Preprint Review Version 1 This version is not peer-reviewed

Ecosystems Monitoring Powered by Environmental Genomics: A Review of Current Strategies with An Implementation Roadmap

Version 1 : Received: 21 January 2020 / Approved: 24 January 2020 / Online: 24 January 2020 (11:01:41 CET)

How to cite: Cordier, T.; Alonso Sáez, L.; Apotheloz-Perret-Gentil, L.; Aylagas, E.; Bohan, D.A.; Bouchez, A.; Chariton, A.; Creer, S.; Fruhe, L.; Keck, F.; Keeley, N.; Laroche, O.; Leese, F.; Pochon, X.; Stoeck, T.; Pawlowski, J.; Lanzén, A. Ecosystems Monitoring Powered by Environmental Genomics: A Review of Current Strategies with An Implementation Roadmap. Preprints 2020, 2020010278 (doi: 10.20944/preprints202001.0278.v1). Cordier, T.; Alonso Sáez, L.; Apotheloz-Perret-Gentil, L.; Aylagas, E.; Bohan, D.A.; Bouchez, A.; Chariton, A.; Creer, S.; Fruhe, L.; Keck, F.; Keeley, N.; Laroche, O.; Leese, F.; Pochon, X.; Stoeck, T.; Pawlowski, J.; Lanzén, A. Ecosystems Monitoring Powered by Environmental Genomics: A Review of Current Strategies with An Implementation Roadmap. Preprints 2020, 2020010278 (doi: 10.20944/preprints202001.0278.v1).

Abstract

A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on biodiversity and ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental DNA and RNA to cost-efficiently and accurately monitor biodiversity, technical limitations and conceptual issues still stand in the way of its routine application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception of the methodology as being premature or “in development”, hence restraining regulators from binding these tools into legal frameworks. This review focuses on the strengths and limitations of genomics-based strategies that have emerged over the past ten years and have been classified for this purpose into three broad strategies: (A) Taxonomy-based approaches that focus on known bio-indicators or the diversity of taxonomically described taxa, (B) De novo approaches that do not require well-established taxonomy, and (C) Function-based approaches that rely on community-wide metrics, where taxa are interchangeable, or on functional profiles instead of compositional turnovers. We finally propose a roadmap for the implementation of environmental genomics into routine monitoring programs that leverage recent analytical advancements, upon which some critical limitations are alleviated.

Subject Areas

biomonitoring; metabarcoding; environmental DNA; biodiversity; implementation strategy; ecosystem management

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