Environmental DNA for measuring offshore marine biodiversity: what can DNA in water collected from the RV Investigator tell us?

Samples of eDNA can be collected by filtering seawater and analysed to identify organisms such as bacteria, invertebrates and fishes. This makes it useful for establishing biodiversity baselines and subsequent monitoring, especially in offshore areas that are difficult or expensive to sample. For example, Parks Australia is using eDNA sampling to collect information on biological communities and important species as part of Australian Marine Park management. Research tailored to specific management questions is needed to optimise the use of eDNA in marine environmental management.

This project will identify eDNA from water sampling conducted at ~100 sites during the South-east Australian Marine Ecosystem Survey (July 2023 and May 2024). The survey, from the CSIRO Marine National Facility Research Vessel Investigator, covers offshore sites from Tasmania to New South Wales, including in the South-east Marine Park Network. Nets, cameras, and acoustics are also used to collect biodiversity data.

The project will evaluate eDNA sampling methods, including how they complement conventional sampling approaches, and contribute to the design of effective, scalable, and non-extractive biomonitoring tools for marine ecosystems. It will:

• provide an eDNA biodiversity baseline for the South-eastern temperate region;
• compare biodiversity inside and outside two Australian Marine Parks;
• provide an initial eDNA baseline for the Gippsland priority area for offshore renewable energy infrastructure; and
• evaluate the ability of eDNA to detect some priority shark species in the region.

Approach

The project team expects to collect about 600 eDNA samples during the two voyages. Three hundred samples were collected at ~50 research stations during the first 30-day voyage. Niskin bottles are used to sample at points through water column (50–500 m depths) before trawl sampling at each site. Two-litre water samples are filtered through fine 0.2 µm pore filters (for small plankton) and 10-litre samples are filtered through 0.45 µm pore filters (for fishes). A CSIRO-developed auto-sampler is deployed on the deep tow camera system to collect eDNA along the video-recorded transect. From these samples eDNA markers will be sequenced to document fish, shark and plankton diversity. The evaluation will also compare eDNA results collected through different collection and water filtering protocols.

The project will investigate these practical questions of interest to biodiversity managers.

• Can eDNA based observations be used as a proxy for traditional observations of benthic/pelagic fish diversity/abundance?
• Can eDNA based observations be used to measure diversity and abundance of pelagic plankton to monitor the health of the pelagic (open ocean) ecosystem?
• What is the horizontal and vertical distribution of eDNA signal?
• Compared with conventional datasets how structured is the eDNA data (do eDNA observations from surface waters reflect what is seen in deep samples and the benthic community)?
• Using a shark-specific marker, how often is eDNA from relatively rare species of interest detected (such as white sharks and grey nurse sharks).

Expected outcomes

This project is expected to facilitate the better understanding and use of eDNA sampling for monitoring by Parks Australia and in fisheries, oil and gas production, and emerging renewable energy industries. Marine managers will have a new baseline and unique eDNA-based perspective on the biodiversity of the south-east marine region to help address specific questions in Freycinet and Flinders marine parks and broader implications for future monitoring.

Results of the project will complement a new eDNA species mapping and monitoring partnership between Parks Australia and the Minderoo Foundation (funded through the Ocean Discovery and Restoration Program).

Project location

Freycinet Marine Park and Flinders Marine Park