Applications of environmental DNA (eDNA) to detect subterranean and aquatic invasive species: A critical review on the challenges and limitations of eDNA metabarcoding

Environmental Advances, Journal Year: 2023, Volume and Issue: 12, P. 100370 - 100370

Published: April 19, 2023

The world is struggling to solve a devastating biodiversity loss that not only affects the extinction of treasured species and irreplaceable genetic variation, but also jeopardizes food production, health, safety people. All initiatives aimed conserve rely heavily on monitoring both populations get accurate spatial patterns overall population assessments. Conventional techniques, such as visual surveys counting individuals, are problematic due challenges in identifying cryptic or immature life stages. Environmental DNA (eDNA) relatively new technology has potential be faster, non-invasive, cost-effective tool for biodiversity, conservation, management practices. eDNA been extracted from materials ancient present, its applications range identification individual study entire ecosystems. In past few years, there substantial increase usage research pertaining ecological preservation conservation. However, several technological problems still need solved. To reduce number false positives and/or negatives produced by current technologies, it necessary improve optimize calibration validation at every stage procedure. There significant greater information about physical constraints use, well synthesis, state, expected lifespan, modes movement. Due widespread use research, essential assess extent breadth these studies. this article, we critically reviewed primary subterranean aquatic invasive species. Through review, readers can better understand limitations metabarcoding.

Language: Английский

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The Application of eDNA for Monitoring Aquatic Non-Indigenous Species: Practical and Policy Considerations

Diversity, Journal Year: 2023, Volume and Issue: 15(5), P. 631 - 631

Published: May 6, 2023

Aquatic non-indigenous species (NIS) threaten biodiversity, ecosystem functions, and the economy worldwide. Monitoring NIS is of immediate concern to identify newly arriving species, assess efficacy mitigation measures, report long-term indicators introduction, spread, impacts. The challenges associated with conventional methods specimen collection morphological identification have led development alternative methods, such as DNA-based which could offer rapid cost-effective detection NIS. Depending on whether a few (targeted monitoring) or many (passive are being monitored, environmental DNA (eDNA) can infer presence-absence relative abundances, enabling informed decisions actions be made based patterns detection. Compared more eDNA tools increase levels sensitivity for rare elusive even noticeable some taxa when using targeted monitoring. use not only minimizes onus taxonomic expertise reduces resource demands but also sensitive cost-efficient in detecting NIS, thus proving its value an early warning tool. As nucleic acid (DNA/RNA) advance rapidly detection, there must balance between method sensitivity, logistical requirements, costs, factored into future management decisions. While complementary reviews available, our aim emphasize importance incorporating surveys highlight available opportunities this field.

Language: Английский

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eDNA metabarcoding reveals the role of habitat specialization and spatial and environmental variability in shaping diversity patterns of fish metacommunities

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(1), P. e0296310 - e0296310

Published: Jan. 2, 2024

Information is scarce on how environmental and dispersal processes interact with biological features of the organisms, such as their habitat affinity, to influence patterns in biodiversity. We examined role specialist vs. generalist species, spatial configuration, connectivity, different characteristics river-floodplain habitats get a more mechanistic understanding alpha beta diversity fish metacommunities. used DNA metabarcoding characterize species (taxa) richness composition two separate floodplains river Danube (Austria Hungary) during hydrological conditions. Results showed that differences number responses connectivity gradients influenced diversity. Of components diversity, difference (nestedness) consistently higher values than replacement (turnover), mainly due decrease along gradient (i.e., from mainstem most isolated oxbows). Variance both could be well predicted by set local regional variables, despite high variability, which characterizes ecosystems. these, joint or shared variance fractions proved important, indicates effects cannot unambiguously separated these systems. Local scale variables were important determinants low water period period. These results indicate differential community organization Maintenance are thus preservation floodplain metacommunities, should considered management.

Language: Английский

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Signal and noise in metabarcoding data

PLoS ONE, Journal Year: 2023, Volume and Issue: 18(5), P. e0285674 - e0285674

Published: May 11, 2023

Metabarcoding is a powerful molecular tool for simultaneously surveying hundreds to thousands of species from single sample, underpinning microbiome and environmental DNA (eDNA) methods. Deriving quantitative estimates underlying biological communities metabarcoding critical enhancing the utility such approaches health conservation. Recent work has demonstrated that correcting amplification biases in genetic data can yield template concentrations. However, major source uncertainty stems non-detections across technical PCR replicates where one replicate fails detect observed other replicates. Such are special case variability among data. While many sampling processes underlie variation data, understanding causes an important step distinguishing signal noise studies. Here, we use both simulated empirical 1) suggest how may arise 2) outline steps recognize uninformative practice, 3) identify conditions under which amplicon sequence reliably signals. We show with simulations that, given species, rate function concentration species-specific efficiency. Consequently, conclude datasets strongly affected by (1) deterministic during (2) stochastic amplicons sequencing-both model-but also (3) rare molecules prior PCR, remains frontier metabarcoding. Our results highlight importance estimating efficiencies critically evaluating patterns non-detection better distinguish inherent detections targets.

Language: Английский

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Linking antibiotic resistance gene patterns with advanced faecal pollution assessment and environmental key parameters along 2300 km of the Danube River

Water Research, Journal Year: 2024, Volume and Issue: 252, P. 121244 - 121244

Published: Jan. 31, 2024

The global spread of antimicrobial resistance (AMR) in the environment is a growing health threat. Large rivers are particular concern as they highly impacted by wastewater discharge while being vital lifelines serving various human needs. A comprehensive understanding occurrence, and key drivers AMR along whole river courses largely lacking. We provide holistic approach studying spatiotemporal patterns hotspots antibiotic genes (ARGs) 2311 km navigable Danube River, combining longitudinal temporal monitoring campaign. integration advanced faecal pollution diagnostics environmental chemical parameters allowed linking ARG concentrations to major sources explaining observed patterns. Nine markers, including conferring five different classes clinical relevance, one integrase gene were determined probe-based qPCR. All targets could be quantified River water, with intI1 sul1 ubiquitously abundant, qnrS, tetM, blaTEM intermediate abundance blaOXA-48like, blaCTX-M-1group, blaCTX-M-9group blaKPC rare occurrence. Human from municipal discharges was dominant factor shaping River. Other significant correlations specific ARGs discharge, certain metals pesticides. In contrast, not associated but already established water microbiome. Animal contamination detected only sporadically correlated sampling set. During monitoring, an extraordinary hotspot identified emphasizing variability within natural waters. This study provides first baseline lays foundation for future trends evaluating potential reduction measures. applided proved valuable methodological contribution towards better occurrence AMR.

Language: Английский

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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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Predicting trawl catches using environmental DNA

ICES Journal of Marine Science, Journal Year: 2024, Volume and Issue: 81(8), P. 1536 - 1548

Published: Aug. 7, 2024

Abstract Quantifying the biomass, or number of individuals, diversity, and distribution marine species is a critical aspect understanding managing ecosystems. In recent years, there has been growing interest in using environmental DNA (eDNA) for ecosystem management biodiversity assessment. However, main challenge hindering eDNA applicability inability to infer absolute abundances from multispecies analysis (eDNA metabarcoding). this study, we demonstrate way forward by estimating abundance commercially important fish Norwegian fjord joint Bayesian statistical model traditional trawl-catch data molecular derived eDNA. Using model, accurately predict out-of-sample trawl catches alone. Moreover, our provides empirical estimates key processes linking concentration population estimated observations, including catchability, shedding, degradation, dilution, transport, recovery rate, isolation efficiency. These processes, amplification efficiencies correcting Polymerase Chain Reaction (PCR) bias, are species-specific enable translation metabarcoding into abundances. findings have broad implications use conservation efforts.

Language: Английский

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Considerations for first field trials of low-threshold gene drive for malaria vector control

Malaria Journal, Journal Year: 2024, Volume and Issue: 23(1)

Published: May 21, 2024

Sustainable reductions in African malaria transmission require innovative tools for mosquito control. One proposal involves the use of low-threshold gene drive Anopheles vector species, where a 'causal pathway' would be initiated by (i) release system target leading to (ii) its subsequent generations, (iii) increase frequency and spread populations, (iv) simultaneous propagation linked genetic trait aimed at reducing vectorial capacity Plasmodium, (v) reduced parasites populations as reaches fixation causing (vi) decreased incidence prevalence. Here scope, objectives, trial design elements, approaches monitoring initial field releases such dive systems are considered, informed successful implementation trials biological control agents, well other tools, including insecticides, Wolbachia, larvicides, attractive-toxic sugar bait systems. Specific research questions addressed identified, adaptive is explored potentially constructive flexible approach facilitate testing causal pathway. A fundamental question decision-makers first will whether there should selective focus on earlier points pathway, efficacy via measurement or wider interrogation entire pathway entomological epidemiological efficacy. How when eventually assessed an essential consideration before decisions any protocols finalized implemented, regardless exclusively efficacy, broader aspects Statistical modelling currently under active development inform design, locations, endpoints. Collectively, considerations here advance realization developer ambitions within next 5 years.

Language: Английский

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Ultra-sensitive detection of ecologically rare fish from eDNA samples based on the RPA-CRISPR/Cas12a technology

iScience, Journal Year: 2023, Volume and Issue: 26(9), P. 107519 - 107519

Published: Aug. 3, 2023

Environmental DNA (eDNA) research holds great promise for improving biodiversity science and conservation efforts by enabling worldwide species censuses in near real-time. Current eDNA methods face challenges detecting low-abundance ecologically important species. In this study, we used isothermal recombinase polymerase amplification (RPA)-CRISPR/Cas detection to test Ctenopharyngodon idella. RPA-CRISPR-Cas12a detected 6.0 copies/μL within 35 min. Ecologically rare were identified the Three Gorges Reservoir Area (TGRA) using functional distinctiveness geographical restrictiveness, with seven fish (9%) classified as potentially including three investigation. RPA-CRISPR/Cas12a-FQ outperformed high-throughput sequencing (HTS) qPCR (AUC = 0.883∗∗). A significant linear correlation (R2 0.682∗∗) between HTS quantification suggests its potential predicting abundance enhancing eDNA-based monitoring. This study highlights value of a tool advancing efforts.

Language: Английский

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Environmental DNA complements scientific trawling in surveys of marine fish biodiversity

ICES Journal of Marine Science, Journal Year: 2023, Volume and Issue: 80(8), P. 2150 - 2165

Published: Aug. 22, 2023

Abstract Environmental DNA (eDNA) metabarcoding is a method to detect taxa from environmental samples. It increasingly used for marine biodiversity surveys. As it only requires water collection, eDNA less invasive than scientific trawling and might be more cost effective. Here, we analysed data both sampling methods applied in the same survey targeting Northeast Atlantic fish Bay of Biscay. We compared regarding distribution taxonomic, phylogenetic, functional diversity. found that captured taxonomic phylogenetic richness bottom at local scale. was selective detected species communities spanning larger breadths, especially as large pelagic escaped trawl, even though flat fish. indicated differences community composition were comparable those based on trawling. However, consistency between abundance estimates provided by trawl catches low, after accounting allometric scaling production. conclude promising can complement multi-component monitoring presence/absence, but not yet abundance.

Language: Английский

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