• This study, led by AZTI in collaboration with the University of the Basque Country, ICM-CSIC and the Technical University of Kaiserslautern-Landau (Germany), has led to the publication in Scientific Data of the first-ever gene catalogue of estuarine sediments.
  • The gene catalogue contains more than 108 million genes and nearly 500 microbial genomes, opening up new ways to understand the role of microorganisms in environmental health and climate change.

Pasaia, December 10, 2025. An international research team led by the technology centre AZTI has created the first gene catalogue of estuarine sediments along the Basque coast. This groundbreaking scientific resource provides an in-depth look at the microbial biodiversity that thrives in these ecosystems. The work, entitled the Basque Coast Estuarine Sediment Gene Catalogue, has been published in the journal Scientific Data (Springer Nature).

This marks the first comprehensive effort to genetically characterise estuarine sediments through metagenomic techniques, building on methodology adapted from major international initiatives such as the TARA Oceans and Malaspina expeditions, the later in which AZTI also took part. With this achievement, the Basque Country takes its place on the global map of marine environmental genomics, contributing an important reference for temperate coastal ecosystems.

The study examined 92 sediment samples collected between 2013 and 2020 from twelve Basque estuaries, within the Basque Environmental Monitoring Network. Using metagenomic techniques, the team identified more than 108 million unique genes and reconstructed 471 high- and medium-quality microbial genomes, belonging to bacteria, archaea, eukaryotes and viruses.

“This genetic catalogue allows us to explore how microorganisms support the functioning of estuarine ecosystems and how they respond to human pressures such as pollution or climate change,” explains Ion L. Abad-Recio, a researcher at AZTI and the study’s lead author. “It also opens the door to innovative biotechnological applications, for example in bioremediation or in the search for genes with industrial potential.”

A tool to protect and restore coastal ecosystems

Beyond its scientific value, the catalogue represents a strategic resource for environmental management and the sustainable use of coastal ecosystems. The genetic information it contains will make it possible to identify markers linked to pollution or loss of ecological quality, strengthen DNA-based environmental monitoring models, and support conservation, restoration and coastal management policies.

This resource also provides a solid basis for bioprospecting and biotechnology, facilitating the detection of genes with potential applications in sectors such as blue energy, aquaculture, sustainable agriculture and the food industry.

Among its most relevant practical applications are the development of DNA-based ecological status indices, port biosecurity and monitoring through early detection of invasive species or pathogens, environmental management of dredging and discharges, blue carbon monitoring in estuaries (MRV: measurement, reporting and verification), and targeted bioremediation.

An essential yet little-known ecosystem

Estuaries are transitional zones between marine, river and terrestrial environments. They recycle nutrients, remove pollutants and store organic carbon, playing a crucial role in climate regulation. However, their microbial biodiversity remains largely unexplored.

Thanks to the large-scale sequencing of 3.35 terabases of environmental DNA, the catalogue offers an unrivalled view of the microscopic life that sustains these habitats. The data reveal key ecological functions and genes that act as indicators of environmental disturbance, paving the way for enhanced biological monitoring and coastal management.

Open science serving knowledge

In keeping with the principles of open science, all materials generated, including sequences, functional and taxonomic annotations, and reconstructed genomes, are publicly available in international repositories (the ENA Sequence Read Archive and BioStudies) so that the global scientific community can reuse them in future research.

“Making this resource publicly available will enable comparisons with other coastal ecosystems around the world and help develop new tools for DNA-based environmental assessment,” notes Anders Lanzén, Senior Investigator at AZTI and IKERBASQUE Research Associate Professor.

An international collaborative effort

The project was developed by AZTI, the University of the Basque Country (UPV/EHU), the Rheinland-Pfalz Technische Universität Kaiserslautern-Landau (Germany), the Institute of Marine Sciences (ICM-CSIC) and IKERBASQUE, with support from the Spanish Government, the Deutsche Forschungsgemeinschaft (DFG) and the Horizon Europe programme.

This initiative reinforces the Basque Country’s position as a leader in marine ecology and environmental genomics, providing key reference data on estuarine biodiversity and its role in the global carbon cycle.

Scientific article:

  • Abad-Recio, I. L., Rubel, V., Filker, S., Garate, L., Stoeck, T., Logares, R., … Lanzén, A. (2025). The Basque Coast Estuarine Sediment Gene Catalogue. Scientific Data, 12, Article 1909. https://doi.org/10.1038/s41597-025-06163-6

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