Similar autonomous sampling technology is being used by several research teams to find out what’s living on tropical reefs, where scientists have placed multi-layer structures to attract the tiny organisms that call the reef home. The idea is to assess the diversity and density of “cryptic fauna”–the corals, sponges and soft-bodied animals that make up a big portion of the reef’s biodiversity–but are usually not counted by a census of marine life, says Allen Collins, director of NOAA’s National Systematics Lab and an adjunct curator at the Smithsonian Institution. Understanding the tiny animals that underlie the ecosystem is key to determining how well the whole system is faring. A collapse among an important yet overlooked animal–a type of shrimp, for example–might be a harbinger of problems among animals higher up the food chain.

A team of Australian marine biologists recently used remote eDNA samplers at an Indian Ocean coral reef as part of a population diversity study. Their goal was to identify new ranges for species that are facing climate change-driven pressures from rising temperatures and seawater acidity. Using the samplers, they found 376 kinds of fish and invertebrates over the study site, and that each reef had a different mix of marine life.

Experts say that these eDNA sampling techniques are improving quickly, but they still have a couple of drawbacks. DNA degrades in the water after only a few days, so samples collected by AUVs only provide a genetic snapshot of whatever passed by recently. Along coastal areas or near cities, scientists are also finding contamination from people. “The biggest monkey wrench is that we get human DNA almost everywhere,” says Mark Stoeckle, a senior research associate at Rockefeller University who has been using eDNA techniques to assess the health and diversity of underwater life in New York Harbor and along the New Jersey Shore. “And in New York Harbor, we get DNA of fish that people eat: Nile tilapia, branzino, barramundi.”

AUV device in sea
Photograph: Todd Walsh/MBARI

They also found a healthy amount of goldfish DNA. “It could be that there is a big goldfish population,” Stoeckle adds, “but it could also be people releasing goldfish.”

Stoeckle has been working with New Jersey state biologists to conduct DNA-based counts of commercial fish species by dropping one-liter bottles into the ocean at various depths and sampling the water inside. It’s part of a census of commercial species that has been ongoing since the 1960s, information that helps resource managers determine catch limits for local fishermen. But in addition to the target species, they are finding that some species of fish are moving north from their normal range along the coast of Florida and the Carolinas; they’re environmental refugees who are trying to escape increasing temperatures. The researchers found DNA from the gulf kingfish, which normally resides in the Chesapeake Bay and has never before been identified in New Jersey, as well as the Brazilian cownose ray, which is native to the Gulf of Mexico and has been unknown in northeastern waters.

Stoeckle says once some of the bugs can be worked out, eDNA sampling may soon prove to be a faster and cheaper way to assess the health of the marine ecosystem as humans increasingly rely on the ocean to provide more food and energy. “There’s a need to monitor the oceans more closely, because we are doing more in the ocean, such as building wind farms and pipelines and natural gas and oil extraction,” he says. “These are all things that may be beneficial economically, but we want to know what we are doing to the environment.”

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