Fishing for cephalopod DNA allows for efficient marine surveying

(Press-News.org) New DNA probes allow for efficient surveying of the hidden lives of squids and octopuses in the deep sea. This development by Kobe University provides an effective tool for marine ecological research and conservation efforts.

Squids and octopuses eat and are eaten, and in between that they move around a lot. “Cephalopods play an important role in marine ecosystems, contributing to the distribution of energy and nutrients in the food web,” explains Kobe University marine ecologist WU Qianqian. And while for ecological research it is therefore essential to know about the distribution of the various species of squids and octopuses, collectively known as cephalopods, their deep-sea habitat is largely inaccessible to direct surveys. Wu says, “The deep sea covers a large portion of Earth’s surface and is home to many unknown organisms whose ecology remains largely unexplored.”

Wu and her team therefore set out to develop a detection system based on DNA released to the environment. In the technique known as “environmental DNA metabarcoding,” the environmental DNA is probed with small pieces of DNA specific to the target, similar to how anglers use specific bait to catch a particular species. The challenge is creating probes that is specific enough to just the group one tries to detect, but also general enough to catch anything within that group. “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,” says Wu.

In the journal Marine Environmental Research, the Kobe University researcher now reports that they developed DNA probes, called “primers,” that could specifically detect DNA from a broad range of cephalopod species. This worked both in mock samples created from tissues from the Osaka Museum of Natural History and in sea samples from the surface all the way down to 2,000 meters deep. In the latter, their ability to detect some species of cephalopods in the waters around Japan for the first time is a testament to the power of their technique. One possible key element in their success was that Wu and her colleagues were fishing for longer DNA fragments than had been attempted before. Although longer DNA fragments might degrade more quickly, this is not as big of a problem in the deep, cold sea, and it also ensures that the DNA is relatively “fresh,” more accurately representing the distribution of species. Having more DNA per sample also allows for more precise identification of exactly what species it came from.

The Kobe University team detected octopus DNA only in samples from the deepest seas. From their trials with mock samples, the team can be confident that this is not because their primers don’t work properly; rather, they see it as their technique’s ability to even infer the target organisms’ lifestyle from the results, as octopuses are mostly ground dwelling, hidden and solitary.

“In future studies, we need to nevertheless revise our sampling strategy to account for life history and behavioral patterns of different cephalopods. In addition, 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” says Wu. She adds: “Nevertheless, our technique is expected to open new possibilities for deep-sea cephalopod research and to serve as a foundation for marine life conservation.”

This research was funded by the Ministry of Environment of Japan. It was conducted in collaboration with researchers from Kyoto University, the Osaka Museum of Natural History, the Natural History Museum and Institute, the Japan Agency for Marine-Earth Science and Technology (JAMSTEC) and the Okinawa Churashima Foundation.

Kobe University is a national university with roots dating back to the Kobe Higher Commercial School founded in 1902. It is now one of Japan’s leading comprehensive research universities with nearly 16,000 students and nearly 1,700 faculty in 10 faculties and schools and 15 graduate schools. Combining the social and natural sciences to cultivate leaders with an interdisciplinary perspective, Kobe University creates knowledge and fosters innovation to address society’s challenges.

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