As the urgency to monitor and protect aquatic biodiversity intensifies, the need for reliable and interoperable DNA-based data infrastructures becomes increasingly vital. The eDNAqua-Plan project sets out to address this need by building a European FAIR-based digital ecosystem for environmental DNA (eDNA) repositories and reference libraries. A major milestone within this mission is the audit and gap analysis conducted by Work Package 2, which critically examines the current landscape of aquatic DNA reference databases across Europe. In this blog, we interviewed Filipe Costa, Professor at University of Minho (UMinho) and member of the project’s team, on the outcomes of this analysis and focus on key insights on the challenges, opportunities, and next steps in creating a harmonised and trustworthy digital ecosystem for DNA-based biodiversity monitoring.
eDNAqua-Plan: Audit & gap analysis of the digital landscape of European aquatic DNA
eDNAqua-Plan aims to create a European FAIR-based digital ecosystem for eDNA repositories and a dynamic species reference library to support future biodiversity monitoring initiatives in marine and freshwater ecosystems. Within these aims, and in the first half of the project implementation, a gap analysis developed by Work Package 2 “Audit & gap analysis” has been completed to assess the digital landscape of aquatic DNA sequence repositories.
According to Filipe Costa, Professor at UMinho specialised in marine biology and molecular ecology, and member and task leader within Work Package 2, the objective has been to identify and analyse which repositories are being used, their characteristics, how the data is accessible and curated, and to map existing initiatives in Europe. Collectively, this information will finally reveal which gaps are present in the landscape and how they can be solved or improved whilst understanding the data workflow, as well as stakeholder data management and distribution needs.
The outcome of the gap analysis
DNA reference libraries serve to identify species when using DNA-based tools in environmental research or biodiversity monitoring, for example. Without them or with an uncomplete reference library DNA sequences can lack context therefore interfering with the correct identification of organisms. That’s why having well curated, complete and standardised reference library is of main importance.
Nonetheless, DNA reference libraries can present gaps therefore potentially mining the trustability in the results of organisms identification. The work carried out by eDNAqua-Plan’s Work Package 2 and the survey developed by Task 2.1 “Inventory, overview and gap analysis of DNA barcoding initiatives and reference libraries” has demonstrated that there is not a common procedure for the creation and management of these libraries. For example, there is a large variety of aquatic organisms used in environmental monitoring, and different practices of working with them in cell cultures, museum vouchers specimens, or tissue collections. Plus a suite of genetic marker regions can be used, depending on the target organism, and there are diverse ways to access the data of a reference library.
A common challenge: harmonising the digital landscape
The analysis from Work Package 2 have allowed to determine the weaknesses of today’s data workflows concerning aquatic DNA reference libraries. According to Filipe, though there are some standardised workflows there is an issue on the collection of data from the related repositories and the communication between the corresponding databases, therefore creating a challenge from the perspective of bioinformatics. Furthermore, there is a lack of harmonisation making it hard to have interoperability among the data.
Therefore, Filipe, further suggest to have a harmonisation on the metadata requirements and implementing systems to validate and curate the record of the different reference libraries which will allow to have a harmonised digital landscape of aquatic DNA reference libraries.
Monitoring and decision making: developing strategies for aquatic biodiversity
Decision-makers can play a pivotal role in addressing the gaps that eDNAqua-Plan team has identified through its work. As Filipe says:
“Policy-makers can help by understanding the key aspects of the data that is required for aquatic DNA based monitoring therefore grasping what is behind the technology they based their decisions on”
The understanding of the data itself and how it is use for environmental or biodiversity monitoring, for example, can help develop a future European digital ecosystems based on aquatic DNA reference libraries that is not only useful for the scientific community but also to the individuals or organisations that do the actual monitoring. The influence of policy-makers in the development and implementation of a strategy on this topic can be crucial to have a trustworthy monitoring system.
A call to action: collaboration between stakeholders
Though challenges remain in the world of European aquatic DNA reference libraries there is already an agreement in the scientific community that there needs to be a harmonised environmental DNA sequenced data, and how the corresponding reference libraries are dealt with. For Filipe, the main takeaway message is to collaborate and coordinate among stakeholders to define the harmonisation of such system. eDNAqua-Plan aims to further facilitate this collaboration.