From Molecules to Ecosystems: A Review on Environmental DNA and Metabarcoding in Biodiversity Science

Traditional biodiversity monitoring methods often struggle to detect elusive, rare, or cryptic species due to their reliance on direct observation and specimen collection. In an era of accelerating habitat loss and climate change, there is an urgent need for rapid, reliable, and non-invasive tools to assess biodiversity across ecosystems. This review aims to synthesize the emerging field of environmental DNA (eDNA) and metabarcoding, focusing on their principles, methodologies, and transformative applications in ecological monitoring, species detection, and conservation management. We summarize global research developments on eDNA collection from environmental matrices such as soil, water, and air, explain the integration of PCR-based metabarcoding with high-throughput sequencing, and analyze bioinformatics pipelines used for taxonomic identification and community composition assessment. Additionally, we highlight advances in combining eDNA with remote sensing, machine learning, and conservation genomics. The synthesis demonstrates that eDNA metabarcoding provides a cost-effective, scalable, and highly sensitive framework for biodiversity assessment, enabling detection of rare, invasive, and cryptic species. Its integration with ecological and bioinformatics tools bridges molecular data with environmental management, offering a transformative frontier for global biodiversity monitoring and conservation planning under changing climatic and anthropogenic pressures.