Networks of sponges could capture DNA to track ocean health

To track the biological health of oceans, researchers use cameras, satellite images, and, increasingly, DNA shed directly into the water. But capturing genetic material in the sea is a tough task: Scientists must sift through massive amounts of water to dredge up their samples. Now, marine biologists have discovered that sponges are very good at “sponging” up DNA. More research is needed, but eventually a network of sponges planted throughout the oceans could provide an easy readout of how the diversity of plants and animals nearby is doing.

“It’s a clever idea,” says Eske Willeslev, an evolutionary geneticist at the University of Copenhagen who was not involved with the work. “It could make studies of biodiversity easier and more consistent.”

Across the planet, biologists are scrambling to catalog all the world’s plants and animals before they disappear. Traditionally, that meant going out and collecting samples of every species. In the past 20 years, however, researchers have been collecting and sequencing DNA from soil, water, air, and even the guts of other organisms. This so-called environmental DNA, or eDNA, can tell what plants, animals, or microbes are present in a given environment.

At the University of Salford in the United Kingdom, marine ecologist Stefano Mariani had focused his eDNA efforts on the marine environment. But he always found the processing of samples to be “fiddly, cumbersome, stressful, and wasteful.”

So he decided to see whether animals that filter seawater to get their food might also be reservoirs of eDNA. First, he tried shrimp guts, but because these invertebrates are picky eaters, he decided the eDNA they sucked in was not reflective of what was out there. But sponges don’t discriminate. “A sponge the size of a football can filter nearly a swimming pool worth of water in a day,” he explains. Mariani got DNA from nine sponges previously collected from the Mediterranean and Antarctica, and used them as his test cases. To see how the process might work for species conservationists are most concerned about, he tried to isolate any vertebrate DNA inside using special molecular probes. DNA could be in the sponge tissue, or on particles trapped in its channels.

The results were even better than Mariani expected. He and colleagues isolated DNA from 31 types of organisms, including Weddell seals, chinstrap penguins, and rock cod, the team reports today in Current Biology . What’s more, the Antarctic and Mediterranean sponges contained DNA from different sets of creatures, reflecting the different species that lived in the two different places. So it was easy to tell where the sponge—and the eDNA—came from.

Mariani says scientists might one day use these DNA-capturing sponges along with robots and autonomous underwater vehicles to filter water and extract DNA. The robots and vehicles are promising, says Mariani, “but they are also big, expensive, and not the easiest to handle, transport, and maintain.” If sponges could be used instead, even a citizen scientist could retrieve DNA data by simply clipping off a small piece of a sponge, he predicts.

Paul Hebert, a biodiversity scientist at the University of Guelph in Canada, sees limited application for sponges as biodiversity sensors, because the bottom-dwelling creatures don’t live in the open ocean, where it’s really hard to survey creatures by other means. He also notes that because all sponges filter water at different rates, it might be hard to compare eDNA collections from different ones.

Still, Hebert thinks the new work is inspiring. “Forget natural sponges,” he explains. “I like the idea of a techno-sponge,” a humanmade version that would mimic the techniques of real sponges to capture eDNA. He says he can envision schools of techno-sponges plying the seas or sitting on the sea floor collecting valuable data. And even if such sponges—or their natural cousins—prove impractical, Hebert adds, “It was fun to consider the possibility that the ocean bottom is littered with autonomous DNA samplers.”