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Smithsonian National Museum of Natural History
New Blenny species Starksi weighti n. sp., in this case, a male.
A BioCube in place and ready for observation on a mangrove prop root near Carrie Bow Cay, Belize. All of the animals and plants inside the cube were extracted, photographed, and sent to Washington, D.C. for DNA extraction.

In the 40 years that Carrie Bow Cay has been a field station, an impressive array of marine life has been cataloged at the Smithsonian’s National Museum of Natural History (NMNH):  more than 3000 species, spanning 24 plant, algae and animal phyla, containing 670 distinct families and 1518 genera. While this may seem comprehensive, scientists estimate that we have only discovered about 1/3 of the species that live in the ocean, so there is still a long way to go before we have an accurate picture of marine biodiversity. Given the rate that human beings are driving the loss of species, it is more important than ever that we concentrate efforts on better understanding biodiversity. In an attempt to capitalize on new technologies and utilize the resources that have been put into documenting the diversity of the region, scientists at the Smithsonian have set out to generate a genetic library, or a “biocode”, of the major marine ecosystems around Carrie Bow Cay. A biocode is a comprehensive record of the taxonomic and phylogenetic diversity of a given place and time. It can be thought of as a library for our knowledge of biodiversity. When paired with traditional museum-based collections and images, the biocode becomes a powerful resource to understand patterns and address questions about ecological and evolutionary processes for a specific location.

To get started, the team needed a sampling strategy that captured the representative diversity of major habitats surrounding Carrie Bow Cay, but with a manageable amount of effort. The method they chose was the “one cubic foot” approach; that is, collect all the living organisms from one cubic foot sections (or “BioCubes”) of mangrove roots, a sea grass bed, and coral reef. When forced to capture all living organisms within a constrained space, remarkable diversity emerges. For instance, more 200 researchers were given five years to inventory all species on a reef in French Polynesia. A single BioCube from the reef produced more than 335 species (~10% of the total documented organisms) and included at least 17 species not found by previous collectors. Many of these inhabitants are tiny crustaceans like amphipods and juvenile crabs that are often overlooked with other sampling methods.

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The research team sorts through the specimens in a BioCube in the seawater lab at Carrie Bow. Photo- S. Jones

In July 2014, a team of scientists led by Seabird McKeon (Smithsonian Marine Station) traveled to Carrie Bow with an agenda of sampling three BioCubes. They started in the mangroves at Twin Cays, where they had to deal with stinging creatures of all types and visibility that could go from bad to worse with the kick of a fin. They then moved on to a seagrass bed and finally the back-reef lagoon. Once a site was picked, they anchored a BioCube, set up a camera to film all the fish swimming through the cube, and finally extracted the area enclosed by the cube frame. That’s when the fun really gets started. Each sample is brought back to the wet lab to be picked and pulled apart to find every last living organism large enough to see with the naked eye. Every plant and animal was sorted and assigned a number. They sorted each creature and tallied their numbers to get an idea of the relative abundance of each organism and then selected three to be photographed and processed for DNA extraction at NMNH. The specimens that get the extra attention are the voucher specimens that are the beginning of the biocode library of Carrie Bow Cay. In total, the effort netted 680 specimens, 660 DNA vouchers, and 108 genomic tissue samples.

Additionally, McKeon and his colleagues have found exciting ways to use the project as a platform for outreach. In partnership with local non-profit the Biodiversity Center of Belize (BioBelize), they are already using the biocode project to help augment BioBelize’s efforts to support training of the next-generation of Belizean scientists to better understand and use the country's biological resources. After leaving the island, BioBelize utilized the specimen data collected to conduct a DNA barcoding workshop with five Belizean high school students utilizing predatory fish species collected from the BioCube effort. Each student received one fish, removed the gut, extracted the contents, performed DNA extraction, and gene amplification. Preliminary results indicate high quality extractions and high success rate in generating useful DNA sequences.

McKeon hopes the project will continue to grow; an internship will start this winter dedicated to compiling the historical records of specimens, existing DNA sequences, and photos of samples taken from Carrie Bow Cay, in order to highlight ‘gaps,’ and appropriate taxa and ecosystem targets for future field expeditions. If he’s successful, the CBC Biocode will be the first of its kind in the Atlantic Ocean and will serve as template for future initiatives at other marine sites.


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