Predicting downstream transport distance of fish eDNA in lotic environments

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(4)

Published: Feb. 6, 2024

Abstract Environmental DNA (eDNA) is an effective tool for describing fish biodiversity in lotic environments, but the downstream transport of eDNA released by organisms makes it difficult to interpret species detection at local scale. In addition biophysical degradation and exchanges water–sediment interface, hydrological conditions control distance. A new model described this paper considers retention processes combination with hydraulic assumes that sedimentation rate very fine particles a correct estimate deposition rate. Based on meta‐analyses available studies, particle size distribution (PSD), relationship between suspension, influence temperature were successively modelled. After combining results mechanistic‐based model, uptake distances (distance required retain 63.21% riverbed) observed compilation previous experimental studies correctly simulated. negligible low flow has comparable background transfer when allow long The wide prediction intervals associated simulations reflect complexity acting after shedding. This can be useful estimating distance from source point discussing possibility false positive samples, as shown example.

Language: Английский

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Using environmental DNA metabarcoding to monitor fish communities in small rivers and large brooks: Insights on the spatial scale of information

Environmental Research, Journal Year: 2023, Volume and Issue: 228, P. 115857 - 115857

Published: April 12, 2023

Monitoring fish communities is central to the evaluation of ecological health rivers. Both presence/absence species and their relative quantity in local assemblages are crucial parameters measure. Fish lotic systems traditionally monitored via electrofishing, characterized by a known limited efficiency high survey costs. Analysis environmental DNA could serve as non-destructive alternative for detection quantification communities, but this approach still requires further insights practical sampling schemes incorporating transport dilution eDNA particles; optimization predictive power quality assurance molecular method. Via controlled cage experiment, we aim extend knowledge on streamreach small rivers large brooks, laid out European Water Framework Directive's water typology. Using low source biomass two river transects species-poor contrasting discharge rates, found strong significant correlations between abundances per community. Despite decreasing correlation over distance, underlying community composition remained stable from 25 300 m, or up 1 km downstream source, depending rate. Such decrease similarity corresponding eDNA-based profile with increasing distance might be attributed variation species-specific persistence. Our findings offer behaviour characterization riverine communities. We conclude that sampled relatively offers an adequate snapshot total 300-1000 m upstream transect. The potential application other discussed.

Language: Английский

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Combining multiple markers significantly increases the sensitivity and precision of eDNA‐based single‐species analyses

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(5), P. 1065 - 1077

Published: April 24, 2023

Abstract The analysis of environmental DNA (eDNA) is becoming integrated as an established biomonitoring tool, often characterized by detection limits exceeding those conventional counterparts. However, further improving the sensitivity these methods may be invaluable for early invasive species, or locating remnant populations endangered and adequate quantification their abundances. In this study, we provide empirical evidence showing that implementation multiple genetic markers targeting different loci a surprisingly overlooked strategy to increase single‐species detections abundance, particularly at lower end species abundance range. We analyzed 45 natural eDNA samples obtained from wide range water bodies in Belgium, which either American bullfrog ( Lithobates catesbeianus ) rare European weather loach Misgurnus fossilis occurred under variable abundances, compared success precision simplex (single locus) versus multiplex (multilocus) droplet digital PCR (ddPCR) analyses. Multiplexing primer/probe assays independent resulted significantly enhanced probability analyses, gaining twofold reduction limit (LOD). Also improved reactions, especially low concentration samples. This was reflected significant coefficient variation (CV) among technical replicates, resulting associated decrease (LOQ). conclude use can improve analytical eDNA‐based absolute quantifications.

Language: Английский

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Putting eDNA to the test: A field comparison of eDNA metabarcoding to established protocols for assessing biodiversity in Missouri's Ozark Highland streams

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(1)

Published: Jan. 1, 2024

Abstract Aquatic biodiversity monitoring to inform conservation and management efforts in‐stream systems has increasingly begun incorporate environmental DNA (eDNA)‐based sampling methods. We conducted a comparison of eDNA metabarcoding traditional protocol combined seining electrofishing methods assess fish wadeable stream sites in six separate drainages the Ozark Highlands Missouri (USA). The study further focused on headwaters Meramec River, which included 11 seasonal (summer winter). compared estimates diversity across methods, assessed influences water flow (depth, velocity, discharge) season, tested effects method site locality assemblage composition. detected approximately double number species providing higher while maintaining relative ranking sites. detection probabilities were positively associated with depth velocity generally summer than winter but not for all species. Estimated richness was discharge both relationship stronger sampling. Assemblage differences between tributary mainstem attributable small that found predominantly one size category or other, indicating sensitive within‐drainage structure relationships. highlight improved detection, more comprehensive understanding structural dynamics, potential ability integrate data as important benefits encourage use primary collection future assessment programs.

Language: Английский

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Sustainable fisheries management through reliable restocking and stock enhancement evaluation with environmental DNA

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: July 12, 2023

Abstract The practise of restocking and stock improvement as a means managing fisheries aquaculture has been widely used. However, it is difficult to claim that fish stocking effective due number challenges. One those the lack suitable monitoring assessment methods, although all approaches have their strengths weaknesses. If full benefits long-term sustainability are be realised, necessary examine effectiveness enhancement. Therefore, effective, rapid, dependable techniques necessary. In this study, we used an eDNA-based method identify G. cambodgiensis at 14 sites throughout Thailand's enhancement programme. eDNA from species was identified in water samples using quantitative polymerase chain reaction (qPCR) tests with primers probe specific . A successful would show positive results collected studied sites. Only five returned readings, which could considered stocking. locations contained were either confirmed natural habitats or regularly stocked large hatchery fish. demonstrated reliable, fast accurate alternative for measuring improvement.

Language: Английский

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Environmental DNA metabarcoding reflects spatiotemporal fish community shifts in the Scheldt estuary

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 934, P. 173242 - 173242

Published: May 17, 2024

Estuarine ecosystems face increasing anthropogenic pressures, necessitating effective monitoring methods to mitigate their impacts on the biodiversity they harbour. The use of environmental DNA (eDNA) based detection is increasingly recognized as a promising tool complement other, potentially invasive techniques. Integrating such eDNA analyses into frameworks for large still challenging and requires deeper understanding scale resolution at which patterns may offer insights in species presence community composition space time. Scheldt estuary, characterized by its diverse habitats complex currents, one largest Western European tidal river systems. Until now, it remains obtain accurate information fish communities living migrating through this ecosystem, consequently confining our knowledge specific locations. To explore potential monitoring, we simultaneously combine stow net fishing with metabarcoding, assess spatiotemporal shifts estuary's communities. In total, detected 71 estuary using partly overlapping historic data gathered different study locations contrast only 42 during same survey period. Community compositions found both varied among sampling locations, driven clear correlation salinity gradient. Limited effects depth tide were observed metabarcoding data, allowing significant reduction effort future campaigns system. Our results further demonstrate that seasonal occurrence can be metabarcoding. Combining enhances vital waterway's populations, higher more efficient strategy.

Language: Английский

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A new flow path: eDNA connecting hydrology and biology

Wiley Interdisciplinary Reviews Water, Journal Year: 2024, Volume and Issue: 11(6)

Published: July 29, 2024

Abstract Environmental DNA (eDNA) has revolutionized ecological research, particularly for biodiversity assessment in various environments, most notably aquatic media. analysis allows non‐invasive and rapid species detection across multiple taxonomic groups within a single sample, making it especially useful identifying rare or invasive species. Due to dynamic hydrological processes, eDNA samples from running waters may represent broad contributing areas, which is convenient biomonitoring perspective but also challenging, as knowledge required meaningful biological interpretation. Hydrologists could benefit address unsolved questions, concerning water movement through catchments. While naturally occurring abiotic tracers have advanced our understanding of age distribution catchments, example, current geochemical cannot fully elucidate the timing flow paths landscapes. Conversely, tracers, owing their immense diversity interactions with environment, offer more detailed information on sources stream. The informational capacity tracer, however, determined by ability interpret complex heterogeneity at study site, arguably requires both expertise. As data become increasingly available part campaigns, we argue that accompanying surveys observations enhance processes; identify opportunities, challenges, needs further interdisciplinary collaboration; highlight eDNA's potential bridge between hydrology biology, foster domains. This article categorized under: Science Water > Hydrological Processes Methods Life Nature Freshwater Ecosystems

Language: Английский

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eDNA-based seasonal monitoring reveals fish diversity patterns in mangrove habitats of Guinea-Bissau

Regional Studies in Marine Science, Journal Year: 2025, Volume and Issue: unknown, P. 104013 - 104013

Published: Jan. 1, 2025

Language: Английский

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Freshwater fish community assessment using eDNA metabarcoding vs. capture-based methods: differences in efficiency and resolution coupled to habitat and ecology

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

Published: Jan. 10, 2025

Abstract Environmental DNA (eDNA) metabarcoding has revolutionized ecological and environmental research by describing communities without relying on direct observations, making it a powerful, non-invasive, cost-effective tool in biodiversity monitoring. However, implementation of eDNA as standard protocol long-term monitoring programs, that have traditionally relied capture-based methods, poses challenges terms data comparability. Here, we compared freshwater fish assessed through electrofishing, across 35 sampling sites the lower Tagus River basin, Portugal. For most species or species-groups analyzed individually (13 out 17), there was significant correspondence between electrofishing detections. The weaker when comparing number specimens captured with reads, seven 13 taxa showing relationships. Species richness estimates based two methods were very similar at basin level. yielded significantly different compositions, although these differences driven samples collected main channel, which is wider higher flow rates than tributaries. Benthic shoreline showed composition but this not case for pelagic communities, probably due to water turnover zone inefficiency. Our results highlight high potential complementary method monitoring, though further validation needed assess biases related site-specific hydrological conditions ecology target species.

Language: Английский

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International aquatic invasive species early detection efforts in the St. Clair-Detroit River System: A decadal review

Journal of Great Lakes Research, Journal Year: 2025, Volume and Issue: unknown, P. 102531 - 102531

Published: Feb. 1, 2025

Language: Английский

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