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Marine genome campaign nets hundreds of specimens
by Michelle Z. Donahue
An exhaustive effort is underway to catalog some of the Indian River Lagoon's less obvious residents: marine invertebrates. To better understand what lives in the lagoon as well as how they’re getting there, a team of biologists from the Smithsonian Marine Station and several other institutions took part in a two-week collections blitz in March and April.
Their work resulted in hundreds of new specimens for the Smithsonian’s Global Genome Initiative (GGI), a six-year effort to collect, organize, share and study the planet’s genetic diversity. The team aimed to collect at between 650 and 750 samples for DNA analysis and 100–150 samples for cryogenic storage in the Smithsonian’s biorepository—but finished the blitz with 846 specimens for DNA extraction and 650 combined tissue and larval specimens for the biorepository.
“This was an intensive effort, with an impressive number of samples,” said team leader Michael Boyle, a research biologist at the Smithsonian Marine Station.
Boyle’s team included Smithsonian colleagues Dean Janiak, Matthieu Leray and Valerie Paul , as well as Gustav Paulay, of the Florida Museum of Natural History, who brought decades of expertise in marine invertebrate research to the venture. Several other visiting scientists assisted as well, including Dave Burdick, of the University of Guam, and Jaaziel Garcia, of the University of Puerto Rico. Eve Moore, an undergraduate assistant from the University of Florida, also assisted.
In mid-March, Boyle’s team sampled invertebrates at locations along the Fort Pierce Inlet to the Indian River Lagoon (IRL), both in open water and along its shorelines. In a second push in early April, Dr. Boyle, along with Will Jaeckle and Jamie Blumberg from Illinois Wesleyan University, towed the inlet for plankton, which include the mostly unidentified and poorly understood larval forms of adult organisms living in the IRL and flowing into the lagoon from the Atlantic Ocean.
On land and in the water, invertebrates—organisms without a backbone—make up a huge proportion of animal life on Earth; some estimates suggest they comprise as much as 98 percent of Earth's animal species. In marine habitats, invertebrates include familiar creatures like starfish, crabs, worms and snails, but also less mobile creatures like mussels, sponges and tunicates (also called sea squirts.) Yet they’re relatively understudied, and their larval forms even less so. In the IRL, though it’s known that the microscopic larvae of many invertebrate species arise from either local species in the lagoon or the coastal ocean, their origins are generally unknown. Little work has been done on larval genetics, a necessity for matching the larvae with their adult forms.
The 2018 project builds upon earlier work from a Smithsonian project dubbed Streamcode, where Michael Boyle worked with the Smithsonian’s Karen Osborn to collect plankton offshore within the Gulf Stream current.
“We want to see if we can make connections between those larvae and their adults, wherever they’re found,” Boyle said. “They could be coming from South America or across equatorial currents from the other side of the Atlantic Ocean—we just don’t know.”
To prepare the adult specimens for storage in the Smithsonian’s biorepository and addition to the GGI databases, the team photographed each specimen and removed a small portion, such as a leg segment, for DNA sequencing. But rather than sequencing an animal’s entire genome to identify it, the GGI project uses a method known as barcoding.
Barcoding identifies and distinguishes species by a short, unique sequence found in an organism’s mitochondrial COX1 gene. This sequence can be used as a relatively precise identifier—just like a barcode on a product in a store is used to track any item of an inventory. And because few larval forms have been sequenced for barcoding, Boyle is hopeful that the work will turn up quite a few new species.
He added that the entirety of the cataloging effort will also help researchers better track the health of the Indian River Lagoon environment over time.
“If you don’t know what lives here to begin with, then you can’t say how things are getting better or worse over time,” Boyle said. “Understanding plankton and larvae is one of the most critical and overlooked parts of research on biodiversity.”