A bacterium that lives deep underground and feeds on chemical reactions caused by radioactive decay has been doing this unchanged for millions of years, new research shows.
A genetic analysis of microbes of the species Candidatus Desulforudis audaxviator (CDA) collected on three different continents has revealed that the bacterium has hardly evolved since they were last together on the same landmass, Pangea.
That means they have been in what scientists call ‘evolutionary stasis’ for at least 175 million years, making CDA the only known subterranean living microbial fossil. This may have important implications for our understanding of microbial evolution.
“This discovery shows that we need to be careful in making assumptions about the rate of evolution and how we interpret the tree of life,” said microbiologist Eric Becraft of the University of North Alabama.
“It is possible for some organisms to go into an evolutionary full sprint, while others crawl slowly, challenging the establishment of reliable molecular timelines.”
CDA is a curious little organism. It was first discovered in 2008 and lives 2.8 kilometers (1.7 miles) below the Earth’s surface, in the groundwater of a gold mine in South Africa. In addition, it comprised 99.9 percent of the microorganisms in the place where it was found, effectively forming an ecosystem of one species.
As you can imagine, this is quite rare. The tiny microbes live in water-filled cavities on the rock and depend on chemosynthesis for food; Unlike photosynthesis, which relies on sunlight to convert it into energy, chemosynthetic organisms derive their energy from chemical reactions.
In the case of CDA, it is the breakdown of water molecules due to the ionizing radiation generated by the radioactive decay of uranium, potassium and thorium.
Therefore, unlike most of life on Earth, the bacteria does not depend on sunlight or other organisms to survive – it can just keep going down there in the drenched darkness.
The team wanted to learn more about CDA and how it evolved and adapted, so they looked for deep groundwater samples from other continents and found the bacteria in Siberia and California, and other locations in South Africa.
They collected 126 microbes from all three continents, and – being extremely careful, with researchers from each lab not getting close to the others – sequenced their genomes. They thought that by comparing the microbes from different continents, in different physicochemical environments, they would see the ways they had evolved and diversified as they each adapted to their specific circumstances.
“We wanted to use that information to understand how they evolved and which environmental conditions lead to which 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 Darwin studied in the Galapagos.”
They had no reason not to believe this: How could a microbe isolated three kilometers underground in South Africa come into contact with a microbe isolated three kilometers underground in Siberia? But when the team compared the genomes, they found that the microbes on the three continents were nearly identical.
Further investigation revealed no evidence that CDA can survive on the surface, or in the air, let alone travel great distances, and they double checked that there had been no cross-contamination of the samples. When these were all ruled out, the researchers had to find a different answer.
The most plausible explanation? The microbes have hardly evolved.
“The best explanation we have at this point is that these microbes haven’t changed much since their physical locations separated during the breakup of the supercontinent Pangea about 175 million years ago,” said Stepanauskas.
“They look like living fossils from that era. That sounds quite crazy and goes against today’s understanding of microbial evolution.”
We know that bacteria can evolve extremely quickly; in fact, this has been a huge problem in the development of antibiotics, as some microbes have been able to develop resistance to these drugs. However, we don’t really hear about the opposite scenario. Some scientists have suggested that some types of cyanobacteria may be in a state of evolutionary stasis, although that is controversial.
CDA could 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 could reduce mutation rates, along with polymerase – the enzymes that make up long chains of genetic material – that have better accuracy than some other organisms.
This has potential applications in biotechnology, from diagnostic tests to gene therapy, the scientists said. Aside from how we can use it for our own benefit, the finding shows us how little we don’t 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 enormously over time since their last common ancestor,” Becraft said.
“Understanding this is essential to understanding the history of life on Earth.”
The research is published in The ISME Journal