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Microbes of the South African Gold Mines Created by Timothy Ellis

Overview

The gold mines of South Africa host a number of unique microbial species that display resilience to extreme environments. This site hosts the deepest excavations in the world. These mines run over 2.5 miles below the Earth's surface, allowing a detailed exploration of subsurface sediments and microbes. While there is still much to discover in the subsurface, current findings show a high degree of archaeal diversity and one particular species of bacteria of interest.

Description of the Mines

SoAfrica-Mponeng-02062009.png

Mponeng Gold mine was the site where extremophile Desulforudis audaxviator was discovered [1]. Far below the surface, water runs through cracks in the bedrock. It was here that this unusual microbe was found. The environment this far below the surface is harsh; the temperature as high as 60 degrees Celsius can be seen as well as an environmental pH of 9.3.[2] Four other mines in South Africa were used to take stock of the Archaeal diversity: East and West Driefontein along with the Kloof Mines form a group of complexes on the West Rand. These West Rand mines have similar rock composition and stratigraphy. As one ventures deeper, Pretoria Group sandstone gives way to Transvaal dolomites and then moves into Ventersdorp Supergroup volcanic strata and Witwatersrand Supergroup quartzites and carbonaceous gold-bearing reef horizons. The fourth mine, Beatrix Mine, does not have dolomite and Ventersdorp sequences. Temperature gradients at these four sites varied but correlated to the amount of water flowing through the fractures along the dyke.

Candidatus Desulforudis audaxviator

Figure 1: This Candidatus Desulforudis audaxviator bacterium displays a rod-like shape, and the endospore protein coat can be easily seen. The tail-like structure is called a flagellum, and allows the bacterium to move.

Discovered in 2008, Candidatus Desulforudis audaxviator lives independently of any other organism in its habitat which lies 2.8km below the surface of the Mponeng Mine in South Africa. The sun does not contribute to this microbe's energy production. Instead, Candidatus Desulforudis audaxviator creates its energy through the reduction of Sulphate and with the help of excess hydrogen when radiation from uranium minerals breaks down water molecules. As seen in figure 1, this Candidatus Desulforudis audaxviator bacterium is rod-shaped, encapsulates itself in a protective coating known as an endospore, and has a flagellum which allows movement.

Hadesarchaea

The geochemical, biological, and hydrological processes that are present in the mines of South Africa allow a unique archaeal community structure. Generally speaking, the mine water at all sites is acidic. The acidic water was found to host archaeal communities similar to SAGMCG 1 group, which is an archaeal group that thrives in the dolomite aquifer. The water samples obtained from the Beatrix and West Driefontein mines display similarities in this structure. Phylogenetic features such as rDNA sequences belonging to both SAGMEG 1 and SAGMEG 2 and high GC content indicates a shared thermophilic nature between the two communities. The sample of archaea obtained from Kloof Mine was found to be similar to Pyrococcus, which is a thermophilic archaeal species found in deep-sea vents. This is the first discovery of Pyrococcus-like archaea living outside of the marine environment.

Conclusion

The discovery of numerous novel archaea in the South African gold mines suggests the presence of a unique environment that allows certain thermophiles and hyperthermophiles to survive and thrive. Additional analysis of these habitats must take place in order to understand the interaction these archaeal communities have on one another. As for the Mponeng mine's sole organism, Candidatus Desulforudis audaxviator, there is little threat of extinction due to the stability of the mine. This means that future analysis can take place whenever the time is right.

Refrences

1. Starr, Laura (2008). One is the loneliest number for mine-dwelling bacterium https://www.nature.com/news/2008/081009/full/news.2008.1160.html

2. Takai, Ken et al Archaeal Diversity in Waters from Deep South African Gold Mines https://aem.asm.org/content/67/12/5750

3. Baker, Brett et al (2016). Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea https://www.nature.com/articles/nmicrobiol20162

4. Karnachuck, Olga et al (2019). Domestication of previously uncultivated Candidatus Desulforudis audaxviator from a deep aquifer in Siberia sheds light on its physiology and evolution https://www.nature.com/articles/s41396-019-0402-3