'DNA fishing' helps scientists survey marine life in the deep ocean

The deep sea is Earth’s largest habitat, yet remains one of its least explored. In this silent, dark realm, marine animals live in isolation, beyond the reach of most research tools.

Among the many elusive creatures in these waters, squids and octopuses – collectively known as cephalopods – stand out for their intelligence, agility, and ecological importance.

Studying them has always posed a major challenge since traditional tools fail in these lightless depths where cephalopods roam, hunt, and can vanish without a trace.

Recent research led by marine ecologist WU Qianqian at Kobe University may change that. Using cutting-edge molecular tools, her team has developed a new way to detect cephalopods from the faintest traces of their DNA left behind in seawater.

This approach promises to transform how scientists explore life in the deep sea, offering a clearer picture of its biodiversity and the role of these animals in marine ecosystems in general.

Key players in the ocean’s web

Cephalopods are more than just fascinating creatures – they are essential links in the marine food web. “Cephalopods play an important role in marine ecosystems, contributing to the distribution of energy and nutrients in the food web,” noted WU Qianqian.

Cephalopods serve both as hunters and as prey. While young, they are eaten by fish, seabirds, and marine mammals. As adults, they prey on crustaceans, fish, and sometimes even other cephalopods.

Their mobility allows cephalopods to connect distant ecosystems, swimming from shallow coastal waters to the ocean’s depths.

Despite their importance, most cephalopods remain poorly understood. Many live in the deep sea, where light barely penetrates and traditional survey methods such as net captures fail.

These animals can evade traps, change color, and squeeze into impossible spaces. Researchers needed a better way to find and study them without disturbing their world.

Tracking marine animals using DNA

Environmental DNA, or eDNA, refers to genetic material that organisms release into their surroundings through skin, waste, mucus, or decaying tissue.

By collecting water samples and analyzing the DNA they contain, scientists can infer what species are present – even if the animals themselves remain unseen.

In their new study, Wu’s team designed universal primers targeting mitochondrial 16S rRNA genes – genetic regions that are useful for identifying species.

These primers, named Cep16S_D and Cep16S_O, were created specifically to detect squids (Decapodiformes) and octopuses (Octopodiformes).

They allow researchers to perform eDNA metabarcoding, a technique that amplifies and reads many species’ DNA from a single sample.

“For this, our lab, which is renowned for its environmental DNA research, worked together with researchers from the Japan Agency for Marine-Earth Science and Technology (JAMSTEC) who have developed a system for collecting large amounts of deep-sea samples,” said Wu.

Detecting cephalopods of all sizes

Creating these primers was no simple task. Wu’s team had to balance specificity and breadth.

The primers needed to detect all cephalopods while avoiding unrelated organisms. They also needed to perform reliably in both lab settings and the complex chemical environment of deep-sea water.

In tests, the primers showed high sensitivity and could identify species from a wide range of sizes. From small species like Heteroteuthis dagamensis to giants like the elusive Architeuthis dux, the primers succeeded across various water depths.

This success marks a major step forward, especially because earlier primers often failed to detect certain taxa or produced results that lacked resolution.

A key factor in the team’s success was the use of longer DNA segments. While longer fragments usually degrade faster, the cold conditions of the deep sea slow this process. Longer DNA pieces provide better taxonomic resolution, which means scientists can identify species more precisely.

Uncovering hidden biodiversity

The research reveals the technique’s strength in field applications. Wu and her colleagues analyzed samples collected from near the ocean surface all the way down to 2,000 meters.

The new primers helped detect cephalopod species that had not previously been identified in Japanese waters. This shows that the method can uncover hidden biodiversity and correct gaps in our knowledge of regional marine life.

One surprising pattern emerged: octopus DNA was found only in the deepest samples. From mock community tests, the researchers confirmed that the primers themselves worked correctly.

That suggested the result wasn’t an error, but a clue about octopus behavior. These animals are ground-dwelling and solitary, making them less likely to leave traces in midwater or shallow areas.

DNA reveals marine animal behavior

The ability to detect marine animals through DNA is only one benefit of this approach. Wu believes it can also reveal how cephalopods live.

“In future studies, we need to nevertheless revise our sampling strategy to account for life history and behavioral patterns of different cephalopods,” she said.

Environmental DNA can indirectly reflect how species move and interact with their habitat. Since octopuses tend to avoid open water, their limited DNA traces in shallow samples suggest a mostly benthic, hidden lifestyle.

Squids, in contrast, are more likely to roam and leave detectable trails.

A foundation for future ocean research

Even with strong primers and high-quality data, one challenge remains: the reference databases. Species misidentification can occur when available DNA sequences are incorrect or incomplete.

“We need to resolve issues with misidentification of species due to errors in the DNA databases, and for this we intend to strengthen the collaboration between molecular biologists and taxonomists,” Wu said.

She noted that this technique has far-reaching impact. “Nevertheless, our technique is expected to open new possibilities for deep-sea cephalopod research and to serve as a foundation for marine life conservation.”

Tools for marine animal detection

By combining eDNA metabarcoding with precise primer design, Wu and her colleagues have created a sensitive, non-invasive method for tracking cephalopods.

Their work lays the groundwork for future studies into marine biodiversity, population shifts, and ecosystem health.

In a world where human impact on the ocean grows every year, these DNA tools are vital for detection of marine animals.

They help scientists listen to the quiet signals of life below, and to map the rhythms of creatures we’ve barely begun to understand.

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This project involved collaboration between scientists at Kobe University, Kyoto University, the Osaka Museum of Natural History, the Natural History Museum and Institute in Chiba, JAMSTEC, and the Okinawa Churashima Foundation.

Funding came from Japan’s Ministry of Environment, including support for deep-sea research cruises as part of a marine protected area monitoring project.

The study is published in the journal Marine Environmental Research.

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