A universal workflow to monitor animal and plant biodiversity using environmental DNA metabarcoding | LC 25

Biography

Lucas Wange is a Postdoctoral Fellow at the Comparative Genomics Laboratory in Barcelona, led by Tomàs Marquès Bonet. While his core research focuses on mammalian gene regulation, his expertise in the development and optimisation of sequencing protocols led him to work on biodiversity monitoring using environmental DNA metabarcoding.

By providing a scalable workflow from environmental sample to taxonomic identification using nanopore sequencing, he hopes to enable widespread biodiversity monitoring in remote biodiversity hubs like tropical rainforests.

Abstract

Environmental DNA (eDNA) has become a transformative tool for monitoring biodiversity, enabling the non-invasive detection of species across diverse ecosystems. Despite its potential, traditional eDNA approaches often face challenges, including limited sensitivity, reliance on taxon-specific primers, lengthy processing times, computational bottlenecks, and dependence on specialized laboratory infrastructure. To overcome these limitations, we developed an innovative, unified protocol that integrates metabarcoding and barcoding using universal markers cytochrome oxidase I (COI) and internal transcribed spacer 2 (ITS2) for plants and animals. This approach allows for simultaneous detection of diverse taxa, from individual species to entire communities, through complementary molecular experiments. Central to our innovation is the real-time processing capability enabled by Oxford Nanopore Technologies MinION sequencers. By leveraging high-throughput sequencing and an efficient computational pipeline capable of processing over one million reads per hour, our system provides rapid and accurate species identification. This portability and speed make it ideal for field conditions, even without internet connectivity. To enhance usability, we streamlined the library preparation process, enabling robust field deployment. The system's reliability was validated across two sequencing platforms (Illumina and Oxford Nanopore Technologies), with rigorous testing of PCR protocols, primer combinations, and computational pipelines. The inclusion of PCR triplicates and high-quality operational taxonomic units (OTUs) ensures sensitive and precise detection, even for low-abundance species. This unified and efficient eDNA solution represents a significant advancement in biodiversity monitoring. Its versatility, real-time capabilities, and field applicability open new possibilities for ecological research, conservation efforts, and environmental management worldwide.