Assessing fish diversity in abandoned mining ponds in Madre de Dios, Peru, using environmental DNA

The Peruvian region of Madre de Dios is a biodiversity hotspot located in the Andean-Amazon region. Since the 1970s, it has experienced the harsh effects of artisanal and small-scale gold mining (ASGM), which has transformed the primary forests into numerous small mining ponds left abandoned after extraction. Preliminary surveys indicate that these ponds are being recolonized by surrounding biodiversity. These assessments are typically carried out using traditional methods that are costly, difficult to deploy at multiple locations, and have raised safety concerns. In this context, environmental DNA (eDNA) becomes a useful tool for biodiversity monitoring due to its simplicity for sample collection and performance to identify taxonomic groups. In this study, we evaluated fish biodiversity in two mining ponds created by ASGM along with two nearby pristine lakes, unimpacted by mining operations but also influenced by seasonal flooding. We compared two alternative eDNA processing methods and contrasted our results with historic data from traditional biodiversity monitoring. Both eDNA-based methods yielded comparable results, varying only in logistic requirements and costs. In total, we detected 85 fish MOTUs (22 at the species level) from 5 orders, 22 families, and 41 genera. Some of the species identified with eDNA were rarely registered by traditional monitoring, and we could identify 6 genera associated with ASGM mining ponds only. A major restriction of the eDNA approach in this location was the insufficient local taxa registered in genomic databases which limited our taxonomic resolution. Despite this limitation, our results indicate that eDNA could be a powerful tool for biodiversity estimations in the Western Amazon, identifying more taxa, with much less time and money invested than traditional monitoring. Our results also confirm that abandoned mining ponds are being recolonized by surrounding ichthyofauna, reaching richness levels above nearby unmined oxbow lakes used as reference.