Published online 9 October 2008 | Nature | doi:10.1038/news.2008.1160


One is the loneliest number for mine-dwelling bacterium

Sole member of world's first single-species ecosystem depends on rocks and radioactivity for life.

bacteriumThe rod-shaped D. audaxviator was recovered from thousands of litres of water collected deep in the Mponeng Mine in South Africa.Greg Wanger, J. Craig Venter Institute / Gordon Southam, University of Western Ontario

Nestled kilometres down in the hot, dark vaults of Earth's crust, scientists have discovered a remarkably lonely bacterium species.

The rod-shaped bacterium, Candidatus Desulforudis audaxviator, lives independently of any other organism in a part of the Mponeng gold mine near Johannesburg, South Africa, some 2.8 kilometres beneath Earth's surface.

There, water flows from a kilometres-deep fracture in the rock. Researchers led by Tullis Onstott of Princeton University, New Jersey, and Li-Hung Lin of the National Taiwan University, Taipei, had previously found that the water was populated by highly unusual microbes that do not depend on the Sun in any way for their energy1.

Dylan Chivian from the US Department of Energy's Lawrence Berkeley National Laboratory, California, and his colleagues now report in Science that a detailed analysis of genetic material harvested from the mine shows that more than 99.9% of the organisms there are members of just one, previously unknown, species, D. audaxviator2.

"This is the first natural example of a single-species ecosystem," says Chivian. "It's philosophically exciting to know that everything necessary for life can be packed into a single genome."

Going underground

It is thought that D. audaxviator has not seen the surface of the Earth for millions of years. It is highly adapted, surviving independently in its harsh environment that lacks oxygen, and has temperatures as high as 60 ºC and an alkaline pH of 9.3.

mineThe lonely bacteria were found 2.8 km below the ground in a South African gold mine, in water coming from a rock fracture (white area).Li-Hung Lin and Duane Moser

Chivian's team collected DNA from about 5,600 litres of water from the fracture. Their analysis revealed that the bacterium has 2,157 protein-coding genes.

The genome includes genes that code for both sugar and amino-acid transporter molecules, suggesting that the organism can obtain nourishment from the breakdown of organic matter, including the recycling of dead cells. But in leaner times, it can also assimilate carbon from alternative sources, such as carbon monoxide, carbon dioxide or formate (CO2H-).

It gets its energy by reducing sulphate (SO42-) with the help of hydrogen created when radiation from uranium minerals breaks down water molecules.

And despite possessing a nitrogenase enzyme, enabling the bacteria to convert atmospheric nitrogen to ammonia, its nitrogen supply comes from ammonia molecules and ammonium ions amply available in surrounding rocks and fluid.

It also has a tail-like structure, known as a flagellum, allowing the organism to move freely, and a tough protective coat known as an endospore, which shields the organism from harsh conditions.

Ecosystem of one

With only a single species present in the fissure, is one really able to call such an arrangement an ecosystem? According to Chivian, the simple answer is yes, because there are two components present: "The energy and material from the environment interacting with the biological component, which in this case is just one species. It is still an ecosystem, albeit an ultra-simple one."

"Communities are considered to be more stable than single species as they have the genetic potential to adapt to change," points out microbiologist John Parkes, from the University of Cardiff, UK. But D. audaxviator should be in little danger of extinction because the fracture is a stable environment that continues to provide essential nutrients. If the conditions were to alter significantly, however, the bacterium might be in trouble. 

  • References

    1. Chivian, D. et al. Science 322, 275-278 (2008).
    2. Lin, L.-H. et al. Science 314, 479–482 (2006).
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