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Monday 27 February 2012
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Molecular and morphological approaches to biodiversity assessment of soft bottom assemblages


We attempt to estimate benthic biodiversity in Mediterranean marine soft bottoms (macro-and meiobenthic invertebrates), by using metabarcoding and traditional morphological approaches in parallel.
As a first step, we will focus on the establishment of an adequate protocol to extract the most realistic information about benthic biodiversity, trying also to quantify the several OTU’s at the lower taxonomical level possible. We are concerned with issues such as sample manipulation, type of fixative, DNA extraction procedures and finding suitable genes to be used as tags. Our first idea is to work with COI and rDNA 18s barcodes and compare the information gleaned from both genes. We will also compare DNA extractions with RNA extractions in duplicate samples (total vs. “living” DNA).
Our project includes comparisons of soft-bottom communities in submarine canyons (bathyal assemblages vs continental shelf / circalittoral assemblages), and well preserved habitats vs contaminated sites. We will work in close collaboration with a team that will analyse the same samples through conventional methods of sorting and identification.
We also want to explore the capabilities of the method to obtain quantitative, rather than merely qualitative, information. To this end we plan to work with artificial samples with known numbers of individuals and species to assess the reliability of the use of number of reads as a proxy for abundance of taxa.

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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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