Articles Posted in the Green News category

Unique ecosystem found 2,8km down Witwatersrand gold mine

October 14, 2008
Posted in Green News

The rod-shaped D. audaxviator was recovered from water collected in the Mponeng Mine. (Micrograph by Greg Wanger, J. Craig Venter Institute, and Gordon Southam, University of Western Ontario, used with permission)

An organism has been found living in its own little ecosystem 2,8km below the surface of the Earth in the Mponeng gold mine on the Witwatersrand near Johannesburg.

The rod-shaped bacterium, called Desulforudis audaxviator, exists in complete isolation, total darkness, a lack of oxygen, and 60-degree-Celsius heat. It constitutes the first known single-species ecosystem, say researchers.

The bacterium gets its energy from hydrogen and sulphate produced by the radioactive decay of uranium. Because it lives alone, researchers believe that it builds its organic molecules by itself out of water, inorganic carbon, and nitrogen from ammonia in the surrounding rocks and fluid.

Researchers made their remarkable discovery when they drilled into fluid-filled fractures in the mine and extracted about 5,000 litres of water, which they filtered to extract DNA. Using the techniques of environmental genomics, also called metagenomics, the researchers sequenced and analysed the bacterium’s genome.

Just one species

“We knew from previous work in these mines, using molecular biology techniques, that there seemed to be very simple communities living down there,” says Fred Brockman of the Biology Department of Pacific Northwest National Laboratory, where the DNA was extracted from the filtered cells.

“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.”

But, to the surprise of the researchers, only one organism was present in the DNA.

Dylan Chivian, the bioinformatics lead at the Joint BioEnergy Institute in Berkeley, California, says: “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.”

Even before the analysis was complete it was evident that the lone species’s genome was remarkable, the researchers say.

Completely independent

The genome contained everything needed for the organism to sustain an independent existence and reproduce, including the ability to incorporate the elements necessary for life from inorganic sources, move freely, and protect itself from viruses, harsh conditions, and nutrient-poor periods by becoming a spore.

“One question that has arisen when considering the capacity of other planets to support life is whether organisms can exist independently, without access even to the sun,” says Chivian. “The answer is yes, and here’s the proof. It’s sort of philosophically exciting to know that everything necessary for life can be packed into a single genome.”

D. audaxviator not only has the equipment to get its energy from sulphates, it appears to have “borrowed” genes by horizontal gene transfer from archaea. Some 280 types of bacteria and 44 types of archaea have been found in microbial communities in the South African mines.

Carbon sources

D. audaxviator can get its carbon from a number of sources, depending on the local surroundings, the researcher say. It can digest sugars and amino acids, suggesting that one source of carbon might be the dead cells of other microbes. But in the fluid from the Mponeng mine, it gets carbon from carbon monoxide, carbon dioxide, bicarbonate, formate, and other nonbiological sources.

Its nitrogen comes from ammonia released from rocks and dissolved in the fluid, but could, if necessary, extract nitrogen from its surroundings after first converting it to ammonia, say the researchers.

About the only thing D. audaxviator can’t do is resist oxygen, which suggests it hasn’t been exposed to pure oxygen for a very long time – perhaps millions of years.

D. audaxviator’s remarkable capabilities gave rise to its remarkable name. The genus name Desulforudis is from the Latin for “from sulphur” and “rod,” noting its shape and its ability to get energy from sulphates. Audaxviator comes from Jules Verne’s Journey to the Centre of the Earth, in a message in Latin deciphered by Verne’s protagonist, Professor Lidenbrock, which reads in part, “descende, Audax viator, et terrestre centrum attinges.” It means “descend, Bold traveller, and attain the centre of the Earth.”

The researchers reported their results in the 10 October 2008 issue of the journal Science.

Source: Berkley Lab