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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Harnessing decay rates for coastal marine biosecurity applications: A review of environmental DNA and RNA fate

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(5), P. 960 - 972

Published: March 30, 2023

Abstract Marine nonindigenous species (NIS) are spreading at an alarming rate internationally through anthropogenic activities such as shipping and aquaculture, affecting local biodiversity negatively impacting the ecosystem human well‐being. Countries international organizations have recognized this global threat begun implementing biosecurity management programs to ensure early detection, effective surveillance, mitigation of marine NIS spread. Molecular techniques based on environmental DNA RNA (eDNA/eRNA), collectively referred nucleic acids (eNAs), become a popular noninvasive tool for detecting monitoring locally globally. However, uncertainties about eNAs detection probabilities location source population impede broad uptake in programs. It's been hypothesized that most these can be explained by studying molecules' dynamics within environment distribution models. To contribute further knowledge development area, our study reviews data from 20 recent reports degradation mechanisms fate environment. We classified critical factors influencing eNAs' persistence should considered practitioners, outlining complex interaction between processes particular conditions. help guide parameterization models, review also summarizes standardizes decay rates eDNA/eRNA literature. Finally, manuscript outlines guidelines calculate accurate build appropriate “fit‐for‐purpose” tools improved target detectability greater resolution assessing biodiversity.

Language: Английский

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Measuring the state of aquatic environments using eDNA—upscaling spatial resolution of biotic indices

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1904)

Published: May 5, 2024

Aquatic macroinvertebrates, including many aquatic insect orders, are a diverse and ecologically relevant organismal group yet they strongly affected by anthropogenic activities. As of these taxa highly sensitive to environmental change, offer particularly good early warning system for human-induced thus leading their intense monitoring. In ecosystems there is plethora biotic monitoring or biomonitoring approaches, with more than 300 assessment methods reported freshwater alone. Ultimately, macroinvertebrates used calculate ecological indices describing the state systems. Many not only hard compare, but especially difficult scale in time space. Novel DNA-based approaches measure change environments now unprecedented opportunities, also possible integration towards commonly applicable indices. Here, we first give perspective on organisms, focus insects, how move beyond traditional point-based Second, demonstrate proof-of-concept spatially upscaling based DNA, demonstrating novel molecular hydrological models allows an accurate evaluation at catchment scale. This article part theme issue ‘Towards toolkit global biodiversity monitoring’.

Language: Английский

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Comparing eDNA and eRNA Sampling Methodologies From Pond Environments

Aquatic Conservation Marine and Freshwater Ecosystems, Journal Year: 2025, Volume and Issue: 35(2)

Published: Feb. 1, 2025

ABSTRACT Molecular traces are increasingly being applied to assess the presence of species and communities. Studies on environmental DNA (eDNA) have, a large extent, become common practice in detection, but less studies have compared biodiversity estimations with more temporary RNA (eRNA). This study compares metabarcoding results from pond water obtained both molecule types by sequencing V4 region 18S rRNA marker. Water was collected two depths, 20 80 cm, filtered sequentially through filter porosities, 0.45 0.22 μm. Each cut half before fixation either 96% ETOH or RNAlater. The showed no differences between fixatives for molecule. Overall, estimates eDNA significantly overperformed eRNA, likely due higher concentrations terrestrial sources. Comparisons depths variation only, increasing levels found at upper layer. Both pore sizes captured distinctive compositions taxa, where about 30% diversity uniquely identified second, finer filter. Taken together, these findings imply that choice molecular marker, depth size affects pond.

Language: Английский

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Biodiversity Monitoring in Remote Marine Environments: Advancing Environmental DNA/RNA Sampling Workflows

Marine Environmental Research, Journal Year: 2025, Volume and Issue: 206, P. 107041 - 107041

Published: Feb. 26, 2025

Language: Английский

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Sediment Toxicity Tests: A Critical Review of Their use in Environmental Regulations

Environmental Toxicology and Chemistry, Journal Year: 2024, Volume and Issue: 43(8), P. 1697 - 1716

Published: April 10, 2024

Sediments are an integral component of aquatic systems, linking multiple water uses, functions, and services. Contamination sediments by chemicals is a worldwide problem, with many jurisdictions trying to prevent future pollution (prospective) manage existing contamination (retrospective). The present review assesses the implementation sediment toxicity testing in environmental regulations globally. Currently, incorporation most common European Union (EU), North America, Australasian regions, some expansion Asia non-EU Europe. Employing prospective assessments (i.e., before allowed on market) advanced harmonized pesticides. In retrospective assessment risks already contaminating sediments), regulatory practices applied inconsistently global scale. International harmonization tests considered asset has been successful through widespread adoption deployment Organisation for Economic Co-operation Development guidelines. On other hand, benefit from incorporating regional species protocols. Currently used diverse, temperate being often, whereas test protocols insufficiently flexible appropriately address range contaminants, including nanomaterials, highly hydrophobic ionized chemicals. ever-increasing -changing pressures placed resources challenge protection management efforts, calling continuous method improvement insure effective use frameworks. Future developments should focus more subtle specific endpoints (e.g., bioavailability-based vitro tests) genomic techniques, extending single multispecies approaches, providing better link ecological goals. Environ Toxicol Chem 2024;43:1697-1716. © 2024 Authors. Environmental Toxicology Chemistry published Wiley Periodicals LLC behalf SETAC.

Language: Английский

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Evaluating eDNA and eRNA metabarcoding for aquatic biodiversity assessment: From bacteria to vertebrates

Environmental Science and Ecotechnology, Journal Year: 2024, Volume and Issue: 21, P. 100441 - 100441

Published: June 12, 2024

The monitoring and management of aquatic ecosystems depend on precise estimates biodiversity. Metabarcoding analyses environmental nucleic acids (eNAs), including DNA (eDNA) RNA (eRNA), have garnered attention for their cost-effective non-invasive biomonitoring capabilities. However, the accuracy biodiversity obtained through eNAs can vary among different organismal groups. Here we evaluate performance eDNA eRNA metabarcoding across nine groups, ranging from bacteria to terrestrial vertebrates, in three cross-sections Yangtze River, China. We observe robust complementarity between data. relative detectability was notably influenced by major taxonomic groups sizes, with providing more signals larger organisms. Both exhibited similar cross-sectional longitudinal patterns. organisms declined metabarcoding, possibly due differential release decay or sizes. While underscoring potential large river biomonitoring, emphasize need interpretation versus This highlights importance careful method selection studies.

Language: Английский

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Environmental RNA as a Noninvasive Tool for Assessing Toxic Effects in Fish: A Proof-of-concept Study Using Japanese Medaka Exposed to Pyrene

Environmental Science & Technology, Journal Year: 2023, Volume and Issue: 57(34), P. 12654 - 12662

Published: Aug. 16, 2023

Although environmental RNA (eRNA) is emerging as a noninvasive tool to assess the health status of aquatic macroorganisms, potential eRNA in assessing chemical hazards remain largely untested. In this study, we investigated ability detect changes gene expression Japanese medaka fish (Oryzias latipes) response sublethal pyrene exposure, model toxic chemical. We performed standardized acute toxicity tests and collected from tank water tissue after 96 h exposure. Our results showed that over 1000 genes were detected sequenced read counts these correlated with those (r = 0.50). Moreover, 86 differentially expressed pyrene, some which shared by RNA, including suppression collagen fiber genes. These suggest has stressors without need for sacrificing or causing pain fish. However, also found majority reads (>99%) not mapped reference genome they originated bacteria fungi, resulting low sequencing depth. addition, eRNA, particular nuclear genes, was highly degraded median transcript integrity number (TIN) <20. limitations highlight future studies improve analytical methods application.

Language: Английский

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Future-proofing environmental DNA and trait-based predictions of food webs

BioScience, Journal Year: 2023, Volume and Issue: 73(12), P. 862 - 878

Published: Nov. 1, 2023

Abstract Food webs represent trophic interactions within ecosystems. Matching traits of consumers and resources helps infer food-web properties. Environmental (e)DNA, commonly used for detecting species occurrences, is rarely in trait-matching studies because abundance estimates descriptions relevant are generally missing. We synthesized recent literature on inferences with eDNA trait matching to identify challenges opportunities coupled eDNA–trait recording schemes. Our case study shows how coupling data collection improves the ability characterize greater numbers food across multiple scales ranging from spatiotemporal variation. Future-proofing sets requires new or compilation existing at that detect current future changes

Language: Английский

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New prospects of environmental RNA metabarcoding research in biological diversity, ecotoxicological monitoring, and detection of COVID-19: a critical review

Environmental Science and Pollution Research, Journal Year: 2024, Volume and Issue: 31(8), P. 11406 - 11427

Published: Jan. 6, 2024

Language: Английский

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