Environmental barcoding: A next-generation sequencing approach for biomonitoring applications using river benthos
Open accessAbstract
Timely and accurate biodiversity analysis poses an ongoing challenge for the success of biomonitoring programs. Morphology-based identification of bioindicator taxa is time consuming, and rarely supports species-level resolution especially for immature life stages. Much work has been done in the past decade to develop alternative approaches for biodiversity analysis using DNA sequence-based approaches such as molecular phylogenetics and DNA barcoding. On-going assembly of DNA barcode reference libraries will provide the basis for a DNA-based identification system. The use of recently introduced next-generation sequencing (NGS) approaches in biodiversity science has the potential to further extend the application of DNA information for routine biomonitoring applications to an unprecedented scale. Here we demonstrate the feasibility of using 454 massively parallel pyrosequencing for species-level analysis of freshwater benthic macroinvertebrate taxa commonly used for biomonitoring. We designed our experiments in order to directly compare morphology-based, Sanger sequencing DNA barcoding, and next-generation environmental barcoding approaches. Our results show the ability of 454 pyrosequencing of mini-barcodes to accurately identify all species with more than 1% abundance in the pooled mixture. Although the approach failed to identify 6 rare species in the mixture, the presence of sequences from 9 species that were not represented by individuals in the mixture provides evidence that DNA based analysis may yet provide a valuable approach in finding rare species in bulk environmental samples. We further demonstrate the application of the environmental barcoding approach by comparing benthic macroinvertebrates from an urban region to those obtained from a conservation area. Although considerable effort will be required to robustly optimize NGS tools to identify species from bulk environmental samples, our results indicate the potential of an environmental barcoding approach for biomonitoring programs.
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This variation in amplification efficiency might severely bias results, particularly in view of the variation in biomass.
“the amplification efficiency of the COI gene varies among species, and this might severely bias results [34,39] particularly in view of the variation in biomass.”
The amplification efficiency of the COI gene varies among species.
“the amplification efficiency of the COI gene varies among species, and this might severely bias results [34,39] particularly in view of the variation in biomass.”
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- Authors
- Hajibabaei, M., Shokralla, S., Zhou, X., Singer, G. A. C., & Baird, D. J.
- Affiliations
- University of Guelph (CA)
- University of New Brunswick (CA)
- Corresponding author
- Hajibabaei, Mehrdad
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-04-13
- Volume
- 6
- Issue
- 4
- Pages
- e17497
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3076369
- OpenAlex
- W2020200409
- Cited by
- 584
- References
- 25
- Citations by year
- 2026: 14 · 2025: 18 · 2024: 20 · 2023: 35 · 2022: 12 · 2021: 36 · 2020: 53 · 2019: 53 · 2018: 78 · 2017: 46 · 2016: 48 · 2015: 57 · 2014: 45 · 2013: 29 · 2012: 34
- FWCI
- 31.93
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- OCAD University Open Research Repository (OCAD University) (acceptedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- Genome Canada
- Ontario Genomics
- Ontario Genomics Institute
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- DNA barcoding, benthic macroinvertebrates, freshwater biomonitoring, 454 pyrosequencing, species identification, rare species detection, biodiversity assessment
- MeSH terms
- Animals, Electronic Data Processing, DNA, Environmental Monitoring, Fresh Water, Invertebrates, Biodiversity
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