Robot tracks environmental DNA from fish on seabed

At a depth of 15 metres, 5 km off the coast, a contraption most of all resembling a big oil barrel is currently collecting water samples every day. It sucks water in and filters it. It then extracts DNA traces from the organisms in the vicinity, so-called eDNA or environmental DNA. If it recognizes DNA traces from one of four preprogrammed fish species, it propagates enough DNA to be able to transmit a signal to the researchers at DTU Aqua that a bluefin tuna, Atlantic bonito (a small tuna), garfish, or mackerel has passed by.

The barrel contains an ESP – Environmental Sample Processor – and it is the only one of its kind in Europe, and the first in the world being used to measure eDNA.

“Nobody in the whole world has ever carried out autonomous eDNA analyses before, so nobody can tell us what it SHOULD be like. We have to find out for ourselves. And no one can tell us in advance whether it is going to work or not – which is the beauty of this kind of research. It’s a question of trial and error,” says Professor Einar Eg Nielsen from DTU Aqua, who heads the research group behind the ESP study.

Optimized for eDNA analyses in Silkeborg

The ESP was developed in the USA, where it is used to measure algal growth, for example. However, the Danish version has been remodelled to collect DNA traces in the environment—also called eDNA. PhD student Brian Klitgaard Hansen and Postdoc Magnus Jacobsen, who are responsible for the practical experiments at DTU Aqua in Silkeborg, have spent a year designing measuring tools, testing and optimizing, so that the ESP can run eDNA analyses.

“All living organisms leave DNA traces in the environment. Shellfish, fish, people. If you take a spoonful of soil, you will be able to find out which organisms have been in the ground even though there are no visible traces of them. If you spit in a river, and we take a water sample 100 metres further downstream, we may well be able to find your DNA in the water,” explains Einar Eg Nielsen.

Daily samples can show patterns of movement

In addition to sending results home daily, the ESP also stores samples, which the researchers can then examine more closely in the laboratory once the ESP is brought back to shore in about a month’s time.

Right now the researchers are eagerly awaiting the daily transmissions of data from the sea. If the ESP passes the test and is able to track the fish via eDNA and transmit data over a longer period of time, it will be able to add new knowledge, especially about migratory fish. Under normal circumstances, this would require daily trips out to sea to take samples over an equally long period of time.

“Rather than providing just a snapshot, which is essentially what a single water sample can do, the daily samples from the ESP will be able to identify traces of migratory fishes, like garfish, mackerel, and tuna. If the ESP is in the water at the right time, we will observe a steady decline in the traces of mackerel or tuna because we are getting to the time of year when these fishes leave our waters,” says Einar Eg Nielsen.

(Helle Falborg)