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Environmental DNA used to track biodiversity

February 16, 2016

By Paige Welsh
Jesse Port, former Center for Ocean Solutions early career science fellow, is finding a way to identify ocean species without laying eyes on them. A bottle of sea water is laden with trace amounts of DNA sloughed off by passing organisms. Even well-camouflaged organisms leave clues in an ecosystem such as bits of scales, hair and feces that researchers can now detect with eDNA technology. Scientists hope this technology will one day spare them the time and costs of conventional visual surveys and spare ecosystems the harm of destructive survey methods like trawling.

Divers at Hopkins Marine Station set out to survey biodiversity. Photo courtesy of Jesse Port.
The eDNA technology has already proven its value in tracking well-hidden organisms that scientists would like to keep tabs on such as invasive or endangered species. For example, researchers in Florida use eDNA to track invasive anacondas. The giant snakes wreak havoc on ecosystems by eating endemic mammals and birds, but they can blend nearly perfectly in the everglade swamps.Now researchers can track the presence species like the anaconda even if they never see them. However, tracking more than one species in a sample has been considered uncharted waters, until now.
In his latest study, published in Molecular Ecology, Port and his colleagues take eDNA to the next level by moving from species specific identification to identifying entire communities. Port and his team first used eDNA to detect multiple species at the Monterey Bay Aquarium . After a successful trial tracking the tunas and other creatures in a controlled tank, they took the next step to the Aquarium’s back yard: Monterey’s kelp forests.
In the wild, Port and his colleagues found that that eDNA detected eleven of the twelve species groups that scuba divers from Hopkins Marine Station saw in visual surveys. The eDNA even highlighted camouflaged species, such as flat-fish, that divers often overlook.
Port was pleasantly surprised to find that within this dynamic nearshore ecosystem, eDNA could distinguish fish communities located only 60 meters apart.
“You could pick out kelp forest habitats or seagrass habitats. You may think that eDNA may be homogenized in the water because of currents, but there were clear differences even in habitats right next to each other,” said Port, “For community biodiversity, if we can ground truth the method more, eDNA will become a viable monitoring option and be more desirable than visual surveys just because of the ground you can cover.”
While scooping up a cup of water and heading to the lab sounds convenient, analyzing the eDNA of an entire vertebrate community poses unique challenges. Finding the DNA of vertebrates, animals with backbones like fishes and seals, can be like trying to find a few faces in a super-bowl stadium because sea water is packed with plankton DNA and bacteria.

A researcher analyzes eDNA samples. Photo courtesy of Jesse Port.
The current technology uses a technique called PCR to make millions of copies of a choice piece of DNA. A whisper of vertebrate DNA can be found and amplified over the roar of the microbial crowd. The challenge is choosing a gene unique to the desired species for the PCR to latch onto.
Once the team began analyzing the eDNA in Alexandria Boehm’s lab at Stanford University, Port found that sharks and rays were under-represented. Because of unique variances in their DNA, the PCR process could not efficiently multiply the DNA of cartilaginous fishes. The efficiency of the PCR process varies from species to species, and thus using eDNA to measure the number of individual organisms still needs development. In the future, Port hopes to use genetic analysis without PCR to circumvent these problems.
Contamination from human DNA was also an enormous risk.
“Our methods are super sensitive to vertebrates, so even a small amount of human contamination can potentially drown out target DNA in the water,” explained Port.
To compensate, the researchers handled all the samples fastidiously and ran controls at all steps to monitor for contamination.
Port noted that from the aquarium, to the ocean, to the lab, creating this research called for a unique blend of expertise. 
“It was very collaborative. All kinds of skills are needed, and I enjoyed working with all the people and organizations involved,” said Port.
Such research proves the potential strides science can make by pooling resources and collaborating. The Center for Ocean Solutions was proud to facilitate Port’s eDNA work with its partner organizations. The Center is continuing to ground truth eDNA work by partnering with MBARI and Stanford on the CANON (Controlled, Agile, and Novel Ocean Network) project, led by Francisco Chavez and Barbara Block, and Ali Boehm and Francisco Chavez on the Marine Biodiversity Observing Network (MBON) project in the Monterey Bay National Marine Sanctuary. This ongoing work is funded with the generous support of NOAA, NASA and the Seaver Institute.

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