A Hierarchical Model for eDNA Fate and Transport Dynamics Accommodating Low Concentration Samples DOI Creative Commons
Ben C. Augustine, Patrick R. Hutchins, Devin N. Jones

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 2, 2024

Abstract Environmental DNA (eDNA) sampling is an increasingly important tool for answering ecological questions and informing aquatic species management; however, several factors currently limit the reliability of inference from eDNA sampling. Two particular challenges are 1) determining source location(s) 2) accurately precisely measuring low concentration samples in presence multiple sources measurement variability. The recently introduced Integrating Transport Hydrology (eDITH) model provides a framework relating measurements to locations riverine networks, but little empirical work has been done test refine assumptions or accommodate samples, that can be systematically undermeasured. To better understand fate transport dynamics our ability reliably quantify we developed hierarchical used it evaluate experiment. Our addresses by modeling number copies each PCR replicate as latent variable with count distribution conditioning detection quantification on copy number. We provide evidence removal rate declined through time, estimating over 80% was removed first 10 meters, traversed 41 seconds. After this initial period rapid decay, decayed slowly consistent farthest site 1km release location, 250 further allowed us detect extra-Poisson variation allocation replicates. extended continuous effect inhibitors inhibitor hypothesis explore potential implications. While not panacea all faced when quantifying low-concentration more complete accounting uncertainty.

Language: Английский

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward DOI
Meng Yao, Shan Zhang, Qi Lu

et al.

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(20), P. 5132 - 5164

Published: Aug. 16, 2022

Abstract Vast global declines of freshwater and marine fish diversity population abundance pose serious threats to both ecosystem sustainability human livelihoods. Environmental DNA (eDNA)‐based biomonitoring provides robust, efficient, cost‐effective assessment species occurrences trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks facilitate conservation fisheries management. However, the many technical considerations rapid developments underway eDNA arena can overwhelm researchers practitioners new field. Here, we systematically analysed 416 studies summarize research terms investigated targets, aims, study systems, reviewed applications, rationales, methodological considerations, limitations methods with an emphasis on research. We highlighted how technology may advance our knowledge behaviour, distributions, genetics, community structures, ecological interactions. also synthesized current several important concerns, including qualitative quantitative power has recover biodiversity abundance, spatial temporal representations respect its sources. To applications implementing techniques, recent literature was summarized generate guidelines effective sampling lentic, lotic, habitats. Finally, identified gaps limitations, pointed out newly emerging avenues eDNA. As optimization standardization improve, should revolutionize monitoring promote management that transcends geographic boundaries.

Language: Английский

Citations

107
Environmental DNA: The next chapter DOI Creative Commons
Rosetta C. Blackman, Marjorie Couton, François Keck

et al.

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(11)

Published: April 16, 2024

Abstract Molecular tools are an indispensable part of ecology and biodiversity sciences implemented across all biomes. About a decade ago, the use implementation environmental DNA (eDNA) to detect signals extracted from samples opened new avenues research. Initial eDNA research focused on understanding population dynamics target species. Its scope thereafter broadened, uncovering previously unrecorded via metabarcoding in both well‐studied understudied ecosystems taxonomic groups. The application rapidly became established research, field by its own. Here, we revisit key expectations made land‐mark special issue Ecology 2012 frame development six areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour environment (6) reference database development. We pinpoint success eDNA, yet also discuss shortfalls not met, highlighting areas priority identify unexpected developments. In parallel, our retrospective couples screening peer‐reviewed literature with survey users including academics, end‐users commercial providers, which address focus efforts advance eDNA. With rapid ever‐increasing pace technical advances, future looks bright, successful applications best practices must become more interdisciplinary reach full potential. Our retrospect gives towards concretely moving forward.

Language: Английский

Citations

26
Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis DOI
Toshiaki Jo

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2023, Volume and Issue: 290(1999)

Published: May 30, 2023

Environmental DNA (eDNA) analysis allows cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial aquatic environments. However, the eDNA results can sometimes include false-positive inferences of target organisms owing to aged that has long since been released from individual is more likely be detected at site further away its source. In order address issue, this manuscript focuses on state eDNA, proposing new methodologies estimate age eDNA: (1) damage rate, (2) particle size distribution, (3) viable cell-derived eDNA. addition, also shorter persistence environmental RNA (eRNA) compared highlighting application eRNA nucleic acid ratio for assessing genetic materials water. Although substantial research essential support feasibility these methodologies, incorporating time-scale information into would update current analysis, improve accuracy reliability eDNA-based monitoring, refine as useful monitoring tool ecology, fisheries various sciences.

Language: Английский

Citations

22
Environmental DNA (eDNA) removal rates in streams differ by particle size under varying substrate and light conditions DOI Creative Commons
Elise D. Snyder, Jennifer L. Tank, Pedro F. P. Brandão‐Dias

et al.

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 903, P. 166469 - 166469

Published: Aug. 24, 2023

Language: Английский

Citations

22
Sorting states of environmental DNA: Effects of isolation method and water matrix on the recovery of membrane‐bound, dissolved, and adsorbed states of eDNA DOI Creative Commons
Anish Kirtane, Hannah Kleyer, Kristy Deiner

et al.

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(3), P. 582 - 596

Published: April 10, 2023

Abstract Environmental DNA (eDNA) once shed can exist in numerous states with varying behaviors including degradation rates and transport potential. In this study, we consider three of eDNA: (1) a membrane‐bound state referring to enveloped cellular or organellar membrane, (2) dissolved defined as the extracellular molecule environment without any interaction other particles, (3) an adsorbed particle surface environment. Capturing, isolating, analyzing target eDNA provides utility for better interpretation While methods separating different have been developed, they remain poorly evaluated due lack state‐controlled experimentation. We from single sample by spiking species represent state‐specific controls. used chicken state, cultured mouse cells salmon clay particles state. performed separation water matrices, two environmental one synthetic, spiked states. The was only that isolated minimal contamination nontarget also had highest recovery (54.11 ± 19.24%), followed (5.08 2.28%), lowest total (2.21 2.36%). This study highlights potential sort independently analyze them more informed biodiversity assessments. However, further method development is needed improve reduce cross‐contamination.

Language: Английский

Citations

19
Fish community traits near a large confluence: Implications for its nodal effects in the river ecosystem DOI Creative Commons
Saiyu Yuan, Jiajian Qiu,

Hongwu Tang

et al.

Journal of Hydrology, Journal Year: 2023, Volume and Issue: 626, P. 130335 - 130335

Published: Oct. 16, 2023

River confluences are nodes where the unique hydrological processes of two rivers meet, resulting in complex flow structure and water quality mixing processes. Thus, greater food availability habitat complexity can occur at a confluence, making it hotspot for fish productivity diversity. Nonetheless, studies that relate community traits to specific characteristics large river limited. Two field surveys were conducted confluence between Yangtze Poyang Lake outflow channel involving hydroacoustic detection, environmental DNA, acoustic velocity profiling. The discharge ratios this similar, but conditions represented by turbidity differed greatly. results demonstrated high spatial heterogeneity density, size, species near confluence. In with velocity, abundance small-sized was substantially higher than low while large-sized chose their habitats more freely tributaries post-confluence channel. convergence created prominent channel, thus highest biodiversity occurred there. assemblage local greatly affected change quality, e.g., intrusion turbid from into River, exchange communities weakened. present study highlights ecological importance improving regional diversity provides theoretical foundation conservation management aquatic environment whole ecosystem.

Language: Английский

Citations

19
Predicting downstream transport distance of fish eDNA in lotic environments DOI Creative Commons
Didier Pont

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

Citations

8
An overlooked source of false positives in eDNA-based biodiversity assessment and management DOI
Wei Xiong, Hugh J. MacIsaac, Aibin Zhan

et al.

Journal of Environmental Management, Journal Year: 2024, Volume and Issue: 358, P. 120949 - 120949

Published: April 23, 2024

Language: Английский

Citations

6
A comparison of seasonal composition and structure of fish community between environmental DNA technology and gillnetting in the Pearl River Estuary, China DOI Creative Commons
Zhuoying Li, Peiwen Jiang,

Longxin Wang

et al.

Ecological Indicators, Journal Year: 2023, Volume and Issue: 147, P. 109915 - 109915

Published: Jan. 25, 2023

Non-destructive and cost-effective fish diversity monitoring approaches are needed for the management protection of estuarine ecosystems. Environmental DNA (eDNA) technology is a promising, environmentally friendly that has been applied in studies In this study, we investigated seasonal composition, diversity, structure community Pearl River Estuary (PRE) using eDNA gillnetting. We identified 156 PRE, including 26 orders, 58 families, 93 genera, 115 species according to technology. And provided more taxonomic composition information PRE than did Significant or highly significant differences were detected between wet dry seasons. Fifteen eight genus-level indicator taxa differed significantly two seasons gillnetting, respectively. However, study suggest some not overlap approaches. Therefore, should include combination gillnetting comprehensive data analysis. Our findings have important implications ecosystem management.

Language: Английский

Citations

15
Habitat suitability models reveal the spatial signal of environmental DNA in riverine networks DOI Creative Commons
Jeanine Brantschen, Fabian Fopp, Antoine Adde

et al.

Ecography, Journal Year: 2024, Volume and Issue: 2024(8)

Published: May 30, 2024

The rapid loss of biodiversity in freshwater systems asks for a robust and spatially explicit understanding species' occurrences. As two complementing approaches, habitat suitability models provide information about potential occurrence, while environmental DNA (eDNA) based assessments indication actual occurrence. Individually, both approaches are used ecological studies to characterize biodiversity, yet they rarely combined. Here, we integrated high‐resolution with eDNA‐based aquatic invertebrates riverine networks understand their individual combined capacity inform on We eDNA sampling data from 172 river sites the detection taxa three insect orders (Ephemeroptera, Plecoptera, Trichoptera; hereafter EPT) suitable predictions at subcatchment level (2 km 2 ). Overall, find congruence detections. Yet, predicted habitats beyond number detections by sampling, congruent niche being larger than realized niche. For local mismatches, where detected species but was not suitable, calculated minimal distance upstream patches, indicating possible sources signals subsequently transported along water flow. estimated median 1.06 (range 0.2–42 km) transport suitability, this significantly smaller expected null model predictions. This is range previously reported values allows extrapolations distances across many systems. Together, combination scale integrative inferences ultimately needed management protection biodiversity.

Language: Английский

Citations

5