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Title: Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap
Authors: Cordier, Tristan; Alonso-Saez, Laura; Apotheloz-Perret-Gentil, Laure; Aylagas, Eva; Bohan, David A.; Bouchez, Agnes and Chariton, Anthony; Creer, Simon; Fruehe, Larissa; Keck, Francois; Keeley, Nigel; Laroche, Olivier; Leese, Florian and Pochon, Xavier; Stoeck, Thorsten; Pawlowski, Jan; Lanzen, Anders
Citation: MOLECULAR ECOLOGY, 2021, 30, 2937-2958
Abstract: 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 programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
Issue Date: 2021
Publisher: WILEY
Type: Review
DOI: 10.1111/mec.15472
ISSN: 0962-1083
E-ISSN: 1365-294X
Funder: Swiss National Science FoundationSwiss National Science Foundation (SNSF)European Commission [31003A\_179125]
European Cross-Border Cooperation Programme
`Ramon y Cajal' contractSpanish Government [RYC-2012-11404]
Spanish Ministry of Economy and CompetitivenessSpanish Government
Saudi Aramco-KAUST Center for Marine Environmental Observations
French Agence Nationale de la RechercheFrench National Research Agency (ANR) [ANR-17-CE32-011]
UK Natural Environment Research CouncilUK Research \& Innovation (UKRI)Natural Environment Research Council (NERC) [NE/N003756/1, NE/N006216/1]
German Science Foundation (DFG)German Research Foundation (DFG) [STO414/15-1]
New Zealand Ministry for Business, Innovation and EmploymentNew Zealand Ministry of Business, Innovation and Employment (MBIE) [CAWX1904, C05X1707]
DNAquaNet COST ActionEuropean Cooperation in Science and Technology (COST) [CA15219]
European UnionEuropean Commission
IKERBASQUE (Basque Foundation for Science)
Basque GovernmentBasque Government
Office Francais de la Biodiversite (OFB)
Appears in Publication types:Artículos científicos

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