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  • Tristan Cordier
    University of Geneva
  • Laura Alonso-Saez
    AZTI, Spain
  • Apothéloz-Perret-Gentil
    University of Geneva
  • Eva Aylagas
    Red Sea Research Center (RSRC), Saudi Arabia
  • David A. Bohan
    Université de Bourgogne
  • Agnes Bouchez
  • Anthony A Chariton
    Macquarie University, Sydney
  • Simon Creer
  • Larissa Fruhe
    Technische Universität Kaiserslautern
  • Francois Keck
  • Nigel Keeley
    Institute of Marine Research, Tromsø
  • Olivier Laroche
    Institute of Marine Research, Tromsø
  • Florian Leese
    University of Duisburg-Essen
  • Xavier Pochon
    University of Auckland
  • Thorsten Stoeck
    Technische Universität Kaiserslautern
  • Jan Pawlowski
    University of Geneva
  • Anders Lanzen
    AZTI, Spain
A decade after environmental scientists integrated high‐throughput sequencing technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end‐users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or “in development”, hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics‐based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (A) Taxonomy‐based analyses focused on identification of known bioindicators or described taxa; (B) De novo bioindicator analyses; (C) Structural community metrics including inferred ecological networks; and (D) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programs that leverage recent analytical advancements, while pointing out current limitations and future research needs.


  • biodiversity, biomonitoring, ecosystem management, environmental DNA, implementation strategy, metabarcoding
Original languageEnglish
Pages (from-to)2937-2958
Number of pages22
JournalMolecular Ecology
Issue number13
Early online date16 May 2020
Publication statusPublished - Jul 2021

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