National Geographic

The Bacteria That Absorbed Mammoth DNA

An average gram of soil is full of DNA. Some of it is enclosed inside bacteria, worms or insects, but of lot of it is just lying around. It came from living things that died and decomposed, releasing their genetic payload into their surroundings. Exposed to the elements, this environmental DNA breaks, degrades and distorts.

But, sometimes, it finds its way back into a living thing.

Bacteria can feed on bits of DNA from their surroundings. They can also incorporate these fragments into their own genome, as easily as you might put a new book onto your shelf. These horizontal gene transfers give bacteria an edge in the evolutionary race. Rather than just inheriting genes from their ancestors, they can pick up fresh DNA from all around them.

Now, Soren Overballe-Petersen from the University of Copenhagen has shown that they can even do this with extremely short and damaged pieces of DNA. As dramatic proof, he showed that soil microbes can incorporate 43,000-year-old mammoth DNA from a fossilised bone.

Let’s be clear: it’s irrelevant that the DNA came from a mammoth. Mammoth DNA is like human DNA is like cabbage DNA. It’s the same molecule. There’s no special mammothity imbued within strands that small. The microbes aren’t suddenly going to sprout tusks and a shaggy coat.

The point is that the DNA is old. Really damn old. If an Ice Age microbe (or, indeed, a mammoth) could donate DNA to a living bacterium, then “generations long past can influence the evolution of future generations,” says Overballe-Peterson. He calls it anachronistic evolution. “It’s something we’ve not considered before and it’s not in our models of microbe evolution.”

“The idea is something very similar to [a concept called] genome recycling,” says Hendrik Poinar from McMaster University, who studies microbes and ancient DNA. “This idea that DNA of very different ages could make its way back into the evolutionary light of day is certainly a fascinating possibility.”

It’s also possible that the more bacterial there are in the environment, the faster they evolve. If you have a lot of microbes around, you have more DNA in the environment for the survivors to pick up and use.  “There’s the possibility of a positive evolutionary feedback loop,” says Overballe-Petersen.

Scientists have long known that bacteria can efficiently suck up DNA from their surroundings, but these fragments have typically been thousands of ‘letters’ long. “When the fragments become shorter, the efficiency drops very fast,” says Overballe-Petersen. However, his team, led by ancient DNA specialist Eske Willerslev, showed that the soil microbe Acinetobacter baylyi can take up fragments just 20 to 120 letters long.

The bacteria presumably digest much of this DNA, but they can also integrate it into their genomes. This doesn’t require any fancy tricks. Bacteria need to make copies of their DNA whenever they divide, and if the environmental strands are around at the time, they can get slotted in.

“It’s not something that the bacterium tries to do, or necessarily gives it an advantage,” says Overballe-Petersen. “It’s a consequence of feeding on what it finds around itself. I liken it to rummaging through garbage. Most of the time it’ll go nowhere, but you could find all sorts of wonderful things that people have thrown out.”

The team found that this process works even if the environmental DNA is severely damaged, and they wondered if bacteria could take up extremely old and tattered DNA too. The problem is that it’s hard to find DNA that definitely came from ancient microbes—too often, modern bugs contaminate the samples. So, the team turned to a source of DNA that they knew was definitively ancient—a 43,000 year old mammoth bone. “We already had one available,” says Overballe-Petersen. “And we’re pretty confident that a mammoth didn’t run around the lab last week and dropped hair into our samples.

It worked. The soil microbes made the mammoth DNA part of them. This genetic material, broken and shattered by many millennia of decay, is now back in living cells again.

The concept is tantalising but “there is no evidence that this has occurred in nature,” says Howard Ochman from Yale University. “Just from scanning genomes, horizontal gene transfer from [living] sources seems to have had a much, much larger impact on bacterial evolution.”

And it’s still the case that bacteria are much less efficient at transforming their genomes with small pieces of DNA than with larger fragments. On the other hand, Overballe-Petersen argues, there’s a lot of free DNA in the environment. Even if bacteria aren’t great at picking it up, they have many chances to do so.

Poinar says that there are two big questions: how often does this happens in the wild, and how often does the extra DNA changes something meaningful in the bacteria rather than doing nothing? After all, these fragments are far too small to include entire genes. Adding them to a bacterium’s genome is like adding a few letters or words to a book, rather than an entire page.

But the team notes that it doesn’t take many such changes to, say, turn a vulnerable bacterium into a drug-resistant one. That has important implications for hospitals, which are often teeming with drug-resistant bacteria. Medical equipment, toilets and water supplies could all be sources of DNA carrying resistance genes. “In hospital rooms, you’re focused on killing the living bacteria. But that’s not enough to destroy the DNA, which could fragment and potentially be picked up again,” says Overballe-Petersen. “You’d have a vicious cycle of recurring resistance.”

If this is a genuine problem (and that’s not clear yet) it would also be a difficult one to fix. Destroying environmental DNA is very hard. In Willerslev’s lab, they wipe their work surfaces with strong chlorine solutions, and irradiate them at night with ultraviolet lights. “You can’t treat patients in this way, but maybe you could use UV lights in operating theatres, when they’re not in use in the night.”

Reference: Overballe-Petersen, Harms, Orlando, Moreno Mayar, Rasmussen, Dahl, Rosing, Poole, Sicheritz-Ponten, Brunak, Inselmann, de Vries, Wackernagel, Pybus, Nielsen, Johnsen, Nielsen & Willerslev. 2013. Bacterial natural transformation by highly fragmented and damaged DNA. PNAS http://dx.doi.org/10.1073/pnas.1315278110

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There are 3 Comments. Add Yours.

  1. destiney nash
    November 19, 2013

    This is a really cool thing!

  2. Roy Niles
    November 21, 2013

    Bacteria would seem able to inherit lessons that their ancestors have learned. Perhaps there are lessons in these dinosaur leavings that are potentially usable, since all such lessons appear to be predictive, some relating to the expected and others to the relatively unexpected. I’m assuming of course that bacteria exercise evolving forms of intelligence.

  3. Preston Garrison
    November 22, 2013

    Years ago Fred Sherman’s lab showed you could get yeast to incorporate oligos that matched some sequence in a gene. They incorporated single base changes (relative to the genomic sequence) in the center of the oligo that would result in a selectable phenotype, so you could detect the incorporation. It was potentially a very quick way to introduce simple changes in the genome. As I recall there was some evidence that oligos were also being incorporated at non-homologous positions. I was curious whether random sequence oligos would act as general mutagens in yeast, but I never got to test it.

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