A bacterium that lives in the depths of the earth, that lives on the chemical reactions triggered by radioactive decay, has been doing so unchanged for millions of years, new research has found.
Genetic analysis of microbes of the species Candidatus Desulforudis audaxviator (CDA) collection from three different continents has revealed that the bacterium has barely evolved since they were together in the same land mass, Pangea.
This means they have been in what scientists call “evolutionary stasis” for at least 175 million years, making the CDA the only known living underground microbial fossil. This could have important implications for our understanding of microbial evolution.
“This finding demonstrates 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 North Alabama.
“Some organisms may enter a full evolutionary sprint, while others lag behind a trail, challenging the establishment of reliable molecular timelines.”
The CDA is a small peculiar organism. It was first discovered in 2008, living 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 at the site where it was found, effectively constituting an ecosystem of a single species.
This, as you can imagine, is quite rare. Tiny microbes live in cavities filled with rock water, relying on chemosynthesis to feed; unlike photosynthesis, which relies on sunlight to convert it into energy, chemosynthetic organisms obtain their energy from chemical reactions.
In the case of CDA, it is the decomposition of water molecules due to ionizing radiation generated by the radioactive decay of uranium, potassium, and thorium.
Therefore, unlike most life on Earth, the bacterium does not depend on sunlight or other organisms for its survival; it can only continue down there, in the dark.
The team wanted to learn more about ACD and how it has evolved and adapted, so they looked for samples of deep groundwater from other continents and found the bacterium in Siberia and California and other places in South Africa. .
They collected 126 microbes from the three continents and, very carefully, the researchers in each laboratory did not approach the others, they sequenced their genomes. They thought that by comparing microbes from separate continents, in different physicochemical environments, they would see the ways in which they had evolved and diversified as they adapted to their particular circumstances.
“We wanted to use this information to understand how they evolved and what kind of environmental conditions lead to what kind of genetic adaptations,” said microbiologist Ramunas Stepanauskas of the Bigelow Laboratory for Ocean Sciences in Maine.
“We thought of microbes as if they were inhabitants of isolated islands, like the finches Darwin studied in the Galapagos.”
They had no reason not to believe it: how could an isolated microbe 3 kilometers underground in South Africa come into contact with an isolated microbe 3 kilometers underground in Siberia? However, when the team compared the genomes, they found that the microbes from the three continents were almost identical.
A more detailed investigation revealed no evidence that the CDA could survive on the surface or in the air, regardless of traveling long distances, and again verified that there had been no cross-contamination of the samples. Once all were discarded, the researchers had to find a different answer.
The most plausible explanation? Microbes have barely evolved.
“The best explanation we have right now is that these microbes haven’t changed much since their physical locations separated during the rupture of the Pangea supercontinent, about 175 million years ago,” Stepanauskas said.
“They look like living fossils from those days. It sounds pretty crazy and goes against the contemporary understanding of microbial evolution.”
We know that bacteria can evolve extremely quickly; in fact, this has been a huge problem in the development of antibiotic drugs, as some microbes have been able to evolve resistance to these drugs. We don’t really know about the opposite scenario. Some scientists have suggested that some species of cyanobacteria may be in a state of evolutionary stasis, although it has been discussed.
CDA it might be the best case of evolutionary stasis in a microbe. The team believes it could be because microbes have specialized mechanisms that help them resist mutations. The researchers identified genes for DNA repair mechanisms that could reduce mutation rates, along with polymerase (the enzymes that bind long chains of genetic material) that has better accuracy than is seen in some other organisms.
Scientists said this has potential applications in biotechnology, from diagnostic testing to gene therapy. Beyond how we can do it for our own benefit, the finding shows us what little we don’t know about our strange, wonderful, diverse planet.
“These findings are a powerful reminder that the various microbial branches we observe in the tree of life can differ enormously in time from their last common ancestor,” Becraft said.
“Understanding this is critical to understanding the history of life on Earth.”
The research has been published in The ISME newspaper.