The Surprisingly Bold Travels of the Desulforudis audaxviator

Original Article: Labonté, J., Field, E., Lau, M., Chivian, D., Heerden, E., Wommack, K., . . . Stepanauskas, R. (2015). Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. Front. Microbiol. Frontiers in Microbiology.

Post by: Naomi Oliver

Ancient Bold Traveler

Candidatus Desulforudis audaxviator is a rod-shaped, gram positive chemoautotrophic bacteria. Like everyone’s favorite model microbe Bacillus subtilis, it is a member of the phylum Firmicutes which, together with Bacteroidetes, make up about 98% of the microbiota in the human gut. However, D. audaxviator finds its home in the deep subsurface of the earth.  This ancient, monotypic bacterium was aptly named ‘the bold traveler’ (from the Latin: “audax” – bold; “viator” – traveler), based on an eerily prescient line from Jules Vernes’ 1864 French classic, Journey to the Center of the Earth.

“(Latin) Descende, audax viator, et terrestre centrum attinges: 

Descend, bold traveler, and you will attain the center of the Earth.”

- Jules Vernes

  D. audaxviator has proven to be bold, and not just for its travels; this mighty little microbe fixes its own nitrogen and carbon, produces endospores in hostile environments, and can survive with very few sources of energy, possibly as a result of its equally unique ability to derive most of its energy from radioactivity. Like many of its deep subsurface buddies, D. audaxviator exhibits extremely low metabolic rates and generation times that take anywhere from hundreds to thousands of years.

A Biome of Its Own

D. audaxviator’s claim to fame, its unique ability to create and maintain its own ecosystem, was published in a 2008 article by a band of Berkeley microbiologists. The team claimed the species was the first of its kind discovered to have a genome that encoded all of the proteins necessary to create a supportive ecosystem.

Generations of isolation from environmental oxygen rendered the species an obligate anaerobe, or a species sensitive to oxygen. However, the species makes do with its ability to perform sulfate-reduction, an ability it likely picked up, along with several others, from horizontal gene transfer (HGT) events.

That’s So Meta

In April of 2015, Jessica M. Labonte and a motley crew of eight other researchers collected five cell samples of D. audaxviator from 3.14 km (that’s about two miles or 10,300 feet, fellow yankees!) below the TauTona mine in Gauteng, South Africa. The gang was able to amplify, sequence and assemble the individual whole genomes of each collected cell using single cell genomics (SGC).

Most of the Earth’s microbial diversity can’t be grown in culture, and deep subsurface organisms are just that much harder to learn anything about. Metagenomics – processes by which a species’ genome is compiled from multiple clonal cells – is a step closer to phylogenic identification than 16S rRNA sequence comparison, but comes with the caveat of not offering much information about genetic variability or environmental influences. SCG, a sequencing process that that does not require cultivation, may be a solution.

Once the individual genomes were sequenced and single amplified genomes (SAGs) were obtained, they compared these individual genomes to that of MP104C, a metagenomic composite of an indigenous D. audaxviator collected years earlier from the Mponeng gold mine just down the road from the TauTona.

 Where Did You Come From, Where Did You Go?

MP104C has a surprisingly low rate of genomic mutations, with only 32 single nucleotide polymorphisms in its 2.35 million base pair genome, indicating a highly stable one-species ecosystem.

What Labonte & Co. discovered was a series of alterations to the TauTona cells’ single amplified SAGs), including a prophage (a viral infection), a retron, multiple CRISPR genes, and a rather high frequency of transposases for microorganisms in general.

Conclusion

These gene alterations were not present in the original MP104C sample, suggesting that D. audaxviator does in fact coexist with other microbial species, and despite its stable environment and low cell abundance, undergoes HGT events and viral infections that affect its evolution, suggesting that HGT might not be reserved for speedy adaptations in hostile environments after all.

Sources

Labonté, J., Field, E., Lau, M., Chivian, D., Heerden, E., Wommack, K., . . . Stepanauskas, R. (2015). Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. Front. Microbiol. Frontiers in Microbiology.

Desulforudis audaxviator. (n.d.). Retrieved December 1, 2015, from https://microbewiki.kenyon.edu/index.php/Desulforudis_audaxviator#References

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Lasken, R., & Mclean, J. (2014). Recent advances in genomic DNA sequencing of microbial species from single cells. Nat Rev Genet Nature Reviews Genetics, 577-584.

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