Chasing Traces

Crown-of-Thorns Starfish (Acanthaster planci), Lizard Island

Republished from Lateral Magazine December 17, 2018Issue 30, Life Science

Everywhere an animal goes, it leaves behind microscopic samples of its DNA. Can we exploit these traces for a greater good?

In recent decades, the crown-of-thorns sea star has become a scourge on the Great Barrier Reef. Although these coral-eating predators are native to the Indo-Pacific region, large-scale outbreaks have devastated northern parts of the Great Barrier Reef. During the most recent outbreak, which began in 2010, the crown-of-thorns has spread further south every year. Standard monitoring has failed to pick up their presence until they are out of control. Typical surveys require a lot of effort and volunteers, and, even then, are limited to the animals that observers can see or catch. New research at Townsville’s Australian Institute of Marine Science is endeavouring to solve this problem using environmental DNA, or eDNA.

Animals moving through the environment continuously shed skin cells, hair, mucus and faeces, which are all great sources of DNA. These minute DNA traces allow researchers to detect if animals are, or have been, in an area. The easiest way to gather eDNA is from water samples. After these samples are filtered, DNA traces are extracted and can be tested for the presence of a single animal (i.e. a rare or invasive species) or for the composition of the whole ecosystem community.

Researchers collect samples for eDNA analysis at Mt. Hood National Forest in the United States.   Molly McKnight/Flickr  (public domain)

Researchers collect samples for eDNA analysis at Mt. Hood National Forest in the United States. Molly McKnight/Flickr (public domain)

The first use of this technique was to monitor invasive bullfrog populations in France in 2008. However, the use of eDNA is not limited to aquatic animals. Since most terrestrial animals must drink regularly from ponds or streams, they often leave behind skin cells and traces of DNA. More recent advancements are coming in the expansion of the number of species that can be detected from a single sample. This was recently tested as a proof of concept in Japan by Masayuki Ushio and colleagues, who designed universal primers that could detect almost 400 bird species, along with a diverse range of mammals, reptiles and arthropods.

This method can let scientists analyse the interactions of possibly thousands of animals in an environment, while also overcoming the problem of species identification during a typical survey. Some species, especially during the juvenile stages, can be very difficult to differentiate, while DNA samples can be matched to a database in seconds. The availability of eDNA means that this will likely become an additional tool — if not the tool of the future — for ecological monitoring.

One feature of this technique is that eDNA may only be detectable for a few days in warmer climates, due to rapid DNA degradation — this can lead to false negatives when species that are present aren’t detected. For some uses, this is potentially an advantage, as it would mean that each sample offers a very precise look at one point in time. In drier or colder climates, eDNA can be detected for up to thousands of years if the right conditions are maintained, such as in ice cores or certain kinds of soils.

Other issues can emerge from crossover contamination. For instance, some larger animals, such as moose or deer, transport other species’ DNA between ponds and rivers via water carried on their coats. This can be very difficult to identify, especially when monitoring rare and cryptic species that might have a very small home range.

Large terrestrial animals, such as moose, can transport other species’ DNA from one water body to another.   Walter Ezell/Wikimedia Commons  (CC BY 3.0)

Large terrestrial animals, such as moose, can transport other species’ DNA from one water body to another. Walter Ezell/Wikimedia Commons (CC BY 3.0)

Sven Uthicke and Jason Doyle, researchers from the Australian Institute of Marine Science, along with Miles Lamare from the University of Otago, have being using eDNA to look for crown-of-thorns outbreaks. They’ve refined the technique to be able to detect the biomass of crown-of-thorns in an area by measuring the number of copies of a specific crown-of-thorns gene. This can indicate the number of crown-of-thorns in a given area and the severity of an outbreak. This method is incredibly useful for monitoring crown-of-thorns, since they can be very hard to see during underwater surveys, especially when in low numbers.

In a phone call, Sven Uthicke acknowledged that for the time being, this method can be used for initial detection of the crown-of-thorns sea stars, with subsequent visual confirmation still required. But if problems of false positives and false negatives can be solved, eDNA has the potential to give an accurate view of all of the animals in an area without harming them, and with much less effort. This is especially useful for cryptic animals such as the crown-of-thorns, which can go easily undetected while still in the early stages of development.

It’s not unreasonable to assume that eDNA will emerge as an important tool for ecological modelling. The ease of sample collection, and the ability to collect multiple samples at each location during varying time points, could allow researchers to monitor rare, endangered or invasive species without the need to disturb or interact with them. In the near-future, eDNA will accompany other, more typical methods of ecological monitoring, but there are some that are already using eDNA as a sole source of data. This technology is just one more example of the pervasiveness of the DNA in the natural environment and how researchers are harnessing it to better understand the world around us.

Edited by Andrew Katsis

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