TY - JOUR

T1 - Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap

AU - Cordier, Tristan

AU - Alonso-Saez, Laura

AU - Apothéloz-Perret-Gentil, null

AU - Aylagas, Eva

AU - Bohan, David A.

AU - Bouchez, Agnes

AU - Chariton, Anthony A

AU - Creer, Simon

AU - Fruhe, Larissa

AU - Keck, Francois

AU - Keeley, Nigel

AU - Laroche, Olivier

AU - Leese, Florian

AU - Pochon, Xavier

AU - Stoeck, Thorsten

AU - Pawlowski, Jan

AU - Lanzen, Anders

N1 - © 2020 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

PY - 2021/7

Y1 - 2021/7

N2 - 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.

AB - 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.

KW - biodiversity

KW - biomonitoring

KW - ecosystem management

KW - environmental DNA

KW - implementation strategy

KW - metabarcoding

U2 - https://doi.org/10.1111/mec.15472

DO - https://doi.org/10.1111/mec.15472

M3 - Article

C2 - 32416615

VL - 30

SP - 2937

EP - 2958

JO - Molecular Ecology

JF - Molecular Ecology

SN - 0962-1083

IS - 13

ER -