Bacteria: taking up ancient DNA

Short and damaged DNA fragments are found pretty much everywhere and in some environments can survive more than half a million years. But this week a paper published in PNAS showed that bacteria can pick up these stray DNA sequences from their environment and incorporate it into their genomes, even DNA from a 43,000 year old woolly mammoth bone.To find out more we're joined by Eske Willerslev from the Center for GeoGenetics at the University of Copenhagen.

Eske - We wanted to investigate if bacteria can actually incorporate all thebroken DNA, all the damaged DNA that is in the surroundings, if that can be incorporated into the genomes. Obviously, we have known for a long time that long stretches of DNA from two bacteria that are very closely related can actually be swapped between the cells. But it was unknown whether you can say very short and very damaged DNA such as ancient DNA can actually be incorporated into the bacteria genome. This is what we show was possible in the PNAS paper.

Ginny - So, how did the bacteria actually pick up these bits of DNA?

Eske - It seems like it's actually happening more or less spontaneously. So, we think when they eat, some of that DNA can then be incorporated into genomes.

Ginny - Why would they want to do that? Is this useful for them in some way?

Eske - Yeah, it's a good question. You can say, the interesting part here I think is that in principle, that allows for the bacteria to get to stages that might had been lost even for thousands of years. For example let's say, antibiotic resistance and in this case, a bacteria can actually, by taking up a very short piece of DNA become antibiotic resistant.

Ginny - So, does this have an impact on the way we deal with antibiotic-resistant bacteria? So, at the moment, I know there's lots of constraints around medical waste, but they don't have to make sure that the DNA is completely destroyed as far as I know.

Eske - Exactly. I think this is something that this should be investigated further because as you rightfully point out, at hospitals, I mean, people are taking a lot of care to try killing off bacteria on surfaces. But obviously, with alcohol, that doesn't destroy the DNA totally. And that means then in principle, you can say, antibiotic-resistant bacteria that has been on surfaces, had been killed off then a new group of bacteria can come and actually incorporate some of their damaged DNA after even weeks or months, incorporate that into the genomes and then becoming resistant that way. I mean, one of the big questions, of course, that still remains is, how often does this happen in nature? I mean, certainly we know now that it can happen, that it's possible, and it's also possible you can say with the bacteria that we know are out there in the environment. But it's still an open question, how often do they really happen in nature?

Ginny - So, we talked about this DNA being damaged. Does that not have a negative effect on bacteria that pick it up if there's something wrong with the DNA?

Eske - Well, it doesn't seem to be the case and this was one of the really surprising discoveries. I mean first, we tried with very fragmented DNA and was also surprised that they could take up even things like 20 base pair pieces. But when we additionally introduced a lot of different types of damages, I mean, it was a big surprise for us that they actually take it up anyways. It doesn't seem to hold them back. And then finally, we did the experiment with a ground up woolly mammoth's bone and this was just to show that it's not only DNA which has been artificially damaged, or artificially shortened that if we actually use some DNA with just truly ancient, truly damaged then the bacteria can still take it up.

Ginny - Is there a lot of this ancient woolly mammoth type DNA lying around in the real world? Is this something we should actually be worried about?

Eske - Yes, there is a lot of it hanging around. I don't think the most interesting thing though is the mammoth DNA really because what's much more important is that there is chance of ancient bacteria DNA hanging around in the environment. And that bacteria DNA will be potential source for being incorporated into living bacteria. So, if you imagine along river banks, along the surfaces of land masses, etc. We all the time get ancient sediments being released out in the ocean, out in the water, etc and will definitely will release tremendous amounts of ancient bacteria DNA. The question is then, to what extent do this ancient bacteria DNA come into play?