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A Survey Paper on Identifying Taxonomy and Assessing Biodiversity from eDNA Datasets
Abstract
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.
References
R. Haderlé, V. Ung, and J. Jung, “VeTAPRH: A Taxonomic Assignment Protocol for Vertebrates Applied to eDNA Metabarcoding Data, Including Molecular, Taxonomic and Ecological Criteria,” Biodiversity Information Science and Standards, vol. 8, Nov. 2024, doi: 10.3897/biss.8.141746.
M. Baylón and J. L. Ramírez, “A Comparison of eDNA Metabarcoding and Microscopy Techniques to Analyze Algal Diversity in Lake Titicaca, Peru,” Diversity, vol. 17, no. 8, pp. 560–560, Aug. 2025, doi: 10.3390/d17080560.
K. Shi, Y. He, Y. Zhao, and Y. Cui, “The complementary role of detritus in environmental dna monitoring of macroinvertebrates: a case study in qingyi river,” Acta Hydrobiologica Sinica, vol. 49, no. 10, pp. 102507–76, Sept. 2025, doi: 10.3724/1000-3207.2025.2025.0027.
R. González‐Miguéns et al., “A Novel Taxonomic Database for eukaryotic Mitochondrial Cytochrome Oxidase subunit I Gene (eKOI): Enhancing taxonomic resolution at community-level in metabarcoding analyses,” Dec. 2024, doi: 10.1101/2024.12.05.626972.
P. Gauvin, I. Domaizon, A. Bouchez, and F. Rimet, “Environmental Matrices Need Consideration: Insights From Water and Biofilm Environmental DNA for Multi‐Taxonomic
Biomonitoring,” Environmental DNA, vol. 7, no. 2, Mar. 2025, doi: 10.1002/edn3.70079
Y. C. A. Ip, P. F. P. Brandão‐Dias, G. Guri, E. A. Allan, and R. P.
Kelly, “Vertebrate Biodiversity via eDNA at the air-water interface,”
June 2025, doi: 10.1101/2025.06.13.659655.
O. Tournayre et al., “Enhancing metabarcoding of freshwater biotic communities: A new online tool for primer selection and exploring data from 14 primer pairs,” Environmental DNA, vol. 6, no. 4, July 2024, doi: 10.1002/edn3.590.
H. J. Yoon, J. H. Seo, S. H. Shin, M. A. A. Abdelhamid, and S. P. Pack, “Bioinformation and Monitoring Technology for Environmental DNA Analysis: A Review,” Biosensors, Aug. 2025, doi: 10.3390/bios15080494.
N. J. Iacaruso, O. P. Reves, S. J. Merkelz, C. L. Waldrep, and M. A. Davis, “A systematic review evaluating the performance of eDNA methods relative to conventional methods for biodiversity
monitoring,” Ecography, June 2025, doi: 10.1002/ecog.07952.
J. Erens et al., “A field-deployable eDNA metabarcoding workflow including de novo reference assembly for characterizing understudied biodiversity hotspots,” Sept. 2025, doi: 10.1101/2025.09.14.676136.
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