A Curtin University-led study has revealed the extraordinary biodiversity hidden in deep underwater canyons off Western Australia's Nyinggulu (Ningaloo) coast, ranging from species previously undetected in the area, such as the elusive giant squid, to others thought to be new to science.
The Western Australian Museum-led expedition on board the Schmidt Ocean Institute's R/V Falkor surveyed the deep Cape Range and Cloates submarine canyons about 1200km north of Perth, collecting more than 1000 samples from depths of up to 4510m.
Using environmental DNA (eDNA) - genetic material naturally shed by animals into seawater - scientists were able to document what species live in these deep habitats without needing to see or capture them.
Among the most striking finds were traces of the giant squid (Architeuthis dux) detected in both the Cape Range and Cloates Canyons across six separate samples, plus deep‑diving whales such as the Pygmy sperm whale (Kogia breviceps) and Cuvier's beaked whale (Ziphius cavirostris).
Giant squid typically grow longer than a school bus (10 to 13 metres), can weigh from 150 to 275 kg and have the biggest eyes in the animal kingdom at up to 30cm in diameter – the size of a large pizza.
The study detected 226 species across 11 major animal groups, including rare deep‑sea fish, cnidarians, echinoderms, squid, marine mammals and more.
Dozens of species were detected that had never previously been recorded in Western Australian waters, including the sleeper shark (Somniosus sp.), faceless cusk eel (Typhlonus nasus) and the slender snaggletooth (Rhadinesthes decimus).
Lead author Dr Georgia Nester , who conducted the research as part of her PhD studies at Curtin University and is now at the Minderoo OceanOmics Centre at The University of Western Australia, said the results highlighted how little is known about Australia's deep‑sea ecosystems.
"Finding evidence of a giant squid really captures people's imagination, but it's just one part of a much bigger picture," Dr Nester said.
"We found a large number of species that don't neatly match anything currently recorded, which doesn't automatically mean they're new to science, but it strongly suggests there is a vast amount of deep‑sea biodiversity we're only just beginning to uncover."
WA Museum Head of Aquatic Zoology and Curator of Molluscs, Dr Lisa Kirkendale, said there were only two other records of giant squid from Western Australia, but there had not been a sighting or a specimen for more than 25 years.
"This is the first record of a giant squid detected off Western Australia's coast using eDNA protocols and the northernmost record of A. dux in the eastern Indian Ocean," Dr Kirkendale said.
Dr Nester collected water samples from the surface to more than 4 km deep, combining eDNA analysis with genetic reference sequences from physical specimens collected by the remotely operated vehicle SuBastian.
The physical specimens were identified by taxonomists and are now permanently housed in the WA Museum's Collection and Research Facility to aid further taxonomic research.
"The WA Museum contributed expert identification of specimens from the expedition, supporting the development of a local curated genetic reference that strengthened the eDNA analyses," Dr Kirkendale said.
Dr Nester said eDNA allowed the team to detect fragile, rare and fast‑moving species that traditional cameras and nets may miss.
"These canyons are incredibly rich ecosystems and, until now, they've been largely unexplored because of the difficulty of working at such extreme depths," Dr Nester said.
"With eDNA, a single water sample can tell us about hundreds of species at once."
"That means we can dramatically expand our understanding of deep‑water environments in a way that simply hasn't been possible before."
This approach revealed that different water depths host different communities, with neighbouring canyons able to support distinctly different ecosystems.
Senior author Associate Professor Zoe Richards , from Curtin's School of Molecular and Life Sciences , said eDNA had the potential to transform how scientists explore and protect the deep ocean.
"Deep‑sea ecosystems are vast, remote and expensive to study, yet they face growing pressure from climate change, fishing and resource extraction," Associate Professor Richards said.
"Environmental DNA gives us a scalable, non‑invasive way to build baseline knowledge of what lives there, which is essential for informed management and conservation.
"You can't protect what you don't know exists. The sheer number of discoveries, including megafauna, makes it clear that we still have so much to learn about what marine life lives in the Indian Ocean."
Dr Nester said improved knowledge of deep‑sea biodiversity could help guide marine park planning, assess environmental impacts and track changes over time.
"By combining eDNA with conventional deep‑sea survey techniques, we can build a far more complete picture of biodiversity, revealing species, ecosystems and ecological patterns that would otherwise remain hidden," she said.
"This kind of information is critical for marine park planning and management, because it gives us a much clearer picture of what species are present and how communities are structured across depth."
Fieldwork was supported by the Schmidt Ocean Institute, the Western Australian Museum and the study involved a collaboration between researchers at Curtin University, UWA, The Western Australian Museum, Minderoo OceanOmics Centre at UWA, University of Tasmania and Research Connect Blue.
"Environmental DNA Reveals Diverse and Depth-Stratified Biodiversity in East Indian Ocean Submarine Canyons" was published in Environmental DNA .
