Microbes discovered deep underground remain virtually unchanged since 175 million years ago

Microbes discovered deep underground remain virtually unchanged since 175 million years ago

New research has identified what’s very likely the tiniest living fossils so far a group of microbes that feed off radioactive decay.

The team, led by the Bigelow Laboratory for Ocean Sciences, an independent, non-profit oceanography research institute, reports that the microbes have been frozen, evolutionary-speaking, for millions of years. Finding such a case could upturn our current understanding of how microbes evolve and why, and could potentially help guide biotechnology applications in the future (since you want these to not evolve/change over time).

We’re fine as we are

“This discovery shows that we must be careful when making assumptions about the speed of evolution and how we interpret the tree of life,” said Eric Becraft, the lead author on the paper. “It is possible that some organisms go into an evolutionary full-sprint, while others slow to a crawl, challenging the establishment of reliable molecular timelines.”

The microbe species is known as Candidatus Desulforudis audaxviator, and was first discovered in 2008 by a group of researchers led by Tullis Onstott, a co-author of the new study. They live in a gold mine in South Africa almost two miles beneath the surface, swimming merrily in the water-filled cavities inside the rock walls. They feed on chemical products formed by natural radioactive decay processes in minerals at the site, creating a completely independent ecosystem that doesn’t even rely on sunlight to function.

Given their very peculiar living arrangement, the team understandably wanted to know how the microbes evolved to where they are today. They checked other underground samples recovered from around the world and found the species in Siberia, California, and in several other mines in South Africa. Each of these environments was chemically different, the team explains, which spurred them to look for differences among the populations at each site. These groups were obviously separated, and have likely been separate for millions of years, and every one of them had unique conditions they lived in — which would make you think they evolved their own unique quirks.

“We wanted to use that information to understand how they evolved and what kind of environmental conditions lead to what kind of genetic adaptations,” said Bigelow Laboratory Senior Research Scientist Ramunas Stepanauskas, the corresponding author on the paper and Becraft’s postdoctoral advisor.

“We thought of the microbes as though they were inhabitants of isolated islands, like the finches that Darwin studied in the Galapagos.”

So they analyzed the genetic code of 126 individuals retrieved at sites on three different continents — and they were flabbergasted to find that all of them were almost completely identical.

They ruled out the possibility that these microbes could have traveled between the sites. The species is anaerobic and can’t live long in the presence of oxygen, they don’t survive well on the surface; the team also ruled out cross-contamination between these sites.

The best explanation they have so far, the team explains, is that these communities didn’t change all that much, genetically, since they first became separated about 175 million years ago as the supercontinent Pangaea split. 
In essence, they’re living fossils.

“They appear to be living fossils from those days. That sounds quite crazy and goes against the contemporary understanding of microbial evolution,” says Stepanauskas.

The findings offer a unique counterpoint to the much more accelerated rates of mutation and evolution seen in other microbial communities. Populations of bacteria such as E. coli have been noted to evolve (in response to environmental changes) in as little as a few years. The growing antibiotic resistance issue is an example of just how fast bacteria can evolve.

The team’s current hypothesis is that the species’ genetic freeze is due to powerful anti-mutation mechanisms in its genome. We don’t yet know whether that’s true, but if it is, we could have just discovered an extremely rare feature that we can copy and exploit. Developing this into a tool could pave the way towards more stable DNA polymerases (molecules that copy DNA strands), which are a key component of our biotechnology kit. Essentially, it would allow us to make the biological machinery that copies DNA much more stable over time, which sounds unimpressive but is actually a very big deal for the field.

But the findings also have deep implications for how we think about microbial genetics and the rate at which such microscopic organisms mutate.

“There’s a high demand for DNA polymerases that don’t make many mistakes,” Stepanauskas said. “Such enzymes may be useful for DNA sequencing, diagnostic tests, and gene therapy.”

“These findings are a powerful reminder that the various microbial branches we observe on the tree of life may differ vastly in the time since their last common ancestor,” Becraft said. “Understanding this is critical to understanding the history of life on Earth.”

The paper “Evolutionary stasis of a deep subsurface microbial lineage” has been published in The ISME Journal.
Microbes discovered deep underground remain virtually unchanged since 175 million years ago
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