Kirstin Meyer-Kaiser: Digging up DNA from the depths
Image courtesy of Kirstin Meyer-Kaiser
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As we just heard from Elizabeth, eDNA is already being used as a tool to help conservation efforts all around the world, looking for endangered species that would otherwise be hard to spot.
But if you’re anything like me, you’re probably asking whether this could be used to detect human DNA, and how that might be useful. Well one such project is the Missing in Action Recovery and Identification Project, a collaborative effort spanning multiple disciplines of genetics, marine biology and archaeology, hoping to use eDNA to locate the remains of military service personnel.
I had a chat with Dr Kirstin Meyer-Kaiser, a marine biologist at Woods Hole Oceanographic Institution, and one of the leads on this project, and I asked her to tell us more about it…
Kirstin: The project was initiated by DPAA. That stands for the Defense POW MIA Accounting Agency. It's a branch of the US Department of Defense that is tasked with locating the remains of fallen service members and repatriating them so their remains can be buried and their families can have closure. So normally the way DPAA operates is they partner with a lot of archaeologists and they go out and do these extremely complicated, work-intensive excavations where they meticulously go through a site square metre by square metre to try to locate remains. They're sieving sediments. They're documenting everything. And they wanted to speed up that process.
Kirstin: They wanted to figure out a way to prioritise sites that they knew contained human remains, potentially localise those remains to a specific region of the site, and if at all possible, we're not sure if we can do this quite yet, but figure out who the remains might belong to.
Sally: So we've just been hearing about eDNA, environmental DNA, and you've been using this as a tool to try and help find these fallen service members.
Sally: How does that work? Because you are looking in an entire ocean and DNA can move. There are lots of people in the ocean, not just dead ones. So how does eDNA help you pinpoint any level of accuracy?
Kirstin: You have just outlined the questions for our pilot project. This is exactly what we're trying to figure out.
Fishing for eDNA
SCUBA divers take sediment and water samples at the WWII plane wreck in Saipan. Image courtesy of Kirstin Meyer-Kaiser
Kirstin: So DPAA was interested in using eDNA and when they approached us, the first thing that we said was, "Okay, well we need to ground truth this. We need to figure out if this works." And so the current project that we're talking about is designed to do that ground truthing, designed to figure out: is eDNA an effective tool?
Kirstin: How can we refine it? Can we use it to pinpoint remains? Can we use it to just identify a general site where there might be human remains? On what spatial scale, on what temporal scale, in what environments is it the most effective? Those are the questions that we're trying to figure out right now, and the end goal is that we'll come up with a protocol that can be used in the future, but right now it's just like the very basic, does this work?
Sally: Talk me through what it's like to actually collect these samples because the thing I think I love the most about eDNA researchers is that they go to some weird lengths to get their DNA samples.
Kirstin: So we had three different test beds: Saipan; the Great Lakes; and Palermo, Italy.
Kirstin: Saipan and Palermo are both World War II sites. These are plane wrecks that went down during World War II with suspected or known remains. So when I say "suspected", that means there was a loss; somebody died in that plane wreck. We don't know if their body is in the plane, around the plane, or if they ejected and landed somewhere else, but we strongly suspect there's gonna be someone there.
Kirstin: And we wanted to figure out: does eDNA work better in some environments versus others?
Kirstin: And so the three test beds that we had had contrasting conditions for us to be able to test. So Saipan is warm and shallow. The Great Lakes is deep and cold. Palermo, Italy - that's in the Mediterranean - is deep and kind of medium temperature.
Kirstin: And so the combination of those three should show us whether eDNA is a good tool in each of those environments. I kind of suspect that we're gonna find temperature and light exposure to have a significant impact on DNA degradation or our ability to detect something, meaning that something like the Great Lakes where it's deep and it's cold and it's not very highly disturbed would be the best environment.
Sally: How deep and cold is deep and cold?
Kirstin: So the wrecks that we're doing in the Great Lakes are about 70 metres maximum depth and I don't know if you've ever dove in the Great Lakes, but it's pretty darn close to freezing. Like 35, 40 degree Fahrenheit water.
Sally: Oh wow. Yeah. Because 32 is freezing point for Fahrenheit, is that right?
Kirstin: Exactly. Yep.
Sally: And presumably the amount of ocean currents is also gonna have a huge impact on how much of the DNA stays in place. I mean, the Great Lakes are big, but presumably they don't have these same kind of directional currents as the more open ocean sites,
Kirstin: Correct. Yeah. I am a little suspicious about the water samples. So we were collecting sediments and water samples. And I honestly think that the water samples are going to be the least valuable for what we collect because water moves, as you've just said. The current can carry something away. You can have turnover, you can have mixing; any number of oceanographic processes that carry that DNA away from the site, whereas the sediment might be a little more promising.
Kirstin: I'm putting my faith right now in the sediment samples and hoping that those can show us on a localised level where remains might be.
Sampling the sediment
Marine biologists get some of the coolest fieldwork; here two divers are taking sediment samples in Saipan. Image courtesy of Kirstin Meyer-Kaiser.
Sally: And you said that on those sites there's a high probability that there are human remains in there. Surely a dive site that's in beautiful clear water, only 10 metres has had so many tourist divers that by now someone would have spotted a body if there was a body?
Kirstin: Not if the body is inside the plane.
Kirstin: So your standard recreational diver is not gonna be going inside the fuselage. That's the middle part of the plane. That's the body. So we were trying to search using that as our epicentre, getting as close as we could to the fuselage to see if we could find the eDNA signal in the sediment or in the water.
Kirstin: I agree, if there was anything visible, somebody would've spotted it. But, I mean, this has been sitting there since World War II. It's probably been covered by sediment plenty of times. There's probably been typhoons that came through and mixed everything up, and if the body's inside the plane, then it's a lot less visible.
Sally: And then back in the lab, what are the steps you have to go through to extract the DNA from the sediment?
Kirstin: So the field processing for the water samples was pretty simple. It was just filter. We used 0.2 micron filters because that was a pretty good size to get DNA, including anything that was intracellular floating around in the water.
Kirstin: And for the sediment, there was a more complicated procedure of sectioning the sediment cores that we got. This was part of the archaeological influence on the project. Archaeologists usually work in strata of 10cm, so 0-10cm of sediment, and then 10-20cm. So our cores were 20cm long and we split them in half.
Kirstin: Ideally, you're supposed to be able to take the stoppers on the top and bottom off of the core, put it on this little stand, push it down, get the sediment to come up outta the tube and take your subsample. In some cases, it was so difficult to do that, that we ended up having to take the stoppers off, put it on the stand, but you can't push the tube down to get the sediment to come up and out.
Kirstin: So you just take your subsample by pushing a syringe into the top to get like your little mini core and then flip the core over to get to the bottom stratum. That was like the thing that worked best. .
Sally: Yeah. I suppose it's so used to being fully saturated with water that it's not as consolidated as normal soil would be.
Kirstin: Yeah, I come from a deep sea background, and so all of the sediment samples I was used to working thinking with were very fine, very fluffy, and so they're easy to work. You can just push your tube down. It all hangs together. It's not too compacted. But when you're working with a coarser grain like sand, that was at most of our sites, then you've gotta get creative.
Kirstin: And when it came to flipping the core upside down, I was like, oh yes, this is improv science.
Sally: I love the amount of MacGyvering that goes on in science. People think that we have it, all of our ideas properly solidified, that we're using very high tech equipment. But no.
Kirstin: No, we are making it up as we go.
Sally: A hundred percent.
That was Dr Kirstin Meyer-Kaiser, from Woods Hole Oceanographic Institution
