Preprint Review Version 1 Preserved in Portico This version is not peer-reviewed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)

A peer-reviewed article of this Preprint also exists.


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.


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


Biology and Life Sciences, Ecology, Evolution, Behavior and Systematics

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