By Helen Taylor 13/04/2017

I was sceptical about my lab head joining the hunt for the Loch Ness monster, until I realised it was an excellent way to promote the amazing possibilities of environmental DNA.

Making a splash

Last week’s news was full of tales of how my boss, Professor Neil Gemmell, was going to take on the challenge of tracking down the infamous Loch Ness monster. It’s easy to see why people are so excited about finding any evidence that the monster exists. It’s the same reason they are excited about “de-extinction”: it’s where science meets magic. The really exciting part though, is that we now have the technology to detect the presence of pretty much any species in an ecosystem just from a water or earth sample. This is invaluable for understanding how much biodiversity we have, where it is, and how many species we are losing. Welcome to the magical world of eDNA.

A new way to count species

eDNA removes the need to take organisms for biodiversity surveys
Old school biodiversity assessment: great for museums, not so great for conservation. Image credit: Louisiana State Univeristy

Imagine being able to take soil or water samples from an ecosystem and catalogue every species living in that ecosystem.  No more long hours out in the field painstakingly identifying each organism encountered. No more invasive sampling or taking whole organisms back to the lab to ID them under a microscope. The number of species would be assessed, but the species themselves would be relatively undisturbed. This is the principle behind using environmental DNA (eDNA) for biodiversity assessment. eDNA comes from any material that has been sloughed off by species into their surroundings. This could be skin, faeces, slime, even eggs or sperm – anything at all that has come from an organism and contains DNA. The potential for eDNA to rapidly assess biodiversity and detect the presence of invasive species is huge. The technique itself, however, is relatively simple.

The technical stuff

eDNA can detect many species from one sample
What’s in that water sample? Well, quite a lot of DNA, actually. Image credit: FISHBIO

Researchers using eDNA techniques take a sample from the ecosystem they’re interested in (typically water, soil or sediment). They filter out all the DNA contained in that sample and then amplify this DNA back at the lab. At this point, they can use either a technique called metabarcoding, or metagenomics to identify the species contained in the sample. In metabarcoding, the barcodes in question are DNA sequences that are found in almost all species, but that differ between species, so can be used to identify them. Metagenomics, on the other hand, is more of a sledgehammer approach. You literally sequence small, random, fragments of the DNA found in the sample. Simple, right? So simple, that eDNA has already found a wide array of applications.

Endless applications most wonderful

eDNA is fantastic for assessing biodiversity in particularly inaccessible ecosystems. It’s already been used to survey deep-sea communities using sediment samples and insect diversity in Antarctica from soil samples. New Zealand researchers used eDNA from soil samples to assess biodiversity on Hauturu (Little Barrier Island) in the Hauraki Gulf. Biodiversity doesn’t just exist in the wild though. Want to know how many different kinds of bugs or fungus you have in your house? eDNA has you covered. Brilliantly, eDNA lends itself really well to a citizen scientist approach. Almost anyone can take part by providing samples from their local ecosystem. It’s easy to see why the Biological Heritage National Science Challenge has adopted this approach for certain projects.

Searching for species with eDNA

eDNA can help monitor elusive species
Just some of the weird creatures that have been detected with eDNA. Image credit: Arkive

In addition to surveying whole communities, we can also use eDNA to seek out particular species within an ecosystem. Early detection of invasive species is a particularly important application of eDNA. The technique is being trialed as a detector for zebra mussels, and New Zealand’s revenge on the rest of the world for our invasive species issues, the NZ mud snail (now invading river systems pretty much everywhere). eDNA can also be used to monitor rare or elusive species. Researchers have successfully monitored a variety of weird and rare species, including cryptic hellbender salamanders in rivers, cave-dwelling olms, and even golden tree frogs using water samples from inside the bromeliad plants they live in. So why not Nessie using water samples from Loch Ness?

What’s the catch?

Simple and relatively cost effective, eDNA seems like a the perfect panacea for biodiversity assessment. As always with new scientific techniques, we need to iron out the kinks. Several teams (including people in our lab at Otago) are working on best practice methods for eDNA studies. Establishing which filters, sample volumes, and genetic barcodes work best is important. Discovering whether factors like time of day, weather, and tides influence results is also key. How far eDNA can travel between ecosystems is also useful to know, particularly for riverine and marine systems.

Mystery species = MOTUs

One of the biggest issues for using eDNA to survey biodiversity is that many species have not yet been described by taxonomists. Often in eDNA studies, you will see reports of the number of Molecular Operational Taxonomic Units (MOTUs). This means we know how many putative species there are from a genetic standpoint, but we don’t know exactly what they all are.

These mysterious MOTUs partly arise because the universal primers used for many eDNA barcoding studies are not always specific enough to discriminate between closely related species. Researchers can improve this by using more specific primer sets. Even then undescribed species with no recorded barcode are an issue.  This is a longstanding issue for any DNA barcoding technique. Researchers can usually assign these MOTUs to a phylum, so we can still get an idea of community composition, but not to the fine resolution that might constitute a comprehensive biodiversity survey. Finally, we can’t yet judge species abundance using eDNA. It will tell you if a species is present, but not how many individuals, which is usually a key bit of data for conservation. Don’t put away your microscopes yet, taxonomists! We still need you to describe and quantify all the earth’s unidentified species!

In spite of these limitations, eDNA is still an enormously powerful tool with huge potential for conservation. As for Nessie, why stop there? Let’s go look for Bigfoot, the yeti, and Iceland’s Lagarfljót Worm. Just as long as we continue to monitor biodiversity that we know to be real and know to be endangered.