A Survey Paper on Identifying Taxonomy and Assessing Biodiversity from eDNA Datasets

Environmental DNA (eDNA) techniques— particularly metabarcoding and metagenomics—have become essential tools for biodiversity surveys across terrestrial, freshwater, and marine environments. This review summarizes recent methodological and computational developments from 2024–2025, covering sampling strategies, DNA extraction, sequencing technologies, and taxonomic identification approaches. Advances such as multilocus metabarcoding, long- read sequencing, improved reference databases, and integrated bioinformatic pipelines are enhancing the reliability of species detection and ecological interpretation. We additionally review common limitations—including reference gaps, incomplete annotations, and methodological biases—and highlight emerging frameworks that aim to improve accuracy in the generation of taxonomic inventories and biodiversity metrics.