23 June 2024

Sahan Jayasinghe and Cindy Bessey from CSIRO collected eDNA samples on RV Investigator. Image: CSIRO-Rich Little

Scientists on the CSIRO research vessel (RV) Investigator collected hundreds of environmental DNA (eDNA) samples between Hobart and Sydney in May during the South-East Australian Marine Ecosystem Survey (SEA-MES).

They also experimented with a new eDNA collection technique that provided a unique opportunity to directly compare the results with visual sampling.

The eDNA samples are being analysed at CSIRO as part of a Marine and Coastal Hub project that is examining the potential of this biological monitoring technique for use in Australian Marine Park (AMP) management.

The analysis involves amplifying and sequencing the eDNA fragments, then comparing them with known reference samples to identify fish, invertebrates and planktonic organisms. This allows scientists to characterise the lifeforms present in an area without having to capture whole specimens.

The project is drawing from two SEA-MES voyages, the first of which collected 300 samples at ~50 sites in July 2023. This year’s voyage surveyed 53 sites.

The conventional sampling approach. Sahan Jayasinghe collects water from Niskin bottles deployed at various depths on the CTD rosette. Image: CSIRO-Cindy Bessey
Water being filtered. The eDNA is deposited on filter paper that has very small pores. Image: CSIRO-Cindy Bessey
An eDNA sample from filtered water. This sample contains visible colour from phytoplankton and invisible DNA fragments from hundreds of other species. Image: CSIRO-Bruce Deagle

Two approaches were used for eDNA collection.

The more conventional approach involved using fine membranes to filter water samples collected at discrete depths by the CTD platform, prior to trawl sampling and acoustic sampling at each site.

The novel approach involved deploying a CSIRO-developed automatic eDNA sampler mounted on the deep towed camera system. The auto-sampler is opened as the camera collects imagery near the seafloor.

“This ‘paired’ experimental design allows us to take and compare multiple measurements using different techniques at these sites,” project leader Bruce Deagle of CSIRO says.

The novel sampling approach. An eDNA sampler mounted on the deep-towed camera allows the results to be compared with visual sampling. Image: Museums Victoria-Benjamin Heally
Imagery from the deep-towed camera records the presence of jack mackerel at a survey station. Image: CSIRO
Fish samples collected in the trawl net provide additional evidence of the species present (jack mackerel). Image: Rich Little

“Each technique has its strengths and weaknesses.

“For example, with fish biodiversity, acoustic measurements give an estimate of total biomass (based on size of schools), but very poor species resolution; bottom trawl data catch only certain fish near the bottom; and eDNA can potentially give different results depending on depth, or the method of collection.”

Dr Deagle says the eDNA sampler mounted on the deep towed camera is a new way of collecting eDNA, so the goal is to see if it works as well as (or better than) conventional eDNA sampling from the CTD platform, and to compare both eDNA datasets with the deep towed camera.

“We’re evaluating how much data we can get from eDNA with different collection techniques,” he says.

“We’re also doing direct comparisons with conventional biodiversity collection methods, for example by conducting eDNA sampling at the same times and locations as net, camera and acoustic sampling.

“Our initial analysis shows that eDNA from more than 120 fish species was collected, the most common DNA coming from jack mackerel (Trachurus declivis). This familiar species was also very abundant in the trawl nets.”

Dr Deagle says that some of the more interesting eDNA sequences were from the ocean sunfish (Mola mola) and southern sawshark (Pristiophorus nudipinnis).

“Our data will provide the first comprehensive eDNA record in the waters off south-east Australia, which includes Freycinet and Flinders marine parks,” he says.

“While fish eDNA is a focus in the project, integrating this with DNA profiles of the hundreds of plankton that form the basis of the food-web provides a powerful approach to characterise ecosystem health. The sampling can be repeated in future years to detect change.”

Dr Deagle says there is potential for eDNA sampling to be adopted widely as a less extractive means of monitoring in AMPs. The challenge is to develop eDNA approaches that address specific management questions.

This research is supported by grants of sea time on RV Investigator from the CSIRO Marine National Facility, which is supported by funding from the Australian Government’s National Collaborative Research Infrastructure Strategy.

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