Monitoring Marine Biodiversity in the Genomic Era

How effective is the metabarcoding approach as a tool for measuring the status of marine biodiversity?

Project Summary

Rapidly increasing impacts of industrial activities on marine biodiversity strongly affects marine ecosystem health and services. Yet, the growing demand for measuring and mitigating these impacts can hardly be satisfied by classical monitoring tools based on morphological species identification. Next-generation sequencing (NGS) technologies applied to environmental genomics could potentially overcome these limitations, but their application for biomonitoring and environmental impact assessment is currently very limited.

The main objective of this project is to explore the potential utility of NGS – based metabarcoding approach for environmental monitoring of marine ecosystems from biological, legal and economic perspectives. The first part of the project aims to establish the ecogenomic markers for measuring the environmental impact on seabottom diversity in the case of two types of industrial activity: marine aquaculture and deep-sea mining. The second part of the project will focus on understanding the legal and institutional framework surrounding environmental monitoring and future application of ecogenomic markers.

The outcome of the project will be to provide regulators and environmental managers with an evaluation of the effectiveness of the metabarcoding approach as a tool for measuring the status of marine biodiversity. At the same time, the project will provide policy makers and stakeholders at the national and international levels with the information required to implement future decisions necessary to monitor, observe and protect the marine environment.

Academic Output

Executive Summary

The rapid development of marine industries prompts an urgent need for tools able to accurately and rapidly monitor resulting impacts on marine life. Classical methods of biodiversity monitoring based on morphological species identification are time consuming and require a solid taxonomic expertise that is not readily available. The project Monitoring Marine Biodiversity in the Genomic Era proposes to overcome these limitations by using DNA barcoding and metabar coding to identify marine species and to monitor biodiversity changes. These DNA-based approaches are highly effective in terms of both cost and time and offer a unique opportunity to include the small-sized organisms (microbes, meiofauna) that play a key role in marine ecosystem functioning but are generally ignored in routine monitoring. The project examines the use of these genetic methods, focusing on marine aquaculture and deep seabed mining, and provides evidence for their applicability from scientific, economic and legal perspectives. It concludes that emerging DNA-based technologies should be deployed alongside traditional methods to deliver easily-understandable data to environmental managers and authorities, and to ensure the sustainable use of marine resources.



Working Paper

Enabling the use of Environmental DNA for Regulatory Policymaking in the Marine Industrial Revolution

New industrial activities are enhancing the anthropogenic impact on the marine environment, imposing an unprecedented combination of stressors on the ocean ecosystem. The classical methodologies for monitoring impacts on marine life, based on morphological species identification, cannot confront the urgent need for more detailed information to monitor biodiversity changes, and to promptly deliver easily-understandable data to time and budget constrained environmental compliance and enforcement practitioners. This is particularly true for small-sized organisms that are hard to identify and that dominate in some environments, such as deep-sea. Knowledge limitations affect not only the impacts on environmental degradation, but also the lack of adequate understanding of how the cumulative impact of human activities at sea is affecting the provision of the ocean’s many ecosystem services that are fundamental for the sustainability of our planet. High-throughput sequencing (HTS) technologies applied to environmental DNA (eDNA) holds great potential to confront these knowledge gaps, although its use for conducting environmental impact assessments (EIAs) in the marine environment is still limited. In this study, we explored the potential of eDNA HTS approach, called also eDNA metabar coding, for assessing the health of marine ecosystems and the impact of major human actions on it. The study concludes that emerging eDNA-based technologies should systematically be deployed alongside traditional morphological species identification techniques to provide relevant information to ocean resources managers, and environmental compliance and enforcement practitioners; that there are no significant legal constraints to its use; and that its decreasing costs open a unique window of opportunity to enhance human knowledge of the complex marine ecosystems and of the effects of cumulative impacts on them. However, the study also highlights that more research is needed to improve interpretation of eDNA data for impact assessment, with particular concerns in ground truthing species identities and interactions, inferring abundance data and developing molecular indices of ecological status. Major challenges to overcome in eDNA data analysis are associated with signal persistence over time and in non-living material, as well as with the transportation of eDNA in water over long distances.

Research Team

Jan Pawlowski
University of Geneva

Daniel Ariztegui
University of Geneva

Florian Andermatt
Principal Member
Swiss Federal Institute of Aquatic Science and Technology (Eawag)

Philippe Esling
Principal Member
Université Pierre et Marie Curie (Paris 6)

Lisa Levin
Principal Member
University of California San Diego

Kathryn Mengerink
Principal Member

Sandor Mulsow
Principal Member
International Seabed Authority

Tomas Cedhagen
Associated Member
Aarhus Universitet

Kristina Gjerde
Associated Member
International Union for the Conservation of Nature (IUCN)

Andrew Gooday
Associated Member
University of Southampton





Policy domains



All countries

Host Institution