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Sunday 4 March 2012
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Enhancing freshwater ecosystem biomonitoring: Defining and testing a next generation sequencing biodiversity identification framework.

BISTA Iliana

Enhancing freshwater ecosystem biomonitoring: Defining and testing a next generation sequencing biodiversity identification framework.

Evaluation of freshwater faunal biodiversity has been an essential method for the assessment of ecosystem health. The Environment Agency (EA), UK and other regulators have been applying mainly classical taxonomic and morphology-based analysis of benthic macroinvertebrates for biomonitoring of river and lake ecosystems, by either measuring biodiversity or identifying indicator species that can provide information on environment quality. The downside of morphology-based approaches is that they are very demanding. They require taxonomic expertise, the analysis of samples is time consuming and specimens in many cases, cannot be identified to a taxonomic level lower than genus. By employing molecular techniques we have the ability to overcome these difficulties. Using cytochrome oxidase subunit I (COI) barcodes we can accurately identify specimens and resolve taxonomic issues, while with Next Generation Sequencing (NGS) we can achieve high taxonomic resolution for DNA extracted directly from bulk samples (environmental DNA).

In the context of this work we will populate a reference library for about 200 freshwater macroinvertebrate indicator species in the UK, using barcode analysis of the COI mtDNA gene along with classical taxonomic identification. Using this library and the sequences already available in databases (BOLD) we will be able to test the application of large community analysis of benthic macroinvertebrates from bulk environmental samples, through 454 Roche pyrosequencing. Furthermore, we will apply a barcoding analysis system for the identification of Chironomid Pupal Exuviae (CPE Technique), a method which is also extensively used by the EA for the monitoring of lake ecosystems. This work will set a framework for the direct application of molecular methods for the assessment and monitoring of river and lake ecosystem health.

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Editorial board
  • BRANDNER Melissa
    • University of Nordland
    • Bodø (Norway)
  • BROCHMANN Christian
    • National Centre for Biosystematics
    • Oslo (Norway)
  • CHARITON Anthony
    • CSIRO Land and Water
    • Lucas Heights NA (Australia)
  • DEAGLE Bruce
    • University of Victoria
    • Victoria (Canada)
  • Eric Coissac
    • LECA
    • Grenoble (France)
  • KASAPIDIS Panagiotis
    • Hellenic Center for Marine Research
    • Irakleion, Crete (Greece)
    • Université de Genève
    • Genève 4 (Switzerland)
  • TABERLET Pierre
    • LECA,
    • Grenoble (France)
    • Centre for GeoGenetics
    • Copenhagen (Denmark)
  • ZINGER Lucie
    • IBENS
    • Paris (France)
  • Vodka, Bison and Metabarcoding

    31 July 2015, by BRANDNER Melissa

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    The scientists at the Mammal Research Institute PAS in Białowieża National Park hosted this year’s workshop. And our hats go off to them for the organizational skills, warmth and hospitality. During the week, experienced metabarcoders gave lectures on their trials and tribulations in the field of metabarcoding, sparking conversations between the attendees. The end of the first day saw flash talks from all participants of the event, creating an icebreaker and showing the wide variety of applications for metabarcoding, including, dietary studies, environmental health, fundamental ecology and exploration of rare and ancient habitats.
    Pierre Taberlet (who is rumoured to run 8000 PCR a day!) taught technical aspects such as DNA extraction in (...)

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