June 1, 2023

A curious survivor from the age of the dinosaurs

A curious survivor from the age of the dinosaurs
A curious survivor from the age of the dinosaursA curious survivor from the age of the dinosaurs

A LOT HAS happened in the past 165m years. Dinosaurs populated Earth and then died off. The ancestors of whales gave up the land and went back into the oceans. The ancestors of humans gave up the trees and came down to the plains.

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And all the while, a species of bacterium which lives deep underground and feeds on chemicals extracted from rocks continued merrily along without any apparent change at all. The term “living fossil” is much bandied about to describe modern creatures that look like relicts of the past. In this case, though, it really does seem an appropriate description. Not only is Desulforudis audaxviator found, like real fossils, inside rocks, it also seems to have remained unchanged since the Jurassic.

Desulforudis was discovered in 2008, in water collected from a gallery 2.8km below ground in the Mponeng gold mine in South Africa, the world’s deepest. Or, rather, its genetic trace was, for the bacterium itself resists cultivation in a laboratory. The species derives its energy by reacting sulphate ions with hydrogen molecules and it scavenges from the rocks it inhabits the carbon and nitrogen atoms that it requires to assemble the organic molecules from which it is built. From the point of view of organisms living at the surface, which derive their energy ultimately from the sun, via the photosynthesis of plants, this might seem to be a rather specialised way of life. But before photosynthesis evolved, biochemistry of this sort would presumably have been normal.

What is not normal is the implication of a finding reported in ISME Journal by Ramunas Stepanauskas of the Bigelow Laboratory for Ocean Sciences, in Maine, and his colleagues. They have shown that samples of Desulforudis which have been collected from Siberia and California since the bug’s discovery are genetically almost identical to the one from South Africa.

In most species, mutations happen frequently. Such random genetic changes are often damaging, and are eliminated by natural selection. But beneficial or neutral mutations may be preserved, and will accumulate over the course of time. If a population becomes divided, so that its various parts cannot interbreed, their genetic make-up will gradually diverge. The degree of divergence gives clues as to how long ago the separation occurred.

On the face of things, then, the similarity of these three widely separated Desulforudis populations suggests their common ancestor is recent, and that its descendants dispersed rapidly around the planet. How that could be is a mystery. Desulforudis grows and reproduces slowly, so if it simply spread through its rocky, subterranean habitat, the aeons involved should have permitted a lot of mutation. In theory, it could have escaped into the air or the sea, which would have let it travel far and wide. However, both oxygen and salt would be toxic to this species, so that seems unlikely in practice. Moreover, when Dr Stepanauskas and his colleagues searched a big database of genes from surface-dwelling microbes, just in case, they found no trace of any DNA from Desulforudis.

It looks, therefore, as if Desulforudis did indeed migrate across the world through the rocks it lives in. And the likelihood that this happened long ago is made all but certain by the fact that the three populations in question live on separate continents, now barely connected by the sorts of continental rocks the bacteria inhabit.

I met a traveller from an antique land

The last time Africa, Eurasia and North America were well connected was when they were part of a single supercontinent, called Pangaea. That land mass formed about 270m years ago, held together for a while, and then gradually broke up again between 165m and 55m years ago. It is this sequence of events which led Dr Stepanauskas and his colleagues to the conclusion that Desulforudis must have remained essentially unchanged for so long.

Dr Stepanauskas says that Desulforudis seems to have developed mechanisms which replicate DNA with tremendous accuracy, and which correct any errors that do occur. Why such mechanisms might help this particular species, when most others are more fault-tolerant, is unclear. One possibility is that its environment is so stable that “locking in” an optimal genetic configuration is an evolutionarily effective strategy. Such stability might be a consequence of it living in what its original discoverer, Dylan Chivian of the Lawrence Berkeley National Laboratory, in California, called “a single-species ecosystem”. Desulforudis has neither parasites, nor predators, nor prey.

From the human point of view, a hyper-reliable DNA copying mechanism could have applications in biotechnology—and, to this end, the researchers have already applied for a patent on one of the bug’s enzymes. Even if that does not prove useful, though, Desulforudis was already an intriguing organism. It is made more intriguing by this discovery.

A version of this article was published online on April 21st, 2021.

This article appeared in the Science & technology section of the print edition under the headline “Gold bug”