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Freshwater fish community assessment using eDNA metabarcoding vs. capture-based methods: Differences in efficiency and resolution coupled to habitat and ecology

Publication . Curto, Manuel; Batista, Sofia; Santos, Carlos D.; Ribeiro, Filipe; Nogueira, Sofia; Ribeiro, Diogo; Prindle, Benjamin; Licari, Daniel; Riccioni, Giulia; Dias, Diogo; Pina-Martins, Francisco; Jentoft, Sissel; Veríssimo, Ana; Alves, Maria Judite; Gante, Hugo F.

Environmental DNA (eDNA) metabarcoding has revolutionized ecological and environmental research by describing communities without relying on direct observations, making it a powerful, non-invasive, and cost-effective tool in biodiversity monitoring. However, the adoption of eDNA as a standard protocol in long-term monitoring programs, which have traditionally relied on capture-based methods, presents challenges in terms of data comparability. Here, we compared freshwater fish communities assessed through eDNA metabarcoding and electrofishing, across 35 sampling sites in the lower Tagus River basin, Portugal. For the majority of species or species-groups analysed individually (13 out of 17), a significant correspondence was observed between electrofishing and eDNA metabarcoding detections. A weaker correspondence was found between the number of specimens captured by electrofishing with the number of eDNA metabarcoding reads, with seven out of 13 taxa showing significant relationships. Species richness estimates based on the two methods were very similar at the basin level. The methods yielded significantly different species compositions, although these differences were driven by samples collected in the Tagus main channel, which is wider and has higher flow rates than tributaries. Benthic and shoreline fish communities showed similar species composition in the two methods, but this was not the case for pelagic communities, probably due to the higher water turnover of the pelagic zone and electrofishing inefficiency. Our results highlight the high potential of eDNA metabarcoding as a complementary method to electrofishing for freshwater fish monitoring, though further validation is needed to assess biases related to site-specific hydrological conditions and the ecology of the target species.

2025-06Journal article

Embargoed access

Breeding Alnus species for resistance to Phytophthora disease in the Iberian Peninsula

Publication . Cordeiro, Daniela; Pizarro, Alberto; Vélez, M. Dolores; Guevara, M. Ángeles; Marıa, Nuria de; Ramos, Paula; Cobo-Simón, Irene; Diez-Galán, Alba; Benavente, Alfredo; Ferreira, Verónica; Martín, M. Ángela; Rodríguez-González, Patricia M.; Solla, Alejandro; Cervera, M. Teresa; Diez-Casero, Julio Javier; Cabezas, José Antonio; Díaz-Sala, Carmen

Alders are widely distributed riparian trees in Europe, North Africa and Western Asia. Recently, a strong reduction of alder stands has been detected in Europe due to infection by Phytophthora species (Stramenopila kingdom). This infection causes a disease known as alder dieback, characterized by leaf yellowing, dieback of branches, increased fruit production, and bark necrosis in the collar and basal part of the stem. In the Iberian Peninsula, the drastic alder decline has been confirmed in the Spanish Ulla and Ebro basins, the Portuguese Mondego and Sado basins and the Northern and Western transboundary hydrographic basins of Miño and Sil, Limia, Douro and Tagus. The damaging effects of alder decline require management solutions that promote forest resilience while keeping genetic diversity. Breeding programs involve phenotypic selection of asymptomatic individuals in populations where severe damage is observed, confirmation of tree resistance via inoculation trials under controlled conditions, vegetative propagation of selected trees, further planting and assessment in areas with high disease pressure and different environmental conditions and conservation of germplasm of tolerant genotypes for reforestation. In this way, forest biotechnology provides essential tools for the conservation and sustainable management of forest genetic resources, including material characterization for tolerance, propagation for conservation purposes, and genetic resource traceability, as well as identification and characterization of Phytophthora species. The advancement of biotechnological techniques enables improved monitoring and management of natural resources by studying genetic variability and function through molecular biology methods. In addition, in vitro culture techniques make possible large-scale plant propagation and long-term conservation within breeding programs to preserve selected outstanding genotypes.

2024-12Journal article

Open access

Marine microbial community taxonomic and functional indicators to volcanic and anthropogenic stressors in Deception Island, Antarctica

Publication . Duarte, Bernardo; Cruz-Silva, Ana; Feijão, Eduardo; Pereira, Marcelo; Nunes, Mónica; Figueiredo, Andreia; Matos, Ana Rita; Dias, Ricardo; Fonseca, Vanessa; Gameiro, Carla; Cabrita, Maria Teresa

In recent years, the growth in Antarctic tourism has stimulated research on the anthropogenic impacts on the region, boosted by advances in OMIC technologies applied to polar microbial communities. This study aimed to assess the human impacts on marine prokaryotic and viral communities of Deception Island by identifying potential taxonomic, functional, and resistome indicators of both anthropogenic and natural/volcanic pressures. Proteobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla, with notable variations attributed to volcanic activity and anthropogenic pressure. The abundance of Euryarchaeota in regions with increased volcanic activity underlines their adaptability to extreme conditions. Their mercury resistance coupled with their ability to cope with toxic heavy metals is a critical component in managing volcanic mercury concentrations. Actinobacteria, Cyanobacteria, Planctomycetes, and Synergistetes showed distinctive abundance patterns with potential ecological implications related to volcanic environments. Functional analyses revealed the enrichment of functions associated with metal-based, hydrocarbon degradation, and nitrogen metabolism. Submarine volcanic vents contributed significantly to the shape of functional diversity. Identification of specific functions related to nosocomial infections and gastroenteritis highlights the impact of anthropogenic activities on functional traits. Antibiotic resistance genes (ARGs) showed nuanced patterns influenced by both anthropogenic pressure and volcanic activity. Actinobacteria were correlated with increased ARG abundance, which was enhanced by wastewater disposal. Remarkably, Fumarole Bay showed an increased prevalence of certain ARGs, despite a lower anthropogenic impact, suggesting a unique selective pressure induced by volcanic activity. The responsiveness of these indicators to varying levels of pressure characterizes them as valuable tools for assessing and mitigating anthropogenic impacts on the marine waters of Deception Island.

2024Journal article

Open access