Location of Repository

Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos

By Mehrdad Hajibabaei, Shadi Shokralla, Xin Zhou, Gregory A. C. Singer and Donald J. Baird


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

Topics: Research Article
Publisher: Public Library of Science
OAI identifier: oai:pubmedcentral.nih.gov:3076369
Provided by: PubMed Central
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.pubmedcentral.nih.g... (external link)
  • Suggested articles



    1. (2006). A minimalist barcode can identify a specimen whose DNA is degraded.
    2. (2008). Assembling DNA barcodes. Analytical protocols.
    3. (1990). Basic local alignment search tool.
    4. (2003). Biological identifications through DNA barcodes.
    5. (2007). BOLD: The Barcode of Life Data System (www.barcodinglife.org).
    6. (2005). Critical factors for assembling a high volume of DNA barcodes.
    7. (2010). Direct PCR amplification and sequencing of specimens’ DNA from preservative ethanol.
    8. (2007). DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics.
    9. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates.
    10. (1977). DNA sequencing with chainterminating inhibitors.
    11. (2005). Genome sequencing in microfabricated high-density picolitre reactors.
    12. (2009). Googling DNA sequences on the World Wide Web.
    13. (2009). iBarcode.org: web-based molecular biodiversity analysis.
    14. (2009). Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes.
    15. (2007). MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
    16. (2006). Microbial diversity in the deep sea and the underexplored ‘‘rare biosphere’’.
    17. (2006). Microbial ecology: human gut microbes associated with obesity.
    18. (2009). Numbers of Living Species in Australia and the World: A Report for the Australian Biological Resources Study.
    19. (2005). Taxonomy. Will DNA bar codes breathe life into classification?
    20. (2004). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator.
    21. (1985). Time to Revive Systematics.
    22. (2005). Towards writing the encyclopaedia of life: an introduction to DNA barcoding.
    23. (2010). Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises.

    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.