set up a lab even deeper underground to test gene functionality. They are also interested in determining why and how this particular organism has been selected in this environment. “We don’t know why it’s so successful down there,” Onstott said.
Onstott noted that the team is currently trying to secure funding to do similar studies in the Homestake Mine — a former gold mine in South Dakota that’s now a hotspot for neutrino research.

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