Brazilian scientists are pioneering the use of environmental DNA and RNA analysis to assess fish biodiversity in threatened estuarine ecosystems, revealing a complex picture of species distribution and the impact of human activity. A recent study, focusing on estuaries in the state of São Paulo, has identified a diverse range of fish species, including several considered invasive, using cutting-edge molecular techniques.
The research, conducted by a team from São Paulo State University (UNESP) and other institutions, evaluated fish communities in the Juqueriquere and Escuro rivers, two estuaries with differing levels of urbanization. Published in bioRxiv on , the study employed both environmental DNA (eDNA) and environmental RNA (eRNA) metabarcoding, targeting the mitochondrial 12S rRNA fragment, commonly known as MiFish. This approach allows researchers to detect species simply by analyzing genetic material shed into the water – from scales, mucus, or waste – without the need for traditional, often invasive, capture methods.
The team detected a total of 93 species across both systems. EDNA analysis identified 32 fish species, while eRNA analysis, which focuses on genetic material from actively metabolizing organisms, detected 22 species in the more preserved estuary. This integration of eDNA and eRNA provides a more nuanced understanding of the fish community, coupling biodiversity detection with insights into contemporary community composition. The less impacted estuary exhibited significantly higher diversity indices and a more heterogeneous taxonomic composition, indicating a healthier ecosystem.
However, the urbanized estuary presented a different story. Researchers found clear molecular evidence of anthropogenic influence, including the presence of invasive species such as Oreochromis niloticus, O. Aureus, and Clarias gariepinus – commonly known as Nile tilapia, blue tilapia, and African catfish, respectively. The presence of these non-native species, alongside genetic signatures of domestic animals, underscores the impact of human activity on the estuarine environment.
Estuaries, where rivers meet the sea, are crucial ecosystems, serving as nurseries for many marine species and providing vital coastal protection. They are also particularly vulnerable to pollution, habitat destruction, and the introduction of invasive species. Traditional methods of fish biodiversity assessment, such as netting and electrofishing, can be time-consuming, labor-intensive, and may not accurately capture the full diversity of species present, particularly elusive or rare ones. EDNA metabarcoding offers a non-invasive and comprehensive alternative, capable of detecting even trace amounts of genetic material.
This study marks the first application of fish eRNA metabarcoding in Brazil, representing a significant advancement in ecological monitoring techniques within the country. The use of eRNA, in particular, provides a snapshot of the currently active fish population, complementing the broader biodiversity assessment provided by eDNA. According to the research, integrating both methods refines ecological interpretation.
The findings align with a growing body of international research highlighting the effectiveness of eDNA metabarcoding for aquatic biodiversity assessment. A study published in Nature in focused on Norway’s Oslo fjord, demonstrating the utility of eDNA monitoring for temporal analysis of fish communities and the detection of migratory patterns. That research, utilizing MiFish and Elas02 primer sets, detected 63 unique fish species, including commercially important ones, and revealed substantial increases in read abundance during specific migratory cycles.
Similarly, research published in MDPI’s Fishes journal in emphasizes the revolutionary impact of eDNA metabarcoding on fish biodiversity assessments, offering non-invasive and comprehensive sampling. The review highlights how challenges specific to estuarine environments, such as high sediment loads and fluctuating salinity, have been addressed through improved DNA extraction techniques and optimized primers.
The Brazilian study was supported by funding from the São Paulo Research Foundation (FAPESP), the Coordination for the Improvement of Higher Education Personnel (CAPES), and the National Council for Scientific and Technological Development (CNPq). The researchers emphasize the potential of multi-molecule metabarcoding for routine, non-invasive biodiversity assessment in megadiverse and conservation-priority coastal ecosystems. This approach could be crucial for informing conservation and management strategies in Brazil’s Atlantic Forest, a region facing increasing anthropogenic pressures.
The implications of this research extend beyond Brazil. As coastal ecosystems worldwide face similar threats, the adoption of eDNA and eRNA metabarcoding offers a powerful tool for monitoring biodiversity, detecting invasive species, and assessing the health of these vital environments. The cost-effectiveness and non-invasive nature of these techniques make them particularly appealing for long-term monitoring programs and for assessing the impact of conservation efforts.
