New method is fast, cost-effective and designed for non-experts
Can a single bottle of ocean water contain enough scraps of genetic material for researchers to identify virtually all of the fish, plankton, molluscs, marine mammals and other organisms from that location?
Sounds like science fiction, but it’s not. The burgeoning field of environmental DNA (eDNA) is very real, and scientists are rapidly exploring ways to make this breakthrough technology more useful and available for non-scientists.
That’s what motivated NOAA scientist Zachary Gold to lead an effort to write a guide to help marine resource managers who may not have a molecular ecology background understand how to collect samples and extract detailed information about the biodiversity of their study areas. Co-written with a team of researchers from across the country, the guide was recently published in the journal PeerJ .
“The cool thing is that from a field-work perspective, eDNA is incredibly simple,” said Gold, a scientist at the Pacific and Environmental Marine Laboratory. “It’s as easy as filling a bottle with water, so it lends itself really well to community and citizen science projects.”
“Analysis in the lab is where cutting-edge science comes into play.”
What is eDNA metabarcoding?
DNA, or deoxyribonucleic acid, is genetic material found in the cells of almost all organisms. It takes the physical structure of a twisted ladder, or double helix. The precise sequence of four nucleotide bases that make up the “rungs” of the ladder encode all of the instructions needed for an organism to develop, survive and reproduce. Genetic scientists have learned to decode the order of these nucleotides, a process called genetic sequencing, which provides a genetic fingerprint of the organism.
The eDNA revolution emerged from the recognition that every organism is constantly leaving traces of itself as it interacts with the environment, which accumulate in soil, water, snow and air. Rapid advances in genetic sequencing technology have allowed scientists to amplify, sort and then analyze tiny amounts of these jumbled DNA fragments, matching the sequences of genetic code in a sample to previously identified species that are cataloged in a DNA barcode database. Metabarcoding allows for the simultaneous identification of many organisms within the same sample.
New instruments allow sequencing to be performed simultaneously on dozens to hundreds of samples. Analysis of the identified organisms provide insights into species richness in a given area, identify which habitats certain species favor, and – importantly – track the spread of invasive species or shifts in species’ range due to climate change.
“The reference barcode databases are the ‘Rosetta stone’ that connect the unique DNA sequences to the species names of organisms shedding eDNA into their environment,” Gold said. “You can imagine managers would be lost if they got raw sequences,” Gold said. “What do you do with terabytes of As, Cs. Ts and Gs?” he said, referring to the scientific shorthand for the four nucleotides that make up all DNA.
Fortunately, there are now a number of companies that will do the sequencing and barcoding analysis matching the genetic sequences to species – at a cost that’s about a third of a traditional visual survey.
A test run on the Pacific Coast
To test the new approach, Gold and researchers from UCLA, UC Santa Cruz and the Natural History Museum of Los Angeles worked alongside resource managers at the Ports of Los Angeles and Long Beach to implement a pilot program at the nation’s busiest port complex.
“The port managers who were co-authors on the paper were not molecular biologists,” Gold said. “Their big question was ‘We do a lot of midwater trawls, we want to see how they line up with each other.”
The eDNA metabarcoding approach detected 16 of the 17 of species collected in trawl surveys in the same area, he said, and identified an additional 55 native fishes that the trawl surveys did not detect.
“This study indeed demonstrated that eDNA metabarcoding approaches were relatively successful in detecting a broad range of marine taxa within both seaports,” said Justin Luedy, Environmental Planning Specialist at Port of Long Beach, one of the study’s co-authors. He noted that the pilot project produced new reference barcodes for 16 fish species, nine of which had never been cataloged before, including California halibut, queenfish, and kelp bass.
While the team didn’t collect enough trawl data to analyze species abundance, Gold said that for mapping climate range shifts, monitoring endangered or invasive species, and ocean exploration “this tool is ready to go.”
eDNA across NOAA
Across NOAA, scientists are applying eDNA and other methods for measuring biological molecules – a field called ‘omics – to support sustainable fisheries and aquaculture, discover beneficial chemical compounds, and protect vulnerable species and habitats, such as corals, that provide essential fish habitat and fuel tourism economies. They’re implementing eDNA methods at scale in the ocean, demonstrating its accuracy compared with other techniques, and, as with Gold’s project, proving its potential value to resource managers.
One immediate goal is expanding the number of high-quality, publicly available genetic databases. Gold estimates that less than 30% of all species of invertebrates in Southern California have reference barcodes.
“eDNA is a rapidly developing field of science, and NOAA is pushing the envelope on using these tools to understand climate change and ocean acidification impacts on fisheries and marine ecosystems, map endangered and invasive species, characterize harmful algal blooms, and explore our oceans” Gold said. “eDNA has the potential to revolutionize biology and resource management in the way remote sensing revolutionized agriculture, oceanography, hydrology, and weather forecasting. As with remote sensing and satellite technology, NOAA along with our federal partner agencies is helping lead the way on utilizing eDNA at scale”
Take a deep dive into how NOAA uses eDNA and related tools on the NOAA Science Council’s Omics page: https://sciencecouncil.noaa.gov/NOAA-Science-Technology-Focus-Areas/NOAA-Omics