A Microscopic Identity Crisis

Using DNA to identify larval species in the Gulf Stream
The shell of a sea slug

When swimming in the water, the planktonic sea snail, Diacria trispinosa, flutters two wings much like a butterfly. When they retract their bodies into their shells the spikes keep them from quickly sinking.

Credit: © Karen Osborn, Smithsonian

By Danielle Hall

Unseen by the human eye, thousands of microscopic animals hitch rides across the Atlantic on an oceanic highway. These animals, called zooplankton, move at the whim of ocean currents. Off the Eastern Shore of the United States one of the most powerful ocean currents—the Gulf Stream—is transporting zooplankton from the Gulf of Mexico, around the tip of Florida, up to Cape Cod in Massachusetts and then across the North Atlantic Ocean towards Europe. Surprisingly, the identities of most of these animals are completely unknown.

A Smithsonian National Museum of Natural History project is on a mission to change that. StreamCode aims to catalogue the planktonic animals living in the Gulf Stream off the coast of Florida using both photographic images and molecular ‘fingerprints’ in the form of DNA barcodes. Four expeditions between 2017 and 2018 will draw on the expertise of a team of plankton specialists to collect and characterize these tiny creatures based on their physical traits and unique genetic identities. 

“Our interest is not only describing all these amazing forms, but also trying to track who they belong to, where they come from and where they are going. These are huge mysteries,” said Michael Boyle, a developmental biologist, manager of the Life Histories Program at the Smithsonian Marine Station at Fort Pierce, Florida, and a member of the StreamCode team.

A lot of these animals are known as meroplankton, meaning they only spend some of their life drifting in the water column. Take a look in a tide pool where you’ll often see crabs, sea stars, sea urchins, anemones, and perhaps, if you’re lucky, a reclusive octopus tucked within a rocky nook. Many of these familiar animals started out in very unfamiliar forms in what’s called a larval stage. About 70 to 80 percent of benthic dwelling marine invertebrates (animals living on the seafloor) have a larval form, and in many cases, the adult and larva will look nothing alike, even though they’re the same species. Jellyfish are particularly troublesome since they can have a larval stage, a polyp stage, and the more familiar adult medusa stage.

Figuring out larval parentage seems like an easy task—just wait for the parent to give birth and then slide one of the larvae under a microscope. But most animals are stubborn in tanks and getting them to spawn is challenging, time-consuming, and most of time it simply doesn’t work. Some scientists will spend entire careers trying to figure out larval parentage and may only succeed for a handful of species. 

What’s more, at the tiny scale of larvae, many closely related species look almost identical.

“When I look at a bowl full of plankton under a microscope and I pick out certain organisms, especially the ones that I’m most interested in, I don’t know what species they belong to, and it’s almost impossible to tell,” says Boyle. “I know it’s a crustacean, I know it’s a sea star, or a mollusk, but all too often that’s about as close as I can get.”

That’s where genetics comes into play. StreamCode will sequence a specific snippet of DNA from each of the planktonic animals they collect, and store it in a library with an accompanying photograph. This DNA “barcode” is somewhat like the barcode on individual grocery items in the store, and is usually unique to one specific species regardless of whether it is from an adult or a larva. The goal is to have a database where scientists can search with a specific DNA barcode, and a matching picture and identity will pop up on the computer screen.

The barcoding method is already proving to be a powerful tool for discovering larval parentage. In 2010, current StreamCode researcher and National Museum of Natural History zoologist, Allen Collins, was working with a group of jellyfish called hydrozoa, specifically with the living benthic polyp form. After sequencing the DNA barcode of a specific Antarctic polyp, something wasn’t adding up. The sequence wasn’t looking much like other hydrozoan sequences.

“It wasn’t a hydrozoan at all,” says Allen. “It was a staurozoan—their common name are stalked jellyfishes, and it was a life stage of a stalked jellyfish that wasn’t even known.”

Identifying zooplankton serves more than to fulfill an inner curiosity. Many of these larvae will one day grow into economically important species, like lobster or blue crab. For the zooplankton that spend their entire existence as tiny, ocean drifters, they, too, serve an important purpose as tasty meals for bigger predators. Many scientists worry that with climate change the Gulf Stream may one day slow down or die out entirely, and this essential ocean highway will no longer exist to transport animals from the warm equatorial waters up into the north. Before we can understand the potential loss from a disappearing Gulf Stream, we first need to understand what kinds of animals depend on it. 

It’s also pretty amazing that just offshore another type of ‘universe’ exists, with creatures so small we aren’t even aware of them.

“We come back from the ocean after we go out to swim and fish and play, we rinse off our clothes, we splash down our boats, we clean up, and all of that [water] is filled with tiny animals that we never knew were there, swimming on and around us the whole time,” says Boyle.