eDNA Study Uncovers Deep-Sea Secrets Near Ningaloo

PERTH, Australia — Scientists have confirmed the presence of the legendary giant squid in Western Australian waters for the first time using cutting-edge environmental DNA technology, revealing a hidden world of biodiversity in the deep submarine canyons off the Ningaloo Coast.

The discovery, announced this week, marks the northernmost record of Architeuthis dux in the eastern Indian Ocean and comes from a Curtin University-led expedition that detected traces of the elusive creature across multiple water samples collected from extreme depths.

Researchers aboard the Schmidt Ocean Institute’s research vessel Falkor surveyed the Cape Range and Cloates submarine canyons, located about 1,200 kilometers north of Perth, as part of a broader effort to map deep-sea life. They collected more than 1,000 water samples from the surface down to depths exceeding 4,500 meters.

Using environmental DNA — genetic material shed by animals into the surrounding seawater — the team identified 226 species across 11 major animal groups without ever seeing or capturing most of them. The giant squid was detected in six separate samples from both canyons, providing the first molecular evidence of its presence in Western Australian waters.

A Mythical Creature Confirmed

Giant squid, which can grow up to 13 meters long — longer than a school bus — and weigh as much as 275 kilograms, possess the largest eyes in the animal kingdom, measuring up to 30 centimeters in diameter. These deep-sea dwellers have inspired myths of sea monsters like the kraken for centuries, yet they remain notoriously difficult to observe in their natural habitat.

Dr. Lisa Kirkendale, head of aquatic zoology and curator of molluscs at the Western Australian Museum, noted that there had been only two prior records of giant squid in the state, with no confirmed sightings or specimens 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 them in the eastern Indian Ocean,” she said.

The study also uncovered deep-diving marine mammals, including the pygmy sperm whale and Cuvier’s beaked whale, along with dozens of species never before recorded in Western Australian waters, such as the sleeper shark, faceless cusk eel and slender snaggletooth.

Lead author Dr. Georgia Nester, who conducted the research as part of her PhD at Curtin University and now works at the Minderoo OceanOmics Centre at The University of Western Australia, emphasized the broader implications. “Finding evidence of a giant squid really captures people’s imagination, but it’s just one part of a much bigger picture,” she said.

Nester highlighted that many detected species did not match existing genetic databases perfectly, suggesting significant undiscovered biodiversity. “We found a large number of species that don’t neatly match anything currently recorded… it strongly suggests there is a vast amount of deep-sea biodiversity we’re only just beginning to uncover.”

Revolutionary Power of eDNA

Traditional deep-sea exploration relies on cameras, nets or submersibles, which can miss fragile, rare or highly mobile species. Environmental DNA offers a non-invasive alternative: a single water sample can reveal hundreds of species at once.

The expedition combined eDNA analysis with physical specimens collected by the remotely operated vehicle SuBastian. Those specimens, now housed in the Western Australian Museum’s collection, provide reference sequences that strengthen future genetic databases.

Senior author Associate Professor Zoe Richards from Curtin University’s School of Molecular and Life Sciences said the approach transforms ocean science. “Deep-sea ecosystems are vast, remote and expensive to study, yet they face growing pressure from climate change, fishing and resource extraction,” she said. “You can’t protect what you don’t know exists.”

The research revealed distinct communities at different depths and between neighboring canyons, underscoring the complexity of these ecosystems. Such baseline data is crucial for marine park management, environmental impact assessments and tracking long-term changes.

Ningaloo’s Hidden Depths

The Ningaloo Coast, a UNESCO World Heritage site famous for its coral reef and whale sharks, extends into these dramatic underwater canyons. The study highlights how much remains unknown even in relatively accessible deep waters off Australia’s coast.

Nester collected samples across a wide depth range, showing how biodiversity shifts dramatically from surface waters to the abyss. This depth-stratified approach provides a more complete picture than spot surveys could achieve.

The findings, published in the journal Environmental DNA, involved collaboration between Curtin University, the University of Western Australia, the Western Australian Museum, Minderoo OceanOmics and other institutions.

Implications for Conservation and Science

The detection of giant squid and other megafauna in these canyons raises questions about food webs, migration patterns and ecosystem connectivity in the eastern Indian Ocean. It also demonstrates eDNA’s potential for monitoring elusive species amid climate pressures and human activities.

Experts say the technology could revolutionize biodiversity assessments worldwide, particularly in hard-to-reach habitats. As ocean exploration advances, non-invasive methods like eDNA may become essential tools for conservation.

For now, the giant squid remains a symbol of the ocean’s enduring mysteries. While no live footage emerged from this expedition, the genetic traces confirm its presence in waters long thought too far north for the species.

Researchers plan further studies to refine reference databases and expand surveys. The Western Australian Museum continues cataloging specimens to support ongoing taxonomic work.

This breakthrough off Ningaloo adds another chapter to humanity’s quest to understand the deep sea — a realm that covers most of our planet yet remains largely unexplored. As Dr. Nester noted, each water sample opens a window into hidden worlds, reminding scientists and the public alike how much wonder still awaits discovery beneath the waves.