Oceans cover most of the Earth, but ever since our prehistoric ancestors flopped onto land 375 million years ago, we’ve been a little out of touch—the vast majority of the sea remains unexplored.
It’s hard to protect something you know little about, and as we rapidly transform environments around us, we risk losing marine life that we haven’t even discovered yet.
The primary method for ocean exploration used to be trawling. But dragging big nets through the freezing, pitch black, high-pressure deep sea from aboard a tossing ship can only answer so many questions. At the Monterey Bay Aquarium Research Institute (MBARI), autonomous underwater vehicles (AUVs) that drift through the open ocean provide a more advanced solution.
Now, these robots can filter DNA out of seawater to help scientists learn which species live where.
Good Genes
As any living thing goes about its daily business, it leaves evidence of its presence. Shed skin cells, hair, saliva, excrement—it all contains DNA. Scientists collect soil and water samples and use this evidence—called environmental DNA or eDNA—to learn more about the communities in different habitats.
“We’re using eDNA to understand more about a wide range of species—everything from small bacteria all the way up the food chain to blue whales,” says Kobun Truelove, a senior research technician at MBARI and lead author of a recent study about eDNA-collecting AUVs.
Researchers can look for specific types of DNA in water samples to focus on endangered species, commercial fisheries interests or invasive species. They can also do a sort of roll call to evaluate the biodiversity in an area.
This is what the MBARI team and collaborators recently did using a technique called metabarcoding. In metabarcoding, researchers look at short regions of genetic code called DNA barcodes that are unique to different species. These barcodes can be matched to species in an online database.
The process is often compared to collecting fingerprints at a crime scene.
“But instead of a forensic database that looks for potential suspects, this database would be full of different species that are living in the ocean,” says Truelove.
Comparing what lives in different areas or in the same space over time can help researchers visualize the health of ocean environments.
“We have never before been able to look at life in the sea in the detail that eDNA allows us to,” says Francisco Chavez, a senior scientist at MBARI whose lab contributed to the work.
Making a Splash
The process only requires around a quart of water. Previously, scientists had to lower bottles from research ships to collect samples. Once on board the boat, the water passes through tiny filters that trap the DNA for extraction and sequencing in a lab.
MBARI scientists and collaborators automated the process of filtering and storing DNA and created a “laboratory in a can” that fits on the AUV.
Equipping robots to collect and process eDNA at sea makes it possible to explore new locations in great detail.
“These autonomous underwater vehicles can be a lot more agile than a large research vessel,” says Truelove.
The AUVs can get to areas that would be hard to access by ship, and they can stay for longer periods of time.
“We can set them to drift in particular currents in the Monterey Bay and continuously sample in that current,” says Truelove.
Among other things, the technology will help researchers understand how underwater communities shift over time in response to climate change.
“Having more of these autonomous vehicles out continuously monitoring will give us a much better idea of how things are changing,” says Truelove.
In their recent paper, Truelove, Chavez and collaborators showed that AUVs collect samples that are similar in quality to those collected manually in bottles.
The scientists sampled water from different sites around northern Monterey Bay using both methods and compared the results.
They used metabarcoding to identify different types of bacteria, “and then we just moved our way up the food chain,” says Truelove. From microbes to mammals, the results were consistent enough to inspire confidence in the unmanned system.
“It’s like checking a box … this is a tool that we can use and depend on,” says Ryan Kelly, an associate professor in the school of Marine and Environmental Affairs at the University of Washington.
Kelly was not involved in the project, but he expects it to have an impact on his eDNA work.
“We have a project that we’ve just started—funded by the US Navy—who’s interested in knowing where marine mammals are so they can avoid hurting them,” he says. Autonomously collected eDNA could help reveal the locations of some of the more elusive species.
Tiny Labs
The long-term goal is to have several of these AUVs roaming the oceans collecting eDNA. But right now, “they’re kind of still like a Model A Ford or something like that in terms of how much care it takes,” says Chavez.
Researchers are still figuring out the best methods when it comes to how much water to collect, what filters to use, etc. And to combine and operate automated eDNA sampling and AUVs together “takes a little fleet of people,” says Chavez.
“That’s a challenge,” he says. “How do you get them out and mass produce them and make them where anybody can use them?”
Another ambitious goal is to automate the entire process. With the current technology, AUVs collect and store eDNA, but they don’t sequence or analyze it.
“The next steps are essentially to take everything that’s inside a small molecular lab and pack it into this small autonomous vehicle,” says Truelove. “We’re currently collaborating with researchers at Johns Hopkins University to basically create a small lab on a chip.”
Each eDNA sample will have its own chip.
“On top of that, we need to have a miniature DNA sequencer on board and also the computing power to be able to make sense out of the DNA sequence data,” Truelove continues.
The team hopes to have it all completed in the next couple of years. The ability to analyze the eDNA live from the ocean will further revolutionize exploration of the deep.
“The robots can be sentinels and tell us where things are interesting, and we could go there with other power,” says Chavez.
“I think it’s too soon to know all of the different uses that are going to come out of it, and that’s one of the reasons it’s exciting,” says Kelly. “It feels like a new way of seeing the living world around us, and that’s a good reason to get out of bed every morning.”
Truelove agrees: “It opens the door up to a lot of possibilities for things that we haven’t even considered yet.”
