Fish Environmental DNA (eDNA)

svEPA

United States
Environmental
Protection Agency

epa.gov/research

Innovative Science for a Sustainable Future
Sampling in Pensacola and Perdido Bays

Background

EPA researchers are conducting a pilot study in
Pensacola and Perdido Bays, Fla. using environmental
DNA (eDNA)1 to assess fish community assemblages
(the variety and abundance offish species in a given
waterbody).

Living organisms constantly shed DNA into their
surrounding environment, and this genetic material can
be used to more precisely identify organisms that live
in, or periodically visit, different aquatic habitats. eDNA
can be readily obtained from environmental samples
such as water.

Goals of this research

Over the next 12 months, genetic material will be
extracted and processed from water samples collected
during fall 2022 through late-spring 2023. The data
produced will provide genetic "fingerprints" that can be
used to identify likely fish species that visit or take refuge
in local estuarine habitats. Results may be indicative of
the suitability of local waters to support thriving fish
populations. Meaningful information gained from this fish
eDNA pilot study may allow for future expansion of this
research effort to other estuarine systems across the
Gulf of Mexico.

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Collect water
sample

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Extract DNA

Fish
eDNA
Metabarcoding



, Sequence
extracted DNA

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I „ Determine presence

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offish species from
DNA sequences

Figure 2. Process for eDNA metabarcoding from sample
collection to species identification.

The goals of this research are to:

•	Assess the use of eDNA methods as a viable and
less environmentally impactful way to detect
changes in fish communities that are dependent on
healthy estuarine habitats, such as seagrasses,
oyster reefs and marsh-edge.

•	Evaluate the use of eDNA results to complement or
add value to existing fish monitoring efforts.

Study Area

The study area includes two estuarine systems:
Pensacola and Perdido Bays, located in northwest
Florida. These bays receive waters from five riverine
watersheds. Land use patterns in the study area are
primarily urban, agricultural, military, and recreational,
with rapid suburban and exurban growth. In total, 25
sites in Pensacola and Perdido Bays are being sampled
as part of this eDNA pilot project.

Figure 1. Map of sampling locations for fish eDNA pilot study in the
Pensacola and Perdido Bays.

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Why study fish communities?

•	Estuaries2 are impacted by many different human
activities including nutrient and sediment loading
from runoff, upland development, dredging, and
overfishing. Restoration of impaired aquatic habitats
can help improve degraded estuarine conditions.

•	Evidence of sentinel (pollution sensitive), keystone3,
and high-value (market value) fish species, such as
those in and around restored locations, can indicate
when estuarine conditions are changing.

•	Fish community data provide important indicators
that can help increase our understanding about
ecological stressor-response relationships; socio-
economic benefits; climate-change impacts; and
restoration/conservation effectiveness.

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