The idea that you can know a creature was present somewhere without ever seeing it has a subtle disorienting quality. No picture, no sonar ping, no unintentional trawl net bringing something bright and frightening to the surface. Just water—regular seawater—carrying imperceptible biological clues that an animal was present, moving through the shadows, and conducting whatever business a giant squid does at depths where sunlight has never reached.
That’s basically what happened off the coast of Ningaloo, Australia, in 2020. The expedition’s findings, which were published earlier this year in the journal Environmental DNA, are still causing a stir in the marine science community. Nearly 200 water samples were taken from two submarine canyons, Cape Range and Cloates, which reach depths of more than 4,500 meters, by researchers from Curtin University, the Western Australian Museum, and several affiliated institutions. They extracted traces of the animals—mucus, feces, shed skin, and the molecular remnants of life in almost complete darkness—from those samples rather than the animals themselves.
The most notable discovery was a giant squid, Architeuthis dux, which was verified by eDNA in six different samples from both canyons. It is the northernmost confirmed occurrence of A. dux in the eastern Indian Ocean and the first time the species has been found in Western Australian waters in more than 25 years. The size of this animal—up to 13 meters long, eyes about the size of a large pizza, and arms designed for dragging prey through water—helps explain why that matters. Despite this, scientists have only been taking pictures of live giant squid since 2006. In 2012, it was first captured on camera in its natural environment. These organisms are not obscure; they can be found in literature, mythology, and sailors’ nervous dreams, but they are still very hard to understand.
Beyond the obvious spectacle of the giant squid detection, this study is intriguing because of what it implies about the range and relatives of the animal. Researchers are still mapping the distribution of Architeuthis dux across ocean basins, suggesting that it is a cosmopolitan species. Its close genetic relatives—populations of the same or closely related lineage—have been found in deep waters off the Pacific coast of the United States, which gives the Australian discovery some geographical weight. The discovery of the species that are active in the submarine canyons of the Indian Ocean supports the idea that it is a diverse, depth-adapted organism that has established a home in the frigid, pressurized zones below, where the majority of ocean research takes place.
Lead investigator Georgia Nester, a molecular ecologist currently employed at the University of Western Australia, characterized the canyons as “incredibly rich ecosystems” that had remained largely unexplored due to the challenging and costly nature of working at such extreme depths. Some of that challenge is avoided with the eDNA approach. In theory, a single water sample can simultaneously contain genetic signatures from hundreds of species, including deep-diving Cuvier’s beaked whales, sleeper sharks, and faceless cusk eels. In the end, the study identified 226 species from 11 major animal groups, some of which had never been identified in Western Australian waters before.
How many of the species that did not match known genetic records actually represent undescribed organisms versus just gaps in current reference databases is still unknown. Nester was cautious about this point, pointing out that while the sheer number of unmatched sequences indicates that deep-sea biodiversity in this area is significantly greater than what is currently known, they do not necessarily indicate the emergence of new species. To be honest, that seems like an understatement. The two nearby canyons displayed significantly different species compositions from one another, and each depth zone produced a unique community of organisms, indicating that even nearby deep-sea habitats can operate as distinct ecological worlds.
Researchers like Zoe Richards, senior author and associate professor at Curtin, have been straightforward about the wider implication of all of this: you cannot protect ecosystems that you have not yet described. Resource extraction, commercial fishing, and climate change are real and increasing threats to deep-sea ecosystems. Environmental DNA adds a layer of knowledge that is quick, scalable, and—most importantly—non-invasive, but it won’t completely replace cameras, nets, or submersibles. As it happens, the ocean is already making a record of itself. The ability of scientists to read it is still relatively new.
