A bacterium that lives deep underground and suffers from chemical reactions caused by radioactive decay has been doing so unchanged for millions of years, new research has found.
A genetic analysis of microbes of the species Candidatus Desulforudis audaxviator (CDA) collected from three different continents revealed that the bacterium has barely evolved since they were last on the same land mass, Pangea.
This means that they have been in what scientists call ‘evolutionary stasis’ for at least 175 million years, making CDA the only known underground microbial fossil. This can have important implications for our understanding of microbial evolution.
“This discovery shows that we need to be careful when making assumptions about the speed of evolution and how we interpret the tree of life,” said microbiologist Eric Becraft of the University of Northern Alabama.
“It is possible that some organisms go into an evolutionary full sprint, while others become slow to crawl, challenging the establishment of reliable molecular timelines.”
CDA is a peculiar small organism. It was first discovered in 2008 and lives 2.8 kilometers below the earth’s surface in the groundwater of a gold mine in South Africa. In addition, it covered 99.9 percent of the microorganisms in the place where it was found – effectively forming a single species ecosystem.
It is, as you might think, quite rare. The small microbes live in cavities on the rock filled with water and rely on chemosynthesis for food; Unlike photosynthesis, which depends on sunlight for conversion into energy, chemosynthetic organisms derive their energy from chemical reactions.
In the case of CDA, it is the decomposition of water molecules due to the ionizing radiation generated by the radioactive decay of uranium, potassium and thorium.
Therefore, unlike the majority of life on earth, the bacterium is not dependent on sunlight or other organisms to survive; he can keep going on, there in the softer dark.
The team wanted to know more about CDA and how it evolved and adapted, so they searched deep groundwater samples from other continents and found the bacterium in Siberia and California and elsewhere in South Africa.
They collected 126 microbes from all three continents, and – extremely carefully – with examiners from each laboratory who did not go near the others – sequenced their genomes. They thought that, by comparing the microbes of separate continents in different physicochemical environments, they would see the ways in which they evolved and diversified as they each adapted to their specific circumstances.
“We wanted to use the information to understand how they evolve and what kind of environmental conditions lead to what kind of genetic adaptations,” said microbiologist Ramunas Stepanauskas of Bigelow Laboratory for Ocean Sciences in Maine.
“We thought of the microbes as if they were inhabitants of isolated islands, like the finches that Darwin studied in the Galapagos.”
They had no reason not to believe it – how can a microbe isolated 3 kilometers underground in South Africa possibly have contact with a microbe 3 kilometers underground in Siberia? When the team compared the genomes, they found that the microbes on the three continents were almost identical.
Closer examination revealed no evidence that CDA could survive on the surface or in the air, nor could it drive long distances, and they checked to see if there was any cross-contamination of the samples. Once all this was ruled out, the researchers had to find another answer.
The most plausible statement? The microbes have barely evolved.
“The best explanation we have at the moment is that these microbes did not change much, as their physical locations separated about 175 million years ago during the decomposition of the supercontinent Pangea,” Stepanauskas said.
“They look like living fossils from those days. It sounds pretty crazy and goes against the modern notion of microbial evolution.”
We know that bacteria can develop very quickly; this was actually a major problem in the development of antibiotics as some microbes could develop resistance to these drugs. However, we do not really hear of the opposite scenario. Some scientists have suggested that some cyanobacterial species may be in an evolutionary state, although this is disputed.
CDA may still be the best case for evolutionary stasis in a microbe. The team believes this may be because the microbes have specialized mechanisms that help them resist mutation. The researchers identified genes for DNA repair mechanisms that can reduce mutation rates, along with polymerase – the enzymes that make up the long chains of genetic material – that have better accuracy than those seen in other organisms.
It has potential applications in biotechnology, from diagnostic tests to gene therapy, scientists have said. Beyond how we can use it to our own advantage, however, the finding shows us how little we do not know about our strange, wonderful, diverse planet.
“These findings are a powerful reminder that the different microbial branches we observe on the tree of life can differ greatly in the time since their last common ancestor,” Becraft said.
“Understanding this is critical to understanding the history of life on earth.”
The research was published in The ISME Journal.