4.3. Cost and effort
The additional cost of adding eDNA analyses to an existing water quality
program is significantly less than the cost of an eDNA-specific
sampling, primarily due to savings in field time and equipment. If
samples can be collected and filtered in conjunction with other water
quality samples that require filtration (nutrients, for example), the
estimated additional resources required for collecting samples,
filtering, and preparing for shipment is $5-$20 and 15-60 minutes of
staff time per sample. If eDNA samples are collected separately, but
leverage existing site personnel and equipment, the per sample cost is
$6-$30 and 1-2.5 hours. Costs vary widely depending on boat charges,
distance to sites, and number of sites sampled in a day. The cost of lab
and bioinformatics analyses varies depending on type of analyses, number
of samples, and available resources. Results may be returned as raw
sequence reads, or may be processed to identify organisms. When raw data
is returned the user must have access to both the skill and
computational capacity to perform bioinformatics, which may be a
significant barrier for some resource managers. Analysis of eDNA samples
is increasingly available from commercial vendors with costs ranging
from $75-$150 per sample for established metabarcoding analyses. Costs
are higher for projects with small sample batches, project advice,
additional analyses etc.
5. CONCLUSIONS
eDNA sampling is relatively easy to implement, and can be applied in
areas which are difficult to reach with traditional surveys (sensitive
habitats, hard to access locations). Sample collection can be added to
existing water quality monitoring programs at less cost than
implementing a new survey, and may increase detection of some species.
Due to the relatively short time required for sampling, higher
resolution sampling (temporally or spatially) can be conducted to gain
more information about species at the sites. Sample extracts can be
re-used for multiple target species or broad biodiversity metrics, and
can be archived for future analyses. While we have not discussed genetic
studies here, emerging methods in understanding sequence variants and
microsatellites are moving towards establishing these methods (e.g.
Dugal et al., 2022; Weitemier et al., 2021). However, there are caveats
to implementing an eDNA monitoring program: Interpretation of results
can be ambiguous, and incomplete sequence data, transport of DNA, and
misidentification of species can lead to errors.
eDNA fish surveys are a potentially powerful addition to standardized
monitoring programs, but have limitations. In Great Bay, extensive eDNA
sampling detected all of the fish likely present, including species that
are difficult to catch in seine nets. In Heʻeia, there was general
agreement with the presence of non-native, freshwater fish found in
estuarine sites through comparison of eDNA with cast net and visual
sampling and eDNA allowed the detection of specific native species that
are cryptic or difficult to locate. However, in the highly turbid
Apalachicola estuary the eDNA sampling and analysis conducted in this
study underperformed traditional sampling and missed many species likely
to be present. At many estuarine locations, more intensive sampling,
additional lab processing, application of more or different primers, and
augmentation of the sequence database using place-specific local fish
voucher specimen will yield better results. In this study we
deliberately apply the same methods at all sites, rather than optimizing
at each location so that we can understand the value of a broad
application of a set of common methods. Managers should consider the
individual goals and needs of their program to determine if this
approach is appropriate and useful. We strongly recommend that resource
managers considering eDNA applications become familiar with the methods,
consult experts with local knowledge about fish species, and work with
sequencing centers or partners that can support accurate interpretation
and troubleshooting of results.
The results of this study support previous work finding that eDNA
sampling is a potentially powerful tool for fish assessments in
estuarine systems. Results will be improved by collecting replicate
samples, focusing sampling in locations or seasons of interest, and by
collecting local voucher specimens for closely related species.
AKNOWLEDGEMENTS
We are grateful to students, interns and collaborators at each site who
assisted in sample collection: Claire Gottsegen, Diana Lopera, Nakoa
Goo, Hoaka Thomas, Aka Beebe, Becca Lensing,
Gus Robertson, Kim Falinski, Anthony Olegario. This work was supported
by the National Estuarine Research Reserve System (NERRS) Science
Collaborative which is funded by the National Oceanic and Atmospheric
Administration (NOAA) and managed by the University of Michigan Water
Center (NAI4NOS4190145).
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DATA ACCESSIBILITY: All raw data and associated metadata is in the
processes of being uploaded to NCBI SRA, under bioproject PRJNA667067.
BENEFITS GENERATED: Benefits from this research accrue from the sharing
of our data and results on public databases and this open access paper
as described above.
AUTHOR CONTRIBUTIONS: A.W, C.P., J.S.G., B.Y., and W.K.T designed the
study. J.S.G., C.P., J.G., M.L., S.S., Y.R., collected samples. D.T.
conducted data analyses, W.K.T oversaw lab analyses. A.W. wrote the
manuscript with review from all authors.
CONFLICT OF INTEREST: The authors declare no conflict of interest