Though they're not going to survive the trip
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| 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. Photos courtesy of ROV SuBastian science camera, Schmidt Ocean Institute. |
A University of Rhode Island professor of Ocean Engineering
and Oceanography, along with a multidisciplinary research team from multiple
institutions, successfully demonstrated new technologies that can obtain
preserved tissue and high-resolution 3D images within minutes of encountering
some of the most fragile animals in the deep ocean.
URI Professor Brennan Phillips, the principal investigator on the project, and a team of 15 researchers from six institutions, including URI, have shown that it is possible to shave years from the process of determining whether a new or rare species has been discovered.
The results of
their work are published in the journal Science Advances. An
advanced copy of the article and press package are available.
Revolutionary advancements in underwater imaging, robotics, and genomic sequencing have reshaped marine exploration, the study reads. 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 this rich digital data is a ‘cybertype’ of a single animal, rather than a physical ‘holotype’ that is traditionally found in museum collections.
“Currently, if researchers want to describe what they believe is a new species, they face an arduous process,” Phillips said.
“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 them 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.
A rotary actuated dodecahedron (RAD-2) encapsulates a holoplanktic polychaete, Tomopteris (a marine worm). Video from remotely operated vehicle, SuBastian science camera, Schmidt Ocean Institute.
“Again, these are deep-sea, thin little wisps of animals. The current workflow is not appropriate. It’s a major reason why we have so many undescribed species in the ocean.”
Information gained from the study—and others that follow—could be useful for extinction prevention studies, as it provides a wealth of information from a single specimen gained during a single encounter.
The work also responds to the growing call among researchers for compassionate
collection, which minimizes harm to animals by using advanced technologies to
collect information. Future studies and development could allow for complete
scans and inventories of life in the deep sea within a catch-and-release framework.
“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, and an Explorer with National Geographic Society.
“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 rates being 100 times higher than background
extinction rates.”
Phillips said because collecting these samples has always
been hard, there are many deep-sea species that have yet to be identified.
“When you look at climate change and deep-sea mining and their potential
effects, it is unsettling,” Phillips said. “You realize you don’t have a full
baseline of species, and you may not know what you’ve lost before it’s too
late. If you want to know what has been there before it’s gone, this is a new
way to do that.”
The mission, which was funded by the Schmidt Ocean
Institute and its 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. The team
collected as many as 14 preserved tissue samples a day, along with terabytes of
quantitative digital imagery. Together, the study provided:
- The first
complete assembled and annotated transcriptome (genes being made in the
animals’ habitat) of Pegea tunicate,
a marine invertebrate animal;
- Details of the
molecular basis of environmental sensing of a holoplanktonic Tomopteris polychaete (marine worm), which
spends its entire life in the water column;
- Details of the
full transcriptomes of two siphonophores, (gelatinous zooplankton composed
of specialized parts growing together in a chain) Erenna sp. and Marrus claudanielis, as well as the Pegea tunicate and Tomopteris polychaete;
- Full
morphological (form and structure) characterizations using digital imaging
of each animal while at depth.
The lead author of the paper, John Burns, a senior research
scientist at Bigelow Laboratory, 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.
“With that information, we can envision how it hunts by
following chemical trails in its open water habitat,” Burns said. “I don’t
think that would have been possible without the innovative technology invented
and employed by the engineers on the team that allowed complete preservation of
the information from the animals within minutes of an encounter.”
“We also discovered that three of the animals we captured have huge genomes: each
having nearly 10 times 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.”
Harvard and URI brought to the mission a rotary-actuated
folding dodecahedron (RAD-2), 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.
“We cannot protect what we do not yet fully understand.
Advanced imaging technologies can accelerate our efforts to document the
diversity of life in the ocean. The faster we can catalog marine life, the
better we can assess and track the impact of human actions like climate change
and mining on ocean environments,” said Kakani Katija, bioengineer and
principal engineer of the Bioinspiration Lab at MBARI.
“We have these remotely operated vehicles out there with advanced imaging systems, which can create a three-dimensional model after only a few minutes,” Phillips said.
“We were able to approach a tiny jellyfish in a matter of seconds, collect high-resolution 3D images to the control room, and our team was able to tell in a matter of minutes that the tentacles were exactly 5 millimeters long. Then, we had extremely well-preserved tissue samples of the same animal within a matter of minutes.”
Roboticists, ocean engineers, bioengineers, and marine and molecular biologists from URI’s Department of Ocean Engineering; the Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine; the School of Engineering and Applied Sciences at Harvard University; Monterey Bay Aquarium Research Institute (MBARI) in California; PA Consulting, a worldwide firm that focuses on innovation; and the Department of Natural Sciences at Baruch College, City University of New York, made up the team. The paper represents five years of research.