Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches

• DOI: 10.7717/peerj.16453
• Publication Date: 2024-01-02T09:01:02Z
• Authors: Ann E. Holmes; Melinda R. Baerwald; Jeff Rodzen; Brian M. Schreier; Brian Mahardja; Amanda J. Finger
• Keywords: Turbidity; Environmental DNA; Filtration (mathematics)

Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt ( Hypomesus transpacificus ), a critically endangered estuarine fish associated with water. sampling the field was first paired trawl survey. Species-specific Taqman qPCR assay showed concordance between methods, weak signal. Informed by results sampling, an experiment designed to assess how turbidity and filtration methods influence rare target. Water from non-turbid (5 NTU) (50 sites spiked small volumes (0.5 1 mL) tank generate low concentrations. Samples were filtered four filter types: cartridge filters (pore size 0.45 μm) 47 mm (glass fiber, pore 1.6 μm polycarbonate, sizes 5 10 μm). Prefiltration also tested as addition protocol for samples. copy numbers analyzed censored data method data. The limits lack PCR inhibition indicated optimized assay. Glass fiber yielded highest rates copies improved only when used polycarbonate filters. Statistical analysis identified significant effect on probability detected; type interaction prefilter effects detected, suggesting that particulate-filter interactions can affect sensitivity. Pilot experiments transparent criteria positive could improve surveys environments.