El pasado 18 de marzo Ion Luis Abad Recio defendió su tesis doctoral titulada: «Metagenomics-based insights into the estuarine benthic microbial community: structure, function and biomonitoring potential» en la Facultad de Química de la Universidad del País Vasco (EHU) en Donosti.
La investigación se ha desarrollado en AZTI, bajo la dirección de los doctores Anders Lanzen (AZTI-Ikerbasque) y Ramiro Logares (ICM-CSIC) y ha obtenido la calificación de sobresaliente cum laude.
By integrating shotgun metagenomics, metabarcoding and ecological network analysis, this thesis evaluates the potential of environmental genomics to improve the biomonitoring of estuarine ecosystems, with a special focus on benthic microbial communities as indicators of environmental health. This innovative approach is developed so that we can overcome several limitations of traditional monitoring based on morphological indicators.
The first chapter compares different methodologies for the functional profiling of microbial communities, including functional inference from metabarcoding, functional microarrays, and shotgun metagenomics, demonstrating the greater capacity of sequencing-based approaches to discriminate ecological states and detect functional responses to environmental stress. The second chapter introduces a multiregion protocol of the 16S rRNA gene that significantly improves taxonomic resolution and the detection of rare taxa, strengthening the identification of microbial bioindicators along environmental gradients. The third and fourth chapters focus on the application of shotgun metagenomics and ecological network analysis. A genetic catalog of the estuarine benthic microbiome was generated from metagenomic data, including putative genes and assembled metagenome genomes (MAGs), providing an unprecedented functional and taxonomic characterization. Integrating these data into co-occurrence networks allowed for the identification of key interactions, core functional genes, and patterns of ecological stability, offering a mechanistic understanding of estuarine functioning. Overall, this thesis demonstrates that environmental genomics, and metagenomics in particular, constitutes a robust, scalable, and highly informative tool for the assessment, conservation, and management of estuarine ecosystems.