Fast, Flexible, Feasible: A Transparent Framework for Evaluating eDNA Workflow Trade-offs in Resource-Limited Settings

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 18, 2025

Abstract Environmental DNA (eDNA) analysis enables biodiversity monitoring by detecting organisms from trace genetic material, but high reagent costs, cold-chain logistics, and computational demands limit its broader use, particularly in resource-limited settings. To address these challenges improve accessibility, we systematically evaluated multiple workflow components, including four extraction methods, two primer sets, three Nanopore basecalling models, demultiplexing pipelines. Across 144 combinations tested an aquarium with 15 fish species, mapped trade-offs between cost, sensitivity, processing speed using a hierarchical Bayesian model, to assess where time resource savings are possible without compromising detection. Workflows the Qiagen Blood Tissue (BT) kit provided highest recovering all species of sampled community within 3–5 hours Oxford sequencing when paired MiFish-U set high-accuracy (HAC) basecalling. Chelex, alternative lower-cost method, required extended (>24 hours) reach comparable species-detection rates. DirectPCR QuickExtract offered field-friendly alternatives that achieved recovery ∼10–12 hours, though their cost-effectiveness varied. While MarVer1 was designed broaden vertebrate detection, it recovered same as MiFish-U, fewer total reads. Real-time trials (0–61 revealed high-efficiency workflows (BT + HAC) reached detection plateaus rapidly, indicating can be reduced sacrificing accuracy. The OBITools4 bioinformatics pipeline enabled automated discarded more reads than alternative, ONTbarcoder2.3, which retained low-abundance taxa at cost manual curation. Rather identifying single “best” workflow, this study provides transparent decision framework for prioritizing speed, sensitivity eDNA applications, supporting scalable, cost-effective monitoring,

Language: Английский

Utilizing aquatic environmental DNA to address global biodiversity targets

Published: April 27, 2025

Language: Английский