How a scoop of 'DNA soup' from our waterways could help preserve biodiversity

How a scoop of 'DNA soup' from our waterways could help preserve biodiversity

DNA is pretty well everywhere. Not just in your cells, not just at crime scenes, but in the very air we breathe and the water we drink.

Rivers and lakes contain a veritable 'soup' of DNA that's washed off any living creatures in the area.

Scientists are now using this natural information source to check on biodiversity.

Just like we use traces of DNA at a crime scene to catch criminals, scientists can use so-called "environmental DNA" (eDNA) left behind by wild animals to identify their presence without even setting eyes on them.

And this is a real plus, because many animals are difficult to catch — especially in waterways.

Think of a freshwater crayfish that burrows into a river bank, a shy platypus that mainly comes out at night, or a threatened fish that is rarely seen and hard to catch in a net.

And some waterways are very fast moving, deep or murky, which makes it even more tricky and dangerous to catch and sample animals.

Researchers hope eDNA can give them a quick and easy snapshot of the presence or absence of animals over a large area.

And early results of a new study suggest it may well do just that.

While eDNA has been used to track single species such as platypus before, the new study used a method — called 'DNA metabarcoding' — that is able to pick up many species of animals within a single sample.

It involved a massive survey for water-based animals in the vast waterway network that feeds Australia's second largest city, Melbourne.

Researchers collected water samples from over 340 sites in 25,000 kilometres worth of waterways during two months in 2016, in an exercise dubbed AquaBlitz.

"I think what's really unique here is the scale at which we're doing this," said Rhys Coleman, Waterways and Wetlands Research Manager at Melbourne Water.

Faster and more animal-friendly

When the eDNA results were compared with the data available from traditional surveys, eDNA metabarcoding came out as a much faster, cheaper and safer way of determining the presence of water-based animals.

"One sampling run captured a large percentage of records that took us decades to collect," Dr Coleman said.

The new method is also a lot more animal-friendly than traditional approaches, such as netting, trapping and electrofishing, which zaps fish to temporarily stun them for collection.

"Here you are just taking a water sample so it's non-invasive and it's not stressful for an animal to be surveyed," Dr Coleman said.

How they did it

After extracting DNA from the water samples the researchers then made multiple copies of it using a method called polymerase chain reaction (PCR).

The PCR process involved using different markers called "primers" to "amplify" genetic material from large groups of animals such as frogs, fish, birds and mammals.

The DNA within each group was then sequenced, and compared with an existing "library" of known animals to identify individual species.

The survey picked up 179 species including platypus, fish, frogs, water birds and water rats.

It also picked up the DNA of land-based animals such as possums, bats, kangaroos, gliders as well as invasive species such as deer, foxes, rabbits, dogs, cats, sheep, cattle and pigs.

Among other things, the survey findings reassured researchers that protected platypus populations were still there.

In fact, the survey identified several new populations of platypus and fish in areas that had not previously been considered worth surveying, or were too difficult to survey.

And it even picked up previously unobserved species, including four new species of burrowing crayfish that would be very hard to find otherwise.

"We believe that eDNA is likely to be the most efficient method for detecting these species," said co-researcher Dr Andrew Weeks, from the University of Melbourne, whose company EnviroDNA applied the eDNA technology used in the survey.

The challenges of using eDNA

Dean Jerry, a geneticist from James Cook University, said the scope of the Melbourne survey was "pretty big".

"I haven't heard of others doing it at that scale."

Professor Jerry has been involved in a project to survey biodiversity in watering holes across Northern Australia using DNA metabarcoding.

But it had been a challenge to get the funding to build up the necessary DNA reference library.

"Metabarcoding doesn't work unless you have good reference libraries for the species."

Evolutionary biologist Jeremy Austin of the University of Adelaide agreed.

He said eDNA had a lot of potential but needed to be used with care.

Apart from the possibility of missing species that were not in the reference library, it's possible that the DNA of some species may be preferentially amplified by the primers used in the PCR process.

"So, if you don't find a species, you're not sure if it's not there or it just hasn't been amplified," Dr Austin said.

And this feature of PCR meant while eDNA could determine the presence of a species, it didn't necessarily tell you the abundance.

Dr Austin said this meant it was important to have some "ground truthing" of eDNA findings, for example by comparing them to historical records, as done by the Melbourne researchers.

Scientist also need strict controls on the collection and analysis of the eDNA to make sure the DNA isn't contaminated and leads to misleading results.

And to ensure that DNA hasn't been brought from another catchment — by a bird flying overhead, for example — they will need to check these findings with multiple samples over time as well as space.

Citizen science

Unlike traditional methods that require experts in the field to identify species, eDNA collection can easily be done by citizen scientists.

All they have to do is to scoop a bit of water out of a stream and squeeze it through a syringe equipped with a 0.22 micron filter, and then send the sample quickly off to a lab to be analysed.

In fact, citizen scientists in Melbourne have already been collecting eDNA for surveys of a single species of platypus.

In the future they may also be able to help with bigger biodiversity snapshots.

But all this doesn't mean scientists won't be needed out in the field any more.

While eDNA can tell you whether an animal is there or not, it can't tell you its age, size, sex, health or whether the population is breeding or not — so traditional surveys will still be needed.

"It will just cut down the number of traditional surveys required," said Dr Coleman, who is looking forward to taking a closer look at the recent eDNA survey results.