When scientists want to know what life-forms live in deep water, they have to send submersibles or cast nets and grabs hung from long cables. These methods are expensive, however, and they offer only a hint of the biodiversity hidden far below the waves. “In the deep sea,” says John Bickham of Battelle Memorial Institute, “we’re back in the 1700s. We have no idea what’s out there.”
On land, genetic methods revolutionized bacterial taxonomy and expanded the world’s count of mammal species. Soon, this approach, which relies on scraps of genetic material floating in ocean water—dubbed “environmental DNA,” or “eDNA”—may dramatically advance our knowledge of deep-sea biodiversity.
All aquatic organisms continuously shed cells, leaving behind packages of DNA in metabolic waste, sloughed-off skin, scales or hair, and other cellular debris. Biologists are using this eDNA to inventory aquatic communities without having to collect a single animal or plant.
Researchers generally begin by filtering water or sediment samples. Then they use chemical treatment and agitation to extract the DNA from material captured on filters. Using polymerase chain reactions to snip off strands of DNA, they obtain what is essentially a unique bar code for each individual species. They match this eDNA to known DNA sequences from thousands of species held in databases such as GenBank and Nucleotide. Each match identifies a species present somewhere close to where the water or sediment sample was collected.
The method shows promise for both general biodiversity surveys and for monitoring ecological impacts associated with effluent or chemical spills. In freshwater it has been used to monitor the spread of invasive species and the presence of amphibian species, which are often considered indicators of environmental health.
Recently researchers from the Natural History Museum of Denmark at the University of Copenhagen demonstrated how useful eDNA methods can be in the marine environment. They compared fish inventories generated from conventional methods with eDNA results. For three years researchers working in the Sound of Elsinore, Denmark, sampled fish with traps, seines, gillnets, push nets, fishing poles, bottom trawls, along with visual observations by snorkelers during the day and at night. In the third year they also processed water samples for eDNA. The eDNA identified 15 fish species, including the European pilchard, not typically found at their sampling location. In an August 2012 article published in PLoS ONE, the authors reported that “eDNA covered the fish diversity better than or equal to any of the applied conventional methods.”
The same researchers investigated the longevity of eDNA in seawater. If eDNA is long-lived, samples might identify species that are no longer present. Results showed that identifiable eDNA disappeared within one week.
Building on that work, Bickham and colleagues from Battelle , along with Alaska’s North Slope Borough Department of Wildlife Management collected water samples from the Beaufort Sea near Barrow, well north of the Arctic circle and about 160 kilometers west of the state’s North Slope oil fields. The work was supported by the North Slope Borough, which is the Alaskan equivalent of a county government, along with a major oil company, both interested in the possibility of applying eDNA methods to environmental impact studies associated with industrial development. Bickham’s team identified not only fish but also clams, worms, algae, waterfowl, seals and whales.
The work near Barrow attracted further interest from another funding source, Shell Oil Corp., but with a twist: the eDNA method was applied in the deep sea. Deepwater offshore oil and gas developments are often accompanied by biological sampling targeting organisms that live on or in the seabed. Conventional methods require the collection of samples around offshore facilities, followed by sieving, manual sorting and time-consuming visual identification by taxonomic experts. At the Society of Environmental Toxicology and Chemistry annual meeting held November 2014 in Vancouver, Bickham and his co-authors said that eDNA methods will inevitably replace “laborious and costly” conventional methods in deepwater biodiversity surveys.
Before eDNA is ready for deep-sea prime time, however, more work is needed. “We got millions of hits,” Bickham said of the samples, “but could only identify 2 or 3 percent.” Some unidentifiable “hits” may be from known species not yet captured in available databases whereas others may be from species unknown to science. Bickham believes that many deep-sea species may turn out to be species complexes—a suite of species, similar in appearance but in fact unique, could masquerade as a single one in taxonomic lists.
Bickham sees the deep sea as a real challenge for biosystematics, the study of taxonomy based on genetic and chemical markers. Although he thinks eDNA methods will be increasingly useful for routine biomonitoring, especially in well-known habitats, Bickham suggests that a major National Science Foundation biosystematics program is justified for the deep sea and other poorly known corners of the planet. With appropriate research support, Bickham believes, eDNA methods will move our understanding of deep-sea biodiversity into the 21st century.