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Innovative DNA Probes Enhance Understanding of Deep-Sea Cephalopods

A recent advancement from Kobe University has introduced novel DNA probes that greatly enhance the ability to study the elusive cephalopods of the deep sea, including squids and octopuses. This innovative development serves as a significant tool for marine ecological research and conservation initiatives.

Cephalopods are essential components of marine ecosystems, involved in intricate food webs as both predators and prey. Wu Qianqian, a marine ecologist at Kobe University, emphasizes the critical role these creatures play in maintaining the ecological balance by facilitating energy and nutrient distribution throughout ocean environments. However, understanding the diversity and distribution of cephalopod species has been challenging due to the inaccessibility of their deep-sea habitats, which are difficult to survey directly.

“The deep sea covers a vast area of our planet and houses countless species whose ecological roles are still largely unknown,” observes Wu. In light of these challenges, her research team aimed to create a detection system using environmental DNA (eDNA), which can be sampled from the water and analyzed to identify various species present in the area.

Utilizing a technique known as “environmental DNA metabarcoding,” the team designed specific DNA probes—referred to as primers—that can identify DNA from a wide variety of cephalopod species. This approach is akin to anglers strategically choosing bait to attract particular fish species. However, striking a balance between specificity and broad applicability of the probes is a key challenge in successful detection.

To address this, the researchers collaborated with scientists from the Japan Agency for Marine-Earth Science and Technology (JAMSTEC), who have extensive experience in gathering deep-sea samples. Their combined expertise has enabled the development of a robust system for capturing eDNA from various depths.

Findings published in the journal Marine Environmental Research indicate that the newly developed primers effectively detected DNA from various cephalopod species, confirming their success in both simulated samples and real-world deep-sea samples ranging from the ocean surface to depths of 2,000 meters. Notably, the study marks the first time several cephalopod species have been identified in Japanese waters using this method. A significant factor contributing to the successful detection was the decision to target longer DNA fragments, which can provide a clearer genetic signature despite being more prone to degradation.

In cold, deep-sea environments, however, the degradation of DNA is less of a concern, allowing for the preservation of genetic information that accurately reflects the species’ distribution. The presence of more DNA per sample allows for improved precision in identifying the specific species present.

Notably, the research revealed octopus DNA was only found in the deepest samples, which aligns with their behavior of being primarily ground-dwelling and solitary. Wu underscores the importance of understanding behavioral patterns and adapting sampling techniques accordingly for future studies. She also highlights the necessity of collaborating with molecular biologists and taxonomists to address issues related to species misidentification arising from inconsistencies in DNA databases.

Wu expresses optimism about the potential of this technique to transform deep-sea cephalopod research, stating, “Our methodology is poised to open new avenues for marine research and conservation efforts.” This groundbreaking work was conducted in partnership with researchers from Kyoto University, the Osaka Museum of Natural History, the Natural History Museum and Institute, JAMSTEC, and the Okinawa Churashima Foundation.

More information: Qianqian Wu et al, Development of universal PCR primers for the environmental DNA metabarcoding of cephalopod (Mollusca) diversity, Marine Environmental Research (2025). DOI: 10.1016/j.marenvres.2025.107094

Citation: Fishing for cephalopod DNA allows for efficient marine surveying (2025, April 14) retrieved April 14, 2025, from phys.org

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