Alternative fish sampling technique saving time and effort

A proof of concept using environmental DNA paves the way for more efficient and affordable sampling to estimate relative fish biomasses in rivers and estuaries.

By Catherine Norwood

Environmental DNA, or eDNA, holds new promise for identifying not only the presence of different species in any given habitat, but also for estimating their relative biomasses over space and time.

Over the past decade, with improved sequencing technology, eDNA has rapidly gained momentum for use in environmental surveillance on land and in water.

Jackson Wilkes Walburn gathering water samples from a Golden Perch larval pond at the Narrandera Fisheries Centre for eDNA testing. Source: NSW DPIRD

What is eDNA?

Environmental DNA (eDNA) is the genetic materials left by organisms in the environment. Every organism sheds its DNA in both life and death. It can be found in tissue fragments skin cells or eggs, in mucus, faeces and urine. Every sample of river or seawater is effectively a kind of DNA soup.

Fisheries scientists can look for DNA of a specific species in a sample - a process particularly suited to biosecurity surveillance. Alternatively, all the DNA in a sample can be sequenced, to identify the community of organisms in a particular habitat.

This process is made possible by the advent of new technology that makes high throughput sequencing possible and cheap.

Both processes rely on having sample DNA in a reference to match DNA sequenced to that of a known organism. Global DNA libraries collectively already contain DNA sequences for hundreds of thousands of organisms, with entries growing daily.

While eDNA is already well recognised for its ability to determine the presence or absence of species, less certain has been its ability to assess the biomass of a species. Biomass is defined as the weight of all individuals in each volume.

This is a "rapidly advancing area of research" says Dr Meagan Duncan from the NSW Department of Primary Industries and Regional Development's (DPIRD) Narrandera Fisheries Centre.

Meaghan leads the new eDNA laboratory at Narrandera and leads an FRDC-funded research project testing whether eDNA can identify fish biomass in rivers and estuaries (2019-016).

"There are potential cost savings with eDNA and also offer a less invasive way of sampling fish biomass than electrofishing or relying on catch-and-effort data which might not be available for many species," she says.

Tank and field trials

Mulloway (Argyrosomus japonicus) was chosen as the marine species for tank trials with Murray Cod (Maccullochella peelii) and Golden Perch (Macquaria ambigua) as the freshwater species.

A juvenile Mulloway used in eDNA tank trials. Source: NSW DPIRD

These trials showed a positive relationship between fish biomass stocked in tanks and eDNA analysed in water samples for both Mulloway and Golden Perch. The results for Murray Cod were less clear.

Field trials for Mulloway were conducted at 12 sites on the Hawkesbury River. Fisheries monitoring consultancy InfoFish used hydroacoustics to identify Mulloway fish numbers at selected sites. Soundwaves have a distinct acoustic pattern or signature when they encounter Mulloway, making the species easy to identify. Water samples to test for eDNA were collected at the same time.

Meaghan says that while Mulloway live in both estuarine and marine waters, depending on the stage of their life cycle, this project focused on estuarine sampling in spring and autumn. The autumn sampling provided a clear positive relationship between the hydroacoustic populations detected and the eDNA results.

Sampling of Golden Perch was done in conjunction with an electrofishing sampling project funded by the Commonwealth Environmental Water Holder. Samples were taken from five sites on each of the Lachlan, Murrumbidgee and Wakool Rivers.

Jarrod Chapman collecting water samples using the eDNA backpack in the upper Murrumbidgee River. Source: NSW DPIRD

The results showed a positive relationship between the biomass of Golden Perch found in the electrofishing and the eDNA sampling.

"We were also able to compare the electrofishing and eDNA results for Bony Bream (Nematalosa erebi) and Murray Cod, and found a positive relationship for both, although the Murray Cod results were the weakest."

eDNA benefits

Meaghan says collecting water samples for eDNA makes it a faster, cheaper and less labour-intensive technique than electrofishing.

"The beauty of eDNA sampling is that anyone can collect water samples because it doesn't require a lot of training.

"Our results essentially provide a 'proof of concept' for using eDNA to assess biomass in freshwater and estuarine environments. But using eDNA to estimate relative biomass is likely going to become feasible in the future," says Meaghan.

FRDC Related Project

2019-016 Estimating the biomass of fish stocks using novel and efficient genetic techniques

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