A DNA Library for Bermuda’s Fish

Among hundreds of preserved fish at the Bermuda Natural History Museum, BIOS interns Jonas Schroder (left) and Maria Granquist (right) select specimens for DNA sequencing.

In an innovative collaboration, BIOS molecular ecologist Leocadio Blanco-Bercial and reef ecologist Tim Noyes are exploring how DNA can be recovered from seawater to reveal which fish species are active on Bermuda’s reefs. As fish swim, water passing over their gills and waste passing through their guts all deliver sloughed off cells to the surrounding seawater, leaving a trail of genetic material behind them. Within that genetic material, a specific short sequence of DNA can be recovered by scientists and traced like a fingerprint to a single fish species. But to learn more about fish communities from the DNA sequences swirling in the seawater, scientists first need to document which sequence belongs to which species.

Thanks to the support of a $9,460 grant from the Bermuda Zoological Society, this summer the BIOS team hopes to sequence 240 of Bermuda’s fish species from the extensive specimen collection in the Natural History Museum at the Bermuda Aquarium, Museum and Zoo (BAMZ). To date, very few of Bermuda’s fish species have had their DNA sequenced. Within the worldwide sequence database GenBank, even many common fish (like grunts) aren’t represented at all. 

From tiny jars housing delicate seahorses, to large jars stuffed with long eels, the Natural History Museum’s collection provides tremendous insight into the diversity of fishes in Bermuda. Many of the specimens were collected by curious Bermudian fishermen, former BIOS visiting scientists such as Bruce Collette in the 1980s, and BIOS’s Chris Flook, a former collector at BAMZ.

“The development of a DNA library of Bermudian fishes will be a great tool to apply to our understanding of the patterns of distribution of fishes around our island, and on the slopes of ‘Mt. Bermuda’,” stated Robbie Smith, Curator of the Natural History Museum and BIOS adjunct faculty.  “We may also uncover more genetic distinctions between Bermuda’s fishes and those in the Caribbean and the southeast U.S. coast.”

Noyes, who has been using Baited Remote Underwater Video (BRUV) cameras to visually survey reef communities, is excited about how this new approach to studying reef fish may reveal more about the ecology of nocturnal species, as well as fish that commute between the reef and deep water offshore.

“In particular, I’m hoping the environmental DNA will provide a better picture of the sharks and rays that we have here,” Noyes said, since they are critical components of reef ecosystems but most active at night, when it is difficult for scientists to observe them.

Blanco-Bercial, who ordinarily uses DNA sequencing to study the ecology of tiny zooplankton, worked last year with Southampton University PhD candidate Luca Peruzza to conduct proof-of-concept sequencing experiments. In collaboration with BAMZ, they used the two North Rock aquaria as controlled systems to test their sampling reproducibility. Blanco-Bercial was initially alarmed when DNA belonging to herring showed up in one sample from the tank – but it turned out that water had been collected just after herring were fed to the predatory fish in the tank, indicating the sensitivity of the method to changes in the tank.

Working with Peruzza and Lehigh University intern Divya Sirdeshpande, Blanco-Bercial and Noyes simultaneously deployed a BRUV camera and sampled the seawater for fish DNA at two sites offshore Bermuda. While bar jacks and rosy razorfish were captured on camera, the environmental DNA revealed the recent presence of at least 14 fish species. 

However, in both the aquarium tanks and the ocean, 60% of the unique DNA sequences that the team recovered from seawater couldn’t be positively matched to any fish in the GenBank sequence database. Other sequences could only be identified to a broad group. For example, while there are three species of barracuda in Bermuda, GenBank only has sequences from a few species found in the Indian and Pacific oceans. The Bermuda sequences are similar enough to be confident they came from a barracuda, but the exact species remains elusive. Hence, the evidence that sequences from local species are essential for environmental DNA to be used as an effective monitoring tool.

In June, Blanco-Bercial and Noyes began training two new interns in the delicate task of removing tissue from the preserved specimens and extracting DNA for sequencing. 

“Leo has demonstrated that we can remove very small amounts of tissue from the specimens without damaging them for future studies, and still get enough DNA,” Noyes said, noting that tissue is taken from the fish’s body by cutting a little flap of skin just above the anal fin, in an area that taxonomists do not use when working on species identification.

Lehigh University intern and molecular biology major Maria Granquist has experience with the next-generation DNA sequencing technology that enables scientists to recover thousands of unique DNA sequences from a few liters of seawater. 

“I have always had a love for the ocean and fish, so it’s exciting to apply my knowledge and skills to something so interesting to me,” she said. 

Because many of the fish at the museum were collected decades ago and the DNA has degraded over time, Granquist is working with Blanco-Bercial to overcome the technical challenges of extracting high-quality DNA from the specimens.

For Bermuda Program Intern Jonas Schroder, the molecular lab work—and the smell of preserved fishes—is a bit different than the field projects he has been involved with at BIOS over previous summers, but offers a whole new set of skills he is excited to master before heading off to Colorado College. An avid diver who got his start through BIOS summer programs, Schroder has spent a lot of time underwater exploring Bermuda’s reefs.

“What surprised me the most was coming to the museum and finding all the specimens that looked like no other fish I’d seen before,” he said. “It puts into perspective how vast and complex the ocean is.”