GEANS extension

30 September 2021 - Published by Nele Jacobs
GEANS applied for an extension under call 12, and our request got approved! GEANS will now run until June 2023. The extension expands GEANS in two directions:

 

  1. Through an additional pilot (WP7 – Towards zero impact monitoring) focusing on eDNA(environmental DNA) instead of bulk DNA. Many organisms release DNA molecules in the marine environment through the excretion of faeces, mucus, gametes or the release of scales and skin cells. This eDNA can be collected in a non-destructive way just by simply sampling and filtering water with a zero impact on marine life as benefit. The eDNA method also offers long-term benefits, since it has the potential for automatic and autonomous sample collection through the use of robotics like AUVs (Autonomous Underwater Vehicles). Our aim is to validate the applicability of eDNA in monitoring studies within the highly dynamic North Sea. To this aim, we have pilots on offshore wind energy, ecosystem restoration and non-indigenous species.
  2. Through addressing important gaps identified during project implementation ensuring that our developed deliverables are future-proof in the fast-developing field of DNA sequencing technology. Some of the gaps to be addressed:
    • For some reference species, it is hard to collect fresh specimens despite all efforts undertaken so far. Therefore, we will extract and amplify DNA from formalin fixed voucher specimens from historical samples in museum collections to further expand the sequence library.
    • The reliable taxonomic identification of marine organisms using DNA requires a high quality and curated taxonomic library of reference DNA sequences. For some specimens inconsistencies exist, which need to be verified by taxonomic experts. For this reason we will organize a taxonomists meeting during which these problematic specimens will be examined by animal-group-specialists in order to reach consensus on the morphological identification of the specimens so that the correct link between DNA sequences and  species level morphological identifications is achieved. This will solve long standing issues that also occur in public databases such as BOLD.
    • So far, the GEANS reference database focused on a short fragment of the COI gene because it has a good species level resolution for animals. Long read DNA sequencing allows to generate complete mitogenomes or even genome skims which provide reference sequences for many other genes than the COI. This could enable primer free methods in the future. Therefore, we will expand the reference database with complete mitogenomes from ecological keystone species that have already been collected within GEANS
    • Reproducibility and robustness is key for implementation of our harmonized protocol. This will be evaluated by conducting a transnational ring test. Subsamples of the same samples will be sent to different partners that will process these samples using a standard protocol (testing reproducibility) and using protocols where small changes to the lab protocol are allowed and where different bio-informatic pipelines will be used to process the sequencing data (testing robustness).
    • We want to support stakeholders in their search for a standardized analytical approach. To this end, we will inventory suitable analytical approaches that are in use within and outside the GEANS consortium. A meta-analysis of available (online) tools and workflows will result in a comprehensible report highlighting the pros & cons, the applicability and requirements of the various analytical approaches in use. In this task, we will work in close connection with existing European research infrastructure initiatives such as LifeWatch, Elixir and EMBRC.

 

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