What's in the water?

Getting DNA out of water is an extremely useful tool for wildlife conversation. You can use genetics to conduct a ‘marine audit’, where you categorise all the living things in an ocean environment to figure out how healthy it is. Mike Bunce, the Chief Scientist at New Zealand’s Environmental Protection Agency, is one of the leading figures in this field. Chris Smith spoke to him last year when he was leading a lab at Australia’s Curtin University, researching trace and environmental DNA. How does it work?

Mike - What environmental DNA is, is our ability to sort of capture DNA that's just exuded into any biological sample. So what we do is, we'll take a big bucket of sea water, we’ll filter that onto a very small membrane to capture all the particles that are floating around in that water column, tease out the DNA molecules or photocopy up specific bits of that DNA, that can tell us things like what fish can we find contained within that.

Chris - So this is like a DNA fishing expedition in the sense that you don't know what's in that bucket of water. You just know there’s some DNA in there and then asking ‘well actually, what is in here" by comparing it to DNA sequences we know.

Mike - That's right. When people generate DNA sequences from known organisms that generates the reference barcode collection, then we can transfer onto an environmental sample like seawater, and we can look at all the fish DNA barcodes within that, or all of the crab DNA barcodes from crustaceans. And we can compare those to the references and then make inferences about what is present there, ‘are we finding new species?’. There’s quite a high profile example of the HMS Sydney, which is a shipwreck that went down in World War II. We got some water from that, extracted the DNA from it, and we found a fish that's only 90 per cent related to anything on the database. So this is probably a fish not yet known, because most of the fish are actually on reference databases now, so I think we've discovered something new.

Chris - Where is this DNA coming from? Is this DNA that's been, for want of a better phrase, pooped out by the fish that you are effectively finding?

Mike - Fecal material that's being pooped out of anything is one major source of it. But organisms in any environment defecate, urinate, slough cells off, things drop off it - it's just that in a marine environment, all of this DNA is sort of homogenized into a nice little soup ready for us to collect up. We've got a natural made blender that's already been sort of blended together for us.

Chris - Someone mentioned to me that, talking of blending things, that you're actually looking at some outputs from one of the largest fish in the sea.

Mike - That's right. That’s part of the work that we're doing with one of our PhD students. They've collected poo from whale sharks. And so, when they defecate, when they're up at the surface, they get out a net and try and scoop some of that material up and then we take it back to the lab. We blend it up, we use our environmental DNA bar coding approaches and look at what we can tease out of it.

Chris - Without being too graphic, what does whale shark poo look like? Is this not just liquid?

Mike - Yeah, it's a big plume of brown goop that comes out the back end and you do have to use a net to collect it because there’s little solids floating around in there, and we literally just scoop it up. So it's not overly pleasant to send a diver swimming through a massive plume of whale shark poo, but you've got to make these sacrifices for science.

Chris - What are you finding in there?

Mike - There's a couple of things we're finding. First of all, we can get whale shark DNA out of the poop, and that's significant because we can then sample that environment for whale sharks non-invasively, without touching the organisms. But we're also getting the window into all those, sort of, zooplankton, copepods, decapods, all these small little krill-like creatures, that big filter feeders pick up. And what we're trying to do, because we've got whale shark samples from around the world that we've collected now, is to try and understand how they're eating different things, at different times of the year, in different geographical locations.

Chris - And you'll be able to track that?

Mike - Well, hopefully. We've only got about 25 different whale shark poo samples that have been sent in by some of our collaborators, because they're quite rare. Most of the time they don’t poo when they're on the surface, apparently. So, we try and pick up what we can, where we can.

Chris - The idea being, then, you'll be able to track not just where they go and what they're eating, but when they're eating it, and therefore what food supplies they depend on where. So we'll have a better idea about conservation, that kind of thing.

Mike - Yeah, well, at its very base, conservation of species is about conservation of habitats. And when you know the food web of whatever species you're trying to conserve, you've got a better indication of how they might respond.

Chris - But how do you know that the signals you're getting correspond to something that the animal has actually eaten and not, given how sensitive your techniques are, not just stuff that’s floating around in the water they've just pooed into?

Mike - Again, it's a good question and the simple answer is we don't. It's probably a combination of both. We end up with these sort of Russian doll effects where even if a large krill has eaten other types of organisms and a whale shark eats that, we end up with, you know, dolls within dolls within dolls. And so to answer that question well frankly, we don't really know,  but it's better than the information that we've got at the moment, which is just looking at a big plume of brown stuff.

Chris - I suppose one of the major benefits of doing this is that you're effectively auditing what's out there, without actually having to go out there apart from armed with a bucket, where previously it would be fishing expeditions, it would be diving expeditions, and relentless counting expeditions. This is much easier

Mike - It is easier. We can literally wade into the ocean and scoop up a bucket. But I will say there's lots of different methods for auditing marine ecosystems from everything from basic underwater cameras, through to visual sensors, and DNA is really just added another quite powerful part of that toolkit. And there's many scientific methods. The more proxies or more ways you've got at looking at a question, the better your answers are going to be. Truly, environmental DNA is a powerful part of this new toolkit because it can look at multiple levels. It doesn't just look at fish, which is historically perhaps how people assayed marine environments, assess them. We get to look at all the crustaceans and even the bacteria that are contained within that and phytoplankton and corals, because collectively that is what makes up the base of the food web and marine ecosystems.