Meet the future - what water samples can tell us about trout and salmon

Imagine being able to scoop water out of a river and tell if fish live upstream, what species they are and if they’re reproducing?

That idea is set to become a reality in the Manawatu.

Above RIght: Dr Adam Canning taking a water sample in the Manawatu.

Dr Adam Canning from Wellington Fish & Game has led a revolutionary project with Massey University to achieve exactly that.

In 2016, Dr Canning went to a conference for the Australian Society for Fish Biology in Hobart. There he attended a presentation on using environmental DNA to identify the presence of Macquarie perch in the Murray Darling Basin.

As organisms interact with the environment, DNA is expelled and accumulates in their surroundings, this is called environmental DNA.

It can be collected from environmental samples such as soil, water, or even air, rather than directly sampled from an individual organism.

Seeing the promise that eDNA showed for fisheries science in New Zealand, and with a focus on identifying trout spawning streams, Dr Canning secured $45,000 in funding from Fish & Game’s National Research Programme.

For background, New Zealand’s trout spawning streams are generally in remote locations, so Fish & Game staff normally walk or fly over them on a regular basis during the spawning season to monitor sports fish populations.

When staff are checking these streams they’re looking for redds, cleared patches where trout have dug down into the gravels to bury their eggs.

These redds can be easy to spot in good conditions, but counting them can be hampered by weather events and poor access so it can be hit and miss.

Being able to take a water sample downstream to identify fish spawning has been viewed by some as the Holy Grail of fisheries science.

So in 18 short months, the project has morphed from an idea in Dr Canning’s head to field trials which are due to start in coming weeks.

The most expensive part was identifying and testing the eDNA “primers” (short strands of DNA akin to barcodes on products) for brown and rainbow trout. Once known, those chemical “barcodes” can be used to rapidly detect trout DNA.

That task undertaken by Dr Richard Winkworth from Massey University is now complete, and initial tests have shown incredibly positive results.

Using a mobile DNA scanner called a BioRanger, scientists will be able to take a water sample, filter out any solids, and place it into a vial that contains a dried chemical that latches on to eDNA.

The vial is inserted in the BioRanger, and scanned for the eDNA “barcodes” of trout in the water with a result produced in about 15 minutes.

The battery-powered device costs around $4000, it’s the size of a block of butter and connects to an Android smartphone with a user-friendly app. The results appear on screen giving you empirical evidence of the existence of fish species in that waterway and whether they’re spawning.

The technology used (known as Loop-Mediated Amplification - LAMP) and the battery-powered portable device, provide the convenience of results in the field at only a couple of dollars test – this compared to common eDNA methods (such as qPCR) that rely on lab equipment and cost $40-plus per test. The time-saving and cost effectiveness will allow many more streams to be assessed each season than traditional methods allow.

Once the trout DNA primers are fully developed, Dr Canning wants to extend the study and develop DNA primers for salmon to enable the technology to assist with monitoring the population and health of this iconic Kiwi sports fish.

There is also no reason why the  LAMP technology can’t be used to identify populations of native fish species in locations that are hard to access.

Dr Canning envisages future refinements, such as being able to use automated water samplers that collect eDNA periodically over a spawning season without having to manually collect the samples.

With field trials approaching, the ground-breaking project is set to take fisheries science in New Zealand into a whole new realm.

Watch a video on the project here: