Environmental DNA is helping to illuminate the deep ocean. We identified thousands of detections for midwater and deep-water associated fish families across all marine parks sampled with 16,901 detections of Myctophidae (lanternfish), 1,107 detections of Stomiidae (dragonfishes), and Sternoptychidae (hatchetfishes).

One striking example identified is Sloane’s viperfish (Chauliodus sloani), a globally distributed deep-sea species known for its enormous teeth and bioluminescence. We found eDNA traces for this species across all marine parks, including 110 detections around the Houtman Abrolhos Island archipelago, 2 around Christmas Island, 1 around Cocos (Keeling) Islands, 38 during open water transects, and 8 across the South-Coast of Western Australia. This species typically inhabits waters deeper than 1,000 metres, far beyond the reach of most biodiversity sampling methods.

The ability of eDNA to detect such elusive organisms makes it a powerful tool for monitoring biodiversity in the deep ocean. Some detections, particularly in regions like the Abrolhos and South-Coast of WA, may be influenced by upwelling, an oceanographic process where nutrient-rich water from deep-canyons rises to the surface, supporting local aggregations of marine life and potentially transporting eDNA for detection.

eDNA has a promising application in supporting species conservation assessments, such as Red List assessments carried out by the International Union for Conservation of Nature. Many marine species are considered Data Deficient (DD) due to limited information about their distribution or population trends and eDNA may be able help fill these gaps by providing additional information and data about species occurrence. We detected 22 species that are currently considered Data Deficient on the IUCN Red List: Polyprion americanus (Atlantic wreckfish), Hippocampus subelongatus (Western Australian seahorse), and Pegasus volitans (long-tailed seamoth). These detections include rare occurrence data for species that are cryptic (hard to find!) or live only in deep waters that are difficult to sample, exactly the kinds of information gaps that eDNA is well suited to fill.

Additionally, we detected four Critically Endangered (CR) species, 8 Endangered (EN) species, 9 that are considered Near Threatened (NT), and 17 that are considered Vulnerable (VU). These include:

• Great hammerhead (Sphyrna mokarran, CR): This large coastal-pelagic shark is facing severe declines due to overfishing and the high demand for its fins.
• Shortfin mako (Isurus oxyrinchus, EN): Known for its speed, this pelagic shark has experienced significant population reductions, primarily due to bycatch and targeted fishing.
• False killer whale (Pseudorca crassidens, NT): A social cetacean found in tropical and subtropical oceans and is vulnerable to threats like bycatch and habitat degradation.
• Great humphead parrotfish (Bolbometopon muricatum, VU): the largest parrotfish species that plays a crucial role in reef bioerosion, this process helps control algae growth and opens space for baby corals to attach to and grow.

These detections underscore the power of eDNA to inform future monitoring and management decisions for high conservation value marine species.

Orange Roughy (Hoplostethus atlanticus) are species of fisheries interest, but they are vulnerable to overfishing due to their long lifespans with estimates of more than 200 years. Maturation ages of 23 to 40 years means that stocks of these fishes are slow to replenish and are thus vulnerable to overexploitation. In the 1970s, Australian and New Zealand stocks were severely depleted within 3 to 20 years of fishing. Government plans are now in place to manage Orange Roughy stocks to ensure that these stocks are not depleted.

eDNA identified this species in two marine parks (29 sightings in Abrolhos Marine Park and 253 sightings across the South Coast marine park network) with an additional two sightings during transit between parks. These findings may be included in future management plans of Orange Roughy and will help assess stock health of these incredibly long-lived species.

The remote south-west coastline of Australia hosts globally significant marine biodiversity and is home to a myriad of regionally endemic and temperate species, many of which remain understudied (Bennett et al., 2016; Sutton & Day, 2021).

Detected fish species include small cryptic taxa such as the Leafy Seadragon (Phycodurus eques), Blackback Snake Blenny (Ophiclinus gracilis), Spotted Dragonet (Repomucenus calcaratus), and Southern Velvetfish (Aploactisoma milesii), as well as larger, commercially important species such as Orange Roughy (Hoplostethus atlanticus), West Australian Dhufush (Glaucosoma hebraicum), Samson Fish (Seriola hippos), and King George Whiting (Sillaginodes punctatus).

Elasmobranchs that were detected in these samples include Southern Eagle Ray (Myliobatis tenuicaudatus), Southern Shovelnose Ray (Aptychotrema vincentiana), and Rusty Carpetshark (Parascyllium ferrugineum). This stretch of coastline encompasses recognized Biologically Important Areas for the reproduction and migration of Southern Right Whales (Eubalaena australis), as well as foraging, breeding, and haul-out sites for Australian Sea Lions (Neophoca cinerea). Southern Right Whales were detected at 11 sites and Australian Sea Lions were detected at 9 sites in these surveys amongst other mammal species including Orca (Orcinus orca), Humpback Whale (Megaptera novaeangliae), and Blue Whale (Balaenoptera musculus).

These surveys demonstrate the power of eDNA-based approaches to reveal a remarkably broad range of marine biodiversity. eDNA enables insights into the distribution of cryptic, reef-associated and benthic fishes, commercially important species, elusive elasmobranchs, and charismatic marine mammals. This underscores the broad applicability of eDNA as a non-invasive, scalable tool for biodiversity monitoring, particularly valuable in environments where traditional survey methods may be logistically challenging to deploy or prone to missing key taxa of interest.