Home > Events > 1 Metabarcoding spring school in French Alps (5-9 March 2012) > Presentations > Benthic vs pelagic contribution in the diet of marine benthic primary (...)

Thursday 1 March 2012
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Benthic vs pelagic contribution in the diet of marine benthic primary consumers: a multi tool approach


My PhD aims at determining the precise diet of three marine benthic primary consumers (abalone, queen scallop and Japanese oyster), in order to discriminate the proportion of benthic primary production versus pelagic production that is assimilated within the benthic food-web. Benthic primary consumers are organisms living on or into the seafloor and that feed on primary producers such as phytoplankton, macroalgae, benthic microalgae, detritus, etc… This study, led within a temperate coastal ecosystem (the Bay of Brest, France) will help us to better understand the links between benthic and pelagic compartments and specially carbon and nitrogen fluxes in aquatic ecosystems undergoing multiple anthropogenic influences (anthropic, river, oceanic…). To try answer to these questions, I intend to develop and use several indicator tools such as stable isotopes, pigments transfers as well as bar-coding. The latter one is yet seldom used in marine organism diet determination, especially in mollusks. In order to determine a working protocol, I am currently making test-analysis on 5 oysters. This involves:
- extracting DNA of their digestive glands as well as within pelagic and benthic seawaters samples (their “food sources”).
- amplify DNA fragments with universal primers (at the moment, I have selected the Cox1 and Cox3 genes)
- separate DNA fragments contained in oyster digestive glands and seawaters by denaturing gradient gel (DGGE). This gel will allow us to compare DNA profiles between seawater samples and of oyster digestive gland samples.
- finally select and sequence matching DNA fragments between food sources and the digestive gland, in order to identify the algal species really consumed by oysters.

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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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