eDNA/eRNA: Scientific Value in What’s Left Behind

eDNA/eRNA: Scientific Value in What’s Left Behind

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December 15, 2022
eDNA/eRNA: Scientific Value in What’s Left Behind
Environmental deoxyribonucleic acid (eDNA) and
sample to be used for various research and decisionmaking
environmental ribonucleic acid (eRNA) are trace amounts
purposes. For example, accurate identification of a
of genetic material collected from an environmental sample,
particular species requires reference sequences of sufficient
such as from soil, terrestrial and aquatic sediments,
quality to exist and be available. Individual databases have
freshwater, seawater, wastewater, or air. This genetic
varying standards that govern access as well as the type and
material can come from shed skin, hair, and other cells;
quality of information they contain. Therefore, the design,
secreted waste or mucus; and carcasses, among other
management, quality standards, and data protocols for
biological sources. It can provide information on the recent
reference databases can affect eDNA/eRNA’s utility.
presence of organisms where a sample was collected
Databases containing certain genetic sequence information,
without directly observing the organisms. Multiple federal
such as for viruses, can also have implications for biosafety
agencies have begun using eDNA/eRNA for various
and biosecurity, depending on who has access to sequences
research, monitoring, and decisionmaking purposes.
and if their use is regulated.
Decreased costs and increased access to eDNA/eRNA
analysis technologies have also allowed other entities to
Some federal agencies are developing, or already have,
develop monitoring projects and programs.
databases for eDNA/eRNA analysis. For example, the U.S.
Geological Survey (USGS) has, and plans to develop,
How It Works
databases for eDNA that include assays and genetic
To analyze eDNA/eRNA, researchers extract partial
markers. The Aquatic eDNAtlas Project, managed by the
DNA/RNA from an environmental sample, amplify it
U.S. Forest Service National Genomics Center for Fish and
(make copies), and compare it against a reference sequence
Wildlife Conservation, is a database that provides
from a previously sequenced organism in order to make a
information on eDNA sampling detection/nondetection
positive match. Depending on research needs, different
results for freshwater species in the United States. The
types of eDNA/eRNA analyses can be performed on an
database, updated annually, contains over 20,000 data
environmental sample (see Figure 1). For example, a
points. Natural resource agencies and nongovernmental
targeted analysis aims to detect a particular species with
organizations use a standardized field sampling protocol to
high accuracy. Alternatively, a non-targeted approach, a
gather and enter environmental samples for the database.
method referred to as “metabarcoding,” can more broadly
characterize the various different species whose DNA/RNA
Nonfederal entities—such as universities, private
is found in the sample.
companies, and international organizations—also compile
their own databases of species sequences. For example, the
Figure 1. eDNA Sampling in Aquatic Environments
International Barcode of Life (iBOL) is an international
research consortium developing DNA reference libraries,
sequencing facilities, informatics platforms, and analytical
protocols to help inventory and assess biodiversity. iBOL
has entered sequences from 500,000 species into reference
libraries and intends to add another 2.5 million species by
2026.
eDNA for Environmental Monitoring
Federal agencies use eDNA for various monitoring
purposes. eDNA data can provide information on the
presence or absence, geographic distribution and range,
relative abundance, and status of organisms. Applications
include tracking species of interest, such as particular native
species, tracking protected species for species assessment
and conservation purposes; identifying the presence of
Source: Songqian Huang, Kazutoshi Yoshitake, and Shugo Watabe,
small or rare (lesser known) species that are difficult to
et al., “Environmental DNA Study on Aquatic Ecosystem Monitoring
observe directly; and detecting the presence of non-native
and Management: Recent Advances and Prospects,” Journal of
species that may adversely affect ecosystems.
Environmental Management, vol. 323, no. 116310 (2022).
eDNA analysis can be limited in its ability to determine
eDNA/eRNA Reference Databases
how many of a particular species may be in the study area.
The availability and quality of a reference sequence can
eDNA data also cannot determine with certainty whether a
affect the analysis of and ability for an eDNA/eRNA
particular species was located in the sampling area at the
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eDNA/eRNA: Scientific Value in What’s Left Behind
time the sample was collected or whether the eDNA
The U.S. Government eDNA Working Group is an informal
collected was transported to that area via other mechanisms
interagency working group comprised of federal employees
(e.g., a species’ DNA present in vessel ballast water).
working with eDNA. The group focuses on the exchange of
Additionally, eDNA degrades at varying rates depending, in
technical information, including sharing best practices,
part, on microbial activity and environmental conditions,
lessons learned, and new advances.
which can affect the utility and accuracy of eDNA.
The Marine Biodiversity Observation Network (MBON) is
eRNA for Disease Surveillance
a global initiative composed of regional networks of
Public Health authorities and researchers increasingly use
scientists, resource managers, and end-users working to
wastewater surveillance—in the form of eRNA—to identify
integrate data from existing long-term programs to
and track disease prevalence. People infected with a virus
understand changes and connections between marine
shed viral RNA in their feces. Wastewater samples can be
biodiversity and ecosystem functions. The U.S. node of
collected and analyzed for the presence of eRNA from a
MBON is a partnership among the National Oceanic and
virus of interest, if that particular virus has been sequenced
Atmospheric Administration, the National Aeronautics and
previously. Similar methods are used to identify non-viral
Space Administration, the Bureau of Ocean Energy
disease (e.g., stool screening for certain types of cancer).
Management, and the Office of Naval Research. The U.S.
Integrated Ocean Observing System Program Office
In response to the COVID-19 pandemic, the Centers for
provides coordination. MBON has developed best practices
Disease Control and Prevention launched the National
and advanced means to collect samples for eDNA analysis
Wastewater Surveillance System in September 2020 to
using autonomous underwater vehicles.
coordinate and build U.S. capacity to track the presence of
SARS-CoV-2, the virus that causes COVID-19. In
Considerations for Congress
September 2021, the Environmental Protection Agency
Congress may consider several eDNA/eRNA policy
released A Compendium of U.S. Wastewater Surveillance to
questions related to protocols, databases, and different uses
Support COVID-19 Public Health Response. The report
for eDNA/eRNA data.
describes different COVID-19 wastewater surveillance
programs, as well as case studies to highlight best practices
Multiple federal agencies have developed protocols for
and lessons learned from programs across the United States.
developing and using eDNA/eRNA. These protocols differ
The report also discusses federal and nonfederal funding
according to scientific purpose, study location, species, and
opportunities that aid in developing and implementing
sampling media. Congress may consider the potential
wastewater surveillance programs for SARS-CoV-2.
benefits and challenges of tasking a federal agency to
develop national standard protocols for sampling,
Selected U.S. Federal eDNA Initiatives
collecting, and analyzing eDNA/eRNA. Standardizing
Federal agencies are engaged in multiple projects and
protocols could aid in research collaboration,
programs that develop and use eDNA. Many of these
interoperability of reference databases, and quality control,
initiatives involve collaborations with international, state,
as well as affect how data is analyzed, shared, and used.
tribal, and local authorities.
Standardizing protocols—for better or worse—could affect
certain research, and potential innovative solutions, where a
One of the longest-standing, best-known applications of
unique or specific protocol is needed. Congress may also
eDNA has been for operational surveillance of invasive fish
consider whether current and proposed agency investments
species in the Great Lakes region. The Great Lakes
in developing and maintaining eDNA/eRNA databases are
Restoration Initiative, made up of nine federal departments
sufficient to meet federal objectives, as well as the need of
and agencies, seeks to continually test and refine the
the broader scientific community and public.
collection, processing, analysis, and interpretation of eDNA
samples and results.
Policymakers may also consider how current federal efforts
related to the collection, use, retention, and access to digital
The USGS, in collaboration with the Monterey Bay
DNA/RNA sequence data address data accessibility,
Aquarium Research Institute, is developing the Rapid
reliability, and biosafety and biosecurity concerns.
eDNA Assessment and Deployment Initiative and Network
Congress may question whether the federal government
(READI-Net). Part of the program’s goal is designing and
should facilitate or regulate access to certain data or
constructing autonomous robotic eDNA samplers that can
regulate certain uses. Congress may also consider how
be deployed as a network in aquatic environments across
local, state, and federal agencies currently use eDNA/eRNA
the United States. USGS intends for READI-Net to enhance
for decisionmaking purposes and whether current policies
early detection and rapid-response methods to aid resource
enable or hamper its use.
managers in containing and controlling aquatic biological
threats.
Todd Kuiken, Coordinator, Analyst in Science and
Technology Policy
The U.S. Forest Service’s National Genomics Center for
Caitlin Keating-Bitonti, Analyst in Natural Resources
Wildlife and Fish Conservation provides eDNA services to
Policy
researchers within and outside the Service, including
sample analysis and assay development, along with
Anna E. Normand, Analyst in Natural Resources Policy
development of protocols and training in eDNA research.
Anne A. Riddle, Analyst in Natural Resources Policy
John F. Sargent Jr., Specialist in Science and Technology
Policy
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eDNA/eRNA: Scientific Value in What’s Left Behind

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