eDNA: how to find hidden species

Whilst it cannot be stated how important the ocean itself is to us and the planet, it is also the home of hundreds of thousands of animal and plant species. And they need all the help they can get. Now, we’ll never be able to monitor and conserve the entire ocean. That would just be a complete waste of our limited time and resources. It makes far more sense to focus our operations on areas that contain the most vulnerable groups of species. But first, we need to know where these biodiversity hotspots are and one of the problems… is that the ocean does not lend itself to being observed. Surveys are expensive and time consuming, and require specialist boats and observers. And realistically they will only be able to observe what happens at the surface, perhaps a bit below it. Yes, you can use sound to try and ID organisms, as long as the stuff you’re trying to find actually makes sound, which plants do not. You could try and fish out what you want to see, but you might just end up killing the stuff you’re trying to preserve. So how could you possibly hope to know what’s there, if you can’t see or hear anything? Well, what if all of our problems could be solved by one bucket of water? Dean Pentcheff is from the Natural History Museum in Los Angeles County, and he is part of a blossoming field of surveying known as eDNA.

Dean - eDNA or environmental DNA is pretty much exactly what it sounds like. It is DNA in the environment. It is reminiscent of all the bad TV shows you've seen where scientists come in and find a trace of someone in a room. We are all leaving a little trail of DNA behind us, and that includes people, that includes mammals, it includes all ocean life, it includes plants. Everybody is leaving a trail of DNA in the environment, and it is now possible to study that DNA from the environment.

Will - So it's sort of our skin cells and, dare I say, it's excreted substances that give us away almost.

Dean - Exactly that. In a lot of cases, it is skin cells that are being sloughed off, but all organisms have a variety of things that, as you imply, come off them and leave a trail in the environment.

Will - What gives it away as to how we can identify a species using it?

Dean - The most popular and most practical way that we use right now, has been sort of put under the umbrella term DNA barcoding. And that term was invented directly analogous to the idea of barcodes for products in stores where you scan a product and there's a numerical code that gets read, and then the store knows what the product is. What we can do with organisms is carefully pick a gene or a couple of genes, a very short segment of DNA through the whole genome that has enough variability that it's different between species, but not so much variability that we can't pick it out of the soup. And so we've identified a few of those genes across organisms across the natural world. And what we can do is from known specimens, we can take tissue samples, isolate those particular genes in those known organisms of known species, and create a library of reference codes more like an old fashioned phone book where you can look up a sequence by its genetic sequence, the sequence of A's and G's and T's and C's in the sequence and get a species name out. So that's how we go about identifying species in the ocean or anywhere using DNA.

Will - On all the marine surveys I've ever been on, it's always been something as indelicate as throwing a bucket into the ocean and analysing what comes out of the bucket. Is that what's going on here?

Dean - It really is. We can make it as high tech as we wish, depending on the question we want to ask, but honestly, yes, you can literally throw a bucket over the side, pull up some seawater and analyse the DNA in it, and that's definitely doable. Obviously, if you want to know things about particular depths or particular areas or particular microenvironments, the sampling can get as intricate as you can imagine. You can put tubes into the water and pump water out to a sampling station, or you can put bottles into the ocean that you release at a known depth, take a sample and then bring back up. So there's pretty much anything you can imagine is somebody's trying with varying degrees of success depending on the question they want to answer.

Will - It's always drilled into me that spooling up an array of equipment to run DNA tests was complicated and expensive. If that is the case, what advantages does eDNA have over your more traditional methods?

Dean - So I'm going to turn your question right around at you and tell you it's a whole lot cheaper. What we think of as the traditional way that you sample things in the ocean seems very straightforward, but is actually very expensive. What we do is we go out in boats, pick up a piece of ocean, whether it's fish in a net or invertebrates in a net or a grab from the ocean bottom. And that is actually really expensive to do. Boats cost a lot of money. Time on boats is very expensive. And then number two, once you've got that sample, if you want to know what's in it, let's say you want to know what the fish species are or what the invertebrate species are, or even more interesting what the microbial community might be, you've got to then get experts who can identify those things, line them up, in many cases literally line them up on the boat, have them do the identifications right there and move on. Again, that's a super expensive thing to do. By contrast, taking a water sample is about as cheap as it gets. You can go out there, grab the water sample, come back, and it's a very, very economical way of sampling the world that can be done much more quickly and in many ways, much more cheaply than the traditional standard ways that we have of sampling the ocean.

Will - Now you mentioned a little while ago about how this is a very useful tool for known species, but there are still unknown species. Is there anything we can do about identifying those?

Dean - Yes, there really is. When I talked about DNA earlier, I said it's, it's kind of like a telephone book and we have these known sequences from known species, but thanks to evolution and the way evolution works, the DNA sequences of closely related species are more similar than the sequences to more distantly related species. So if you are looking through your DNA that you've come up with from the ocean and you sequence all of the sequences that you got from your bucket of water, you will find a bunch that match your, your reference library and tick, tick, tick. Then you've got a list of species that you found almost inevitably you will find sequences that are similar, but not exactly like the sequences that you have in your reference library. Those sequences are very suggestive that there might be something new out there. It might be a new population of a species that you already have sequenced or might be a new species. And because the sequences are somewhat similar to sequences you know about, you can tell a little bit about it. You know, again, a little bit like a phone book, you know, if you find a name that isn't in the phone book, but you find a name that's similar, maybe they're in the same family in this case, maybe it's a species in the same genus, same family, closely related, and that gives you a target to look for. Then it gives you something that, that, you know, you can be looking for something that is similar to things you know, but a little bit different and go after that.

Will - One thing that I've always found a little bit crude about previous forms of marine monitoring was the fact that a lot of the time if we wanted to know what was out there, we'd have to go and fish them out and a lot of them would die in the process. This is presumably far less invasive a means of doing that.

Dean - You've put your finger on one of the beautiful aspects of using environmental DNA. It is non-destructive of the organisms. So we're really, really excited about the possibilities of using that kind of technology to be able to look at the presence or absence of organisms exactly as you said, without having to pull them out of the environment and kill them just to see if they're there.

Will - Okay. I'm really trying hard to catch you out here with some kind of drawback. So let's try this. You said earlier you can get a lovely qualitative list of species in that area, but what about the other side? Can it tell you anything about the number of individuals of that species?

Dean - If you had asked me that question two years ago, I'd have shaken my head and mumbled and said, 'no maybe future, future, we'll get there, we'll get there'. At this most vague obvious nature, you can imagine that the amount of DNA floating around in the ocean from a particular organism is going to have something to do with the amount or number of that organism that's out there. Making that connection quantitatively is really, really challenging, but is increasingly being shown to be practical and doable for particular species, one at a time. What I don't want to imply is that we could take that bucket of seawater and give you a count or a biomass for every species that's out there. That's way, way off. But if there's a particular species of interest, we could talk about fisheries, interested species or endangered species that we really want to know something about. By modelling how the DNA processing works, we can create a model to relate the amount of DNA that you find in the sample to the amount of the organism that's out there, whether that's mass or numbers in ways that are giving us some pretty good numbers.

Will - Putting all this together, then, we've got a non-destructive, non-invasive way of finding out what species are present in an area. How does this help us to help them?

Dean - One of the biggest challenges for any conservation initiative is just answering the question, 'what's there? How's that changing with time?' The only thing that you can serve is what you can see, and the only thing you can see is what you can detect. And so if it's very difficult or very expensive to detect the presence of something, it's very much more difficult to conserve it. So environmental DNA provides us what we think is an incredibly potent tool to let us see how the conservation efforts should be developed, and then once they're developed, how well they're working. And that I think is the biggest promise of environmental DNA for conservation biology.