Scientists recently used environmental DNA technology to discover rich deep-sea biodiversity, including giant squid, in a deep-sea submarine canyon off the coast of Nyingaloo (Ningaloo, also known as Ningaloo) in Western Australia. It may even involve a variety of species that have not been officially recorded by science. The new research, led by Curtin University, shows that in the previously almost blank deep sea area, there is a world of life that is far more prosperous than imagined.
The expedition was led by the Western Australian Museum and took the Schmidt Ocean Institute's research vessel R/V Falkor to conduct a systematic survey of two submarine canyons, the Cape Range and Cloates, off the coast of Ningaloo, about 1,200 kilometers from Perth. The research team collected more than 1,000 water samples from the sea surface to a depth of 4,510 meters to analyze the species composition of the local deep-sea ecosystem.
The researchers used "environmental DNA (eDNA)" technology, which detects the genetic material naturally released by animals into the seawater to identify species that inhabit the sea area without directly photographing or fishing. This method is particularly useful for discovering deep-sea creatures that are large but elusive or extremely fragile and difficult to capture with traditional trawls and camera equipment.
Among the many discoveries, the most eye-catching is that the DNA signal of the giant squid (scientific name Architeuthis dux) has been detected multiple times in water samples in the canyon of the Kopp Mountains and the Klotz Canyon. The research team detected traces of the species in six samples, confirming that this mysterious deep-sea beast haunts the depths off the coast of Western Australia. In addition, the team also identified the DNA of a variety of deep-diving whales, including the sperm whale (Kogia breviceps) and the Cuvier's beaked whale (Ziphius cavirostris).
Giant squid, widely known as the "monster of the sea," can be longer than a school bus, reaching 10 to 13 meters, and weighing between 150 and 275 kilograms. This species also has the largest eyes in the animal kingdom. The diameter of its eyeballs can reach 30 centimeters, which is about the size of a large pizza. It is considered an important feature for its adaptation to the dark deep sea environment.
Comprehensive analysis shows that this study identified a total of 226 species of organisms across 11 major animal groups, including rare deep-sea fish, squid, marine mammals, cnidarians, and echinoderms. Dozens of these species have never been recorded in Western Australian waters before, including deep-sea species such as Somniosus sp., Typhlonus nasus and Rhhadinesthes decimus.
Study lead author Dr Georgia Nester completed the work during her PhD at Curtin University and is currently based at the Minderoo OceanOmics Center at the University of Western Australia. She said the findings highlighted the scientific community's still extremely limited understanding of the deep-sea ecosystems surrounding Australia. In her opinion, the evidence of giant squid is certainly interesting, but more importantly, it is only a small part of the overall picture of deep-sea life.
Nestor noted that the team found a large number of DNA sequences that did not exactly match existing species records. This doesn't necessarily mean they're an entirely new species, but it strongly suggests there's still considerable, under-recognized biodiversity in the deep sea. These "difficult to classify" sequences may become important clues for future taxonomic and genomic research.
Dr. Lisa Kirkendall, head of aquatic zoology and curator of molluscs at the Western Australian Museum, said there have been only two official records of giant squid in Western Australia in the past, and there have been no sighting reports and no physical specimens collected in the past 25 years. She emphasized that this is the first time that the existence of giant squid has been recorded off the coast of Western Australia through environmental DNA technology, and it is also one of the northernmost records of this species in the East Indian Ocean.
In specific operations, Nestor collected seawater samples from different water layers from the sea surface to a depth of more than 4 kilometers, and then compared the eDNA analysis results with the genetic sequences of physical specimens collected by the remotely operated submersible "SuBastian". These physical specimens, identified by taxonomic experts, are now held in the collections and research facilities of the Western Australian Museum, providing the basis for the subsequent establishment of a more complete local genetic reference database.
Kirkendall pointed out that the museum team carefully identified the physical specimens and helped build a locally calibrated genetic reference library, which significantly improved the accuracy and reliability of eDNA analysis. In her view, this combination of "genetic reference + environmental DNA" provides a powerful new paradigm for deep-sea biodiversity investigation.
Nestor further explained that environmental DNA technology allows researchers to detect species that are extremely vulnerable to disturbance, are rare in number, or move extremely fast. This method is particularly critical in the vast depths and complex terrain where traditional cameras and fishing nets are unable to function. She pointed out that these submarine canyons are actually extremely rich ecosystems, but due to the extreme depth and high cost of operation, they have hardly been systematically explored for a long time.
With the help of eDNA, with just a small bottle of water sample, researchers can simultaneously obtain information on the existence of hundreds of organisms, greatly expanding their understanding of the deep-water environment. This method makes it possible to obtain wider and thinner space and depth coverage without adding a lot of ship time and equipment. The study also found that there are significant differences in marine biological communities at different water depths. Even submarine canyons adjacent to each other may have completely different ecological structures.
Zoe Richards, senior author of the paper and associate professor in the School of Molecular and Life Sciences at Curtin University, said environmental DNA has the potential to profoundly change the way the scientific community studies and protects the deep sea. She pointed out that deep-sea ecosystems are vast in scope, remote in location, and expensive to study, but they are increasingly under pressure from climate change, fishery activities, and resource extraction.
Richards emphasized that environmental DNA provides a scalable and non-invasive tool that can help scientists establish baseline information on deep-sea biodiversity, which is critical for formulating scientific management and conservation measures. "You can't protect a species that you don't even know exists." She said that a large number of new discoveries, including giant creatures, clearly show that humans still do not know enough about the marine life of the Indian Ocean.
Nestor believes that more comprehensive information on deep-sea biodiversity will help marine park planning, environmental impact assessment and long-term ecological monitoring. By combining environmental DNA with traditional deep-sea survey methods, researchers can build a more complete species list and ecological landscape, thereby revealing species, ecosystems and ecological patterns that were difficult to observe under previous technical conditions.
She pointed out that this kind of information is crucial for the site selection and management of marine reserves, because it can more clearly show the differences in species composition and community structure between different water depth zones and regions. In the future, with the continuous improvement of the genetic reference database and the advancement of sampling work, the research team is expected to further clarify the true species hidden behind these "unknown sequences".
The relevant research was titled "Environmental DNA reveals diverse and depth-stratified biodiversity in submarine canyons of the Eastern Indian Ocean" and was published in the journal "Environmental DNA" on March 7, 2026. The project's field work is supported by the Schmidt Ocean Institute and the Western Australian Museum, and brings together researchers from Curtin University, the University of Western Australia, the Western Australian Museum, the Minderoo OceanOmics Centre, the University of Tasmania and Research Connect Blue.