Is DNA Barcoding Actually Cheaper and Faster than Traditional Morphological Methods: Results from a Survey of Freshwater Bioassessment Efforts in the United States?

Stein, Eric D.; Martinez, Maria C.; Stiles, Sara; Miller, Peter E.; Zakharov, Evgeny V.

doi:10.1371/journal.pone.0095525

Cited by 153Environmental DNA in Biodiversity StudiesInvertebrate Taxonomy and EcologyFreshwater macroinvertebrate diversity and ecology

Is DNA Barcoding Actually Cheaper and Faster than Traditional Morphological Methods: Results from a Survey of Freshwater Bioassessment Efforts in the United States?

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Stein, Eric D., Martinez, Maria C., Stiles, Sara, Miller, Peter E., Zakharov, Evgeny V.·2014·PLoS ONE

DOI 10.1371/journal.pone.0095525PMC PMC3995707

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Abstract

Taxonomic identification accounts for a substantial portion of cost associated with bioassessment programs across the United States. New analytical approaches, such as DNA barcoding have been promoted as a way to reduce monitoring costs and improve efficiency, yet this assumption has not been thoroughly evaluated. We address this question by comparing costs for traditional morphology-based bioassessment, the standard Sanger sequencing-based DNA barcoding approach, and emerging next-generation (NGS) molecular methods. Market demand for molecular approaches is also assessed through a survey of the level of freshwater bioassessment effort in the United States across multiple habitat types (lakes, streams, wetlands) and indicators (benthic invertebrates, fish, algae). All state and regional level programs administered by public agencies and reported via agency web sites were included in the survey. Costs were based on surveys of labs and programs willing to provide such information. More than 19,500 sites are sampled annually across the United States, with the majority of effort occurring in streams. Benthic invertebrates are the most commonly used indicator, but algae and fish comprise between 35% and 21% of total sampling effort, respectively. We estimate that between $104 and $193 million is spent annually on routine freshwater bioassessment in the United States. Approximately 30% of the bioassessment costs are comprised of the cost to conduct traditional morphology-based taxonomy. Current barcoding costs using Sanger sequencing are between 1.7 and 3.4 times as expensive as traditional taxonomic approaches, excluding the cost of field sampling (which is common to both approaches). However, the cost of NGS methods are comparable (or slightly less expensive) than traditional methods depending on the indicator. The promise of barcoding as a cheaper alternative to current practices is not yet realized, although molecular methods may provide other benefits, such as a faster sample processing and increased taxonomic resolution.

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These limitations have direct consequences for inferred ecosystem assessment metrics and thus management decisions.
“these limitations have direct consequences for the inferred ecosystem assessment metrics [10,14] and thus management decisions.”
From Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol (2015) · cites this paper as [14]
Stein and co-authors showed that ten of 16 assessment metrics had higher statistical power using DNA barcoding than morphological assessment.
“Stein and co-authors showed that ten of 16 assessment metrics had higher statistical power using DNA barcoding than morphological assessment [14].”
From Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol (2015) · cites this paper as [14]
Metabarcoding will widely replace present biomonitoring methods over time because it has higher taxonomic resolution, is cost efficient and fast, and reduces human bias enabling comparisons among studies.
“we are confident that metabarcoding will widely replace present biomonitoring methods over time because 1) it has a higher taxonomic resolution [14], 2) it is cost efficient and fast and, most importantly, 3) it reduces human bias enabling comparisons among studies [57].”
From Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol (2015) · cites this paper as [14]
Several studies show that DNA-based assessments are superior to morphological assessments in freshwater ecosystems.
“Several studies show that DNA-based assessments are superior to morphological assessments in freshwater ecosystems (e.g., [14,25,33])”
From Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol (2015) · cites this paper as [14]

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Self-citation
DNA metabarcoding captures different macroinvertebrate biodiversity than morphological identification approaches across a continental scale
Emmons, S. C., Compson, Z. G., Malish, M. C., Busch, M. H., Saenz, V., Higgins, K. T., & Allen, D. C. (2023) · Environmental DNA · doi:10.1002/edn3.453 · Cited by 18 · see citing works

Authors: Stein, E. D., Martinez, M. C., Stiles, S., Miller, P. E., & Zakharov, E. V.
Affiliations: Southern California Coastal Water Research Project (US)
University of Guelph (CA)
Corresponding author: Stein, Eric D.
ORCID: Stein, Eric D.
Venue: PLoS ONE
Publisher: Public Library of Science (PLoS)
Published: 2014-04-22
Volume: 9
Issue: 4
Pages: e95525
ISSN: 1932-6203 (ISSN-L)
DOI: 10.1371/journal.pone.0095525
PMC: PMC3995707
OpenAlex: W2098534604
Cited by: 152
References: 28
Citations by year: 2026: 12 · 2025: 4 · 2024: 13 · 2023: 14 · 2022: 10 · 2021: 15 · 2020: 15 · 2019: 13 · 2018: 18 · 2017: 17 · 2016: 10 · 2015: 10
FWCI: 10.69
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
Locations: PLoS ONE (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Topics: Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Invertebrate Taxonomy and Ecology
Physical Sciences › Environmental Science › Ecology › Freshwater macroinvertebrate diversity and ecology
Keywords: DNA barcoding, cost comparison, morphological taxonomy, Sanger sequencing, next-generation sequencing, benthic invertebrates, fish, algae, water quality monitoring, taxonomic identification, streams, lakes, wetlands, United States
MeSH terms: Animals, Cost-Benefit Analysis, Environmental Monitoring, Fresh Water, United States, Biodiversity, DNA Barcoding, Taxonomic

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Is DNA Barcoding Actually Cheaper and Faster than Traditional Morphological Methods: Results from a Survey of Freshwater Bioassessment Efforts in the United States?

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