eDNA sampling: Assessing the state of species in bushfire-affected areas

During the summer, bushfires rained hell on the forest streams of southeastern Australia that the iconic platypus calls home.

Before the fires, the shy monotreme was listed as “Near Threatened” on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. In 2016, the IUCN estimated their population was between 30,000 and 300,000. The number is vague because, historically, the number of platypus living in the wild has been difficult to determine.

The most reliable way of counting platypuses has traditionally been through live trapping studies, in which platypuses are trapped and released. It’s labour-intensive but was, until recently, the only way to monitor platypus numbers.

In 2018-19, a new method – environmental DNA, or “eDNA” sampling – was used to discover where, in southeastern Australia, the platypus was hiding out. “All you have to do is arrive at a site and take some water samples, regardless of time of day,” ecologist Reid Tingley says. “It's quite sensitive, and it seems to be applicable to any aquatic animal that you can design a primer for.”

The method will now be used to check the status of a range of animals in bushfire-affected areas. A Sydney University researcher has estimated that one billion animals were lost during the fire season.

The eDNA samples taken before the fires provide researchers with a precious research opportunity. They’ll be compared with post-fire samples to gauge which species of fish, frog, mammal, and crustacean survived the catastrophe.

Dr Tingley, an ecologist from the Monash School of Biological Sciences, has received a $255,000 grant from the Australian Government’s Wildlife and Habitat Bushfire Recovery Program to use the method to assess biodiversity in bushfire-affected areas.

“Essentially, you take a water sample, you filter that water sample with a very fine filter, and the DNA gets trapped on that filter,” Dr Tingley explains. “So that could be a hair cell, a skin cell, any source of DNA that is floating around in the water.”

Read more: Powerless to prevent catastrophic bushfires? No, we're not

The researchers plan to sample water in fire-affected river basins including private land and parks in the Mitchell-Thomson, Snowy, Ovens, Upper Murray, Murrumbidgee, Hawkesbury, Hunter and Shoalhaven catchments, as well as Bega, East Gippsland, and the Clyde-Jervis Bay region.

More than 350 sites were sampled before the fires. Up to 220 of these will be re-sampled to assess the bushfire impacts. Another 80 sites will be examined in the survey to assess the health of priority species, including five varieties of native crayfish, four frog species, and four types of native fish.

Initial testing will assess the short-term impact of the fires. Subsequent testing will be undertaken again next autumn to gauge longer-term impacts. Are populations rebounding? How are introduced species, such as European carp, surviving compared to native fish, such as Macquarie River perch, river blackfish, stocky galaxias, and flathead galaxias?

A versatile method of identification

The method is particularly effective at identifying species that dwell in streams and wetlands, but can also detect more terrestrial species, such as birds and introduced mammals, including feral goats and foxes. But because the bird and land-dwelling animals are intermittent visitors to water bodies, eDNA cannot give as accurate a picture of their distribution, Dr Tingley says.

The eDNA method can be tailored to find specific species, or to cast a wider net using a multi-species meta-coding approach. “This doesn't change how you sample in the field – you still take a water sample and pass it through a filter”, Dr Tingley says. “But back in the lab, you design a more general primer, a short sequence of nucleic acids that is conserved across a whole group – fish or mammals or amphibians, for example – that allows you to sequence all of the DNA that gets amplified with that primer.”

Dr Tingley and his colleagues have already employed the eDNA technique to detect vertebrates in hundreds of waterways. “It's amazing, you can detect native water rats and birds, feral mammals like deer – potentially anything that comes down and spends some time at the waterway. For some fishes and amphibians, or platypus – those organisms that are really tied to a waterway – you can take water samples across a broad area and be fairly confident that if you don't detect a species’ DNA, it may not be present.”

It would be naive to imagine that aquatic species are more protected during a bushfire than tree-dwelling species, such as koalas, he says. “Those rivers are going to get extremely hot, and the ash is another real concern,” Dr Tingley says. “And in some areas, we had the perfect storm, where there were big fires and then a lot of rain, which then just washed all of that ash into the streams.”

"For some fishes and amphibians, or platypus – those organisms that are really tied to a waterway – you can take water samples across a broad area and be fairly confident that if you don't detect a species’ DNA, it may not be present.”

Plants and trees close to the rivers also burned, falling into the water, leaving the streams more prone to erosion and silt.

Initial water samples have already been taken from some of the sites. “My colleague had a hard time even passing water through the filter in one recently-burned area, just because of the quality of the waterway,” Dr Tingley says.

The value of the research is that those species in need of intervention can be quickly identified, so that action to save them can be prioritised.