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Thursday 18 April 2013
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Attempting to characterize marine meiofauna using metabarcoding: what we got and what we wish


Characterizing macro- and meiobenthic marine invertebrates has always been a hard and time-consuming process due to the size of the individuals and scarcity of taxonomic specialists. The uses of environmental DNA coupled with Next Generation Sequencing techniques represent a leap forward in our ability for biodiversity estimation of those organisms. In this way, during the development of my PhD project we intend to establish a generalized protocol for studies of soft- bottom marine fauna using environmental sequences. After optimizing the procedures for DNA extraction, 81 sediment samples from two Mediterranean canyons have been processed for the DNA extraction and the high-throughput sequencing of two fragments from the barcodes 18S and COI. More than 2000 different sequences were obtained for the 18S marker, after cleaning and filtering the sequences (>3 000 000) obtained using an Illumina MiSeq platform. These sequences belonged to 19 different Phyla of Metazoa, with polychaetes and crustaceans being the most abundant in terms of total number of reads. Analysis on the abundance and distribution of the different marine benthic groups are currently being carried out. We were not successful for the amplification of the COI fragment marker, so we are searching for an appropriate COI barcode.

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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

    The start of last month saw the occurrence of the Fifth Metabarcoding Spring School held in Białowieża National Park , Poland. A variety of scientists attended from all over the globe to learn, share and inspire with unique stories of metabarcoding.
    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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