Applicability of eDNA metabarcoding for fish monitoring in high-sediment-laden rivers: a case study of the Lower Yellow River
- 1Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, 430079 Wuhan, PR China; Innovation Team of the Changjiang Water Resources Commission for River and Lake Ecosystem Restoration Key Technology, 430079 Wuhan, PR China
- 2Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, 430079 Wuhan, PR China
- 3Key Laboratory of Underwater Acoustic Communication and Marine Information Technology of the Ministry of Education, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, Fujian, PR China; State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, Fujian, PR China
Abstract
Environmental DNA metabarcoding is widely adopted for aquatic biodiversity surveys, yet strong sediment adsorption and seasonal hydrological fluctuations introduce unquantified detection bias and unstable reliability in hyper-turbid, sediment-laden large rivers, which hinders the establishment of unified, standardized long-term fish monitoring workflows. We implemented synchronous paired seasonal field surveys covering summer and autumn of 2024 along the Lower Yellow River, to systematically compare four core monitoring dimensions-fish community composition characterization, sampling cost efficiency, spatial differentiation resolution, and low-abundance invasive species identification-between eDNA metabarcoding and conventional multi-mesh gillnets-traps capture approaches; all comparisons were quantified and validated via hierarchical clustering, non-metric multidimensional scaling (NMDS), Mantel test, redundancy analysis (RDA) and resampling-based species accumulation statistics. Obvious seasonal divergence in detection performance was detected across two survey periods: extreme high suspended sediment loads in summer significantly suppressed aqueous eDNA persistence and transport, leading to severe underestimation of benthic and herbivorous fish taxa by eDNA, with only 26 species detected versus 51 species captured by gillnets&traps, and a low Jaccard similarity of 0.24; in contrast, stable hydrology and reduced sediment concentration in autumn largely narrowed inter-method discrepancies, yielding comparable species richness (31 for eDNA, 35 for nets) and elevated community similarity (0.32). Conventional net sampling demonstrated prominent advantages in resolving fine-scale spatial partitioning of local fish assemblages across wandering, transitional and narrow river reaches, whereas eDNA signals, despite being blurred by long-distance downstream transport, better captured broad basin-wide environmental gradients and maintained lower stochastic variability under repeated sampling. These findings underscore that eDNA performance in high-sediment rivers is strongly modulated by seasonal hydrology and suspended sediment, calling for context-specific monitoring designs. Future work should integrate paired water-sediment eDNA sampling to validate sediment-mediated suppression and improve monitoring reliability in turbid large river systems.
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BibTeX
@article{zhang2026applicability,
title = {{Applicability of eDNA metabarcoding for fish monitoring in high-sediment-laden rivers: a case study of the Lower Yellow River}},
author = {Hushun Zhang and Yutian Gong and Shuo Lyu and Fang Shi and Qing Yang and Xi Zou and Liming Zhu and Lian Hu},
journal = {Ecological Indicators},
year = {2026},
month = oct,
doi = {10.1016/j.ecolind.2026.115507},
url = {https://doi.org/10.1016/j.ecolind.2026.115507},
note = {CC BY},
}
RIS
TY - JOUR
TI - Applicability of eDNA metabarcoding for fish monitoring in high-sediment-laden rivers: a case study of the Lower Yellow River
AU - Hushun Zhang
AU - Yutian Gong
AU - Shuo Lyu
AU - Fang Shi
AU - Qing Yang
AU - Xi Zou
AU - Liming Zhu
AU - Lian Hu
PY - 2026
DA - 2026/10/23
JO - Ecological Indicators
DO - 10.1016/j.ecolind.2026.115507
UR - https://doi.org/10.1016/j.ecolind.2026.115507
AB - Environmental DNA metabarcoding is widely adopted for aquatic biodiversity surveys, yet strong sediment adsorption and seasonal hydrological fluctuations introduce unquantified detection bias and unstable reliability in hyper-turbid, sediment-laden large rivers, which hinders the establishment of unified, standardized long-term fish monitoring workflows. We implemented synchronous paired seasonal field surveys covering summer and autumn of 2024 along the Lower Yellow River, to systematically compare four core monitoring dimensions-fish community composition characterization, sampling cost efficiency, spatial differentiation resolution, and low-abundance invasive species identification-between eDNA metabarcoding and conventional multi-mesh gillnets-traps capture approaches; all comparisons were quantified and validated via hierarchical clustering, non-metric multidimensional scaling (NMDS), Mantel test, redundancy analysis (RDA) and resampling-based species accumulation statistics. Obvious seasonal divergence in detection performance was detected across two survey periods: extreme high suspended sediment loads in summer significantly suppressed aqueous eDNA persistence and transport, leading to severe underestimation of benthic and herbivorous fish taxa by eDNA, with only 26 species detected versus 51 species captured by gillnets&traps, and a low Jaccard similarity of 0.24; in contrast, stable hydrology and reduced sediment concentration in autumn largely narrowed inter-method discrepancies, yielding comparable species richness (31 for eDNA, 35 for nets) and elevated community similarity (0.32). Conventional net sampling demonstrated prominent advantages in resolving fine-scale spatial partitioning of local fish assemblages across wandering, transitional and narrow river reaches, whereas eDNA signals, despite being blurred by long-distance downstream transport, better captured broad basin-wide environmental gradients and maintained lower stochastic variability under repeated sampling. These findings underscore that eDNA performance in high-sediment rivers is strongly modulated by seasonal hydrology and suspended sediment, calling for context-specific monitoring designs. Future work should integrate paired water-sediment eDNA sampling to validate sediment-mediated suppression and improve monitoring reliability in turbid large river systems.
SN - 1470-160X
SN - 1872-7034
ER -