New Approach Enables Deep-Sea Research on Fragile Animals

A multidisciplinary research team successfully demonstrated a new approach for obtaining preserved tissue and high-resolution 3D images within minutes of encountering some of the most fragile animals in the deep ocean.

The team of 15 researchers from Bigelow Laboratory and five other institutions have shown that it may be possible to shave years from the process of determining whether a new or rare species has been discovered while characterizing how the animal works at the genetic level. The results of their work were recently published in the journal Science Advances.

Led by University of Rhode Island’s Department of Ocean Engineering, the team consisted of roboticists, ocean engineers, bioengineers, marine and molecular biologists from Bigelow Laboratory; the School of Engineering and Applied Sciences at Harvard University; Monterey Bay Aquarium Research Institute in California; PA Consulting; and the Department of Natural Sciences at Baruch College, City University of New York. The paper represents five years of research work.

Revolutionary advancements in underwater imaging, robotics, and genomic sequencing have reshaped marine exploration. The research shows that within minutes of an encounter with a deep-sea animal, it is possible to capture detailed measurements and motion of the animal, obtain an entire genome, and generate a comprehensive list of genes being expressed that point to their physiological status in the deep ocean. The result of these rich digital data is a “cybertype” of a single animal, rather than a physical “holotype” that is traditionally found in museum collections.

The researchers said this approach has the potential to remove a major bottleneck in the process of cataloging life in the ocean, which is vital to understand the impacts of environmental challenges, like climate change and deep-sea mining.

Burns, the lead author on the paper, conducted the genomic analysis on four animals sampled at depths of almost 4,000 feet.

“What we were able to achieve with these animals is remarkable,” Burns said. “For me, this is best seen in the sequence data we generated for the Tomopteris worm. We captured it while it was exploring its environment and were able to infer that it was scanning the water using two long sensory whiskers near its head for ‘sweet’ tastes: likely sugars associated with prey, and possibly for ammonia: a waste product of its typical prey.

That information enabled the team to envision how it hunts by following chemical trails in its open water habitat, something Burns said would have been impossible without the innovative technology invented and employed by the project team.

“Currently, if researchers want to describe what they believe is a new species, they face an arduous process,” said Brennan Phillips, a professor at URI and principal investigator of the project. “The way it is done now is you capture a specimen, which is very difficult because a lot of these animals are so delicate and tissue-thin, and it’s likely you may not be able to collect it at all. But if you successfully collect an animal, you then preserve it in a jar. Then begins a long process of physically bringing that specimen to different collections around the world where it is compared to existing organisms. After a long time, sometimes up to 21 years, scientists may reach consensus that this is a new species.”

“The vision was: how might a marine biologist work to better understand and connect to deep-sea life decades or centuries into the future?” said David Gruber, Distinguished Professor of Biology at Baruch College, City University of New York. “This is a demonstration on how an interdisciplinary team could work collaboratively to provide an enormous amount of new information on deep sea life after one brief encounter. The ultimate goal is to continue down this path and refine the technology to be as minimally-invasive as possible — akin to a doctor's check-up in the deep-sea! This approach is becoming increasingly important with current extinction being 100 times higher than background extinction rates.”

In another study, Gruber and Burns looked at how capture methods affect jellyfish RNA. That sequence information can start to change after about 10 minutes of stressful conditions, even with gentle collection. These technologies overcome this by preserving the information before the animal’s cells start to respond to stress, according to Burns.

“We also discovered that three of the animals we captured have huge genomes: each having nearly 10x the DNA in a cell compared to us humans!” Burns said. “For the fourth, with a more modestly sized genome, about 3% the size of a human genome, we were able to use cutting edge sequencing methods to build the most cohesive and complete genome of a salp to date.”

The mission, which was funded by the Schmidt Ocean Institute’s Designing the Future program and conducted on its research vessel Falkor, included two expeditions off the coast of Hawaii and San Diego in 2019 and 2021.

Harvard and URI brought to the mission a rotary-actuated folding dodecahedron, an innovative origami-inspired robotic encapsulation device, which collected animal tissue samples and almost instantaneously preserved that tissue at depth.

“We are seeing the impact of new types of marine robots for midwater and deep-sea exploration,” said roboticist Robert Wood, the Harry Lewis and Marlyn McGrath Professor of Engineering and Applied Sciences at Harvard University. “Not only are robots going places that are difficult or impossible for humans to reach, our devices investigate, interact with, and collect specimens using a gentle touch, or no touch at all.”

Imaging systems from MBARI’s Bioinspiration Lab that included a laser-scanning imaging device called DeepPIV and a three-dimensional lightfield camera called EyeRIS enabled the measurement and reconstruction of three-dimensional morphology, or body shape, of the animals in their natural environment.

“New imaging technologies like the ones we used here are being deployed in the world’s ocean, and are providing unprecedented detail of ocean life,” said Kakani Katija, lead of the Bioinspiration Lab at MBARI. “Collecting this data in a completely non-invasive way is the cherry on top, and this approach is vital to respectfully exploring and understanding how these systems function in a dynamic ocean.”

Photos:

A composite image of gelatinous deep-sea animals observed and sampled in the study. Clockwise starting from upper left: the holoplanktonic polychaete Tomopteris sp., the siphonophore Marrus claudanielis, the siphonophore Erenna sp., and the salp Pegea sp. Image: ROV SuBastian science camera/Schmidt Ocean Institute

Team members aboard the research vessel Falkor, prepare the RAD-2 for a deep-sea dive in October 2021. From left to right: Dave Casagrande, Brennan Phillips, and Kaitlyn Becker. Image: Jovelle Tamayo/Schmidt Ocean Institute

The marine worm holoplanktonic polychaete about to be encapsulated in the RAD-2. Image: ROV SuBastian science camera/Schmidt Ocean Institute