Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Molecular Ecology, Год журнала: 2022, Номер 31(20), С. 5132 - 5164

Опубликована: Авг. 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.

Язык: Английский

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Environmental DNA/RNA for pathogen and parasite detection, surveillance, and ecology

Trends in Parasitology, Год журнала: 2023, Номер 39(4), С. 285 - 304

Опубликована: Фев. 8, 2023

Язык: Английский

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

Environmental DNA, Год журнала: 2023, Номер 5(5), С. 960 - 972

Опубликована: Март 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.

Язык: Английский

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

Proceedings of the Royal Society B Biological Sciences, Год журнала: 2023, Номер 290(1999)

Опубликована: Май 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.

Язык: Английский

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Environmental DNA methods for biosecurity and invasion biology in terrestrial ecosystems: Progress, pitfalls, and prospects

The Science of The Total Environment, Год журнала: 2024, Номер 926, С. 171810 - 171810

Опубликована: Март 19, 2024

Язык: Английский

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Utilizing aquatic environmental DNA to address global biodiversity targets

Опубликована: Апрель 27, 2025

Язык: Английский

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Environmental nucleic acids: A field‐based comparison for monitoring freshwater habitats using eDNA and eRNA

Molecular Ecology Resources, Год журнала: 2022, Номер 22(8), С. 2928 - 2940

Опубликована: Июнь 22, 2022

Abstract Nucleic acids released by organisms and isolated from environmental substrates are increasingly being used for molecular biomonitoring. While DNA (eDNA) has received much attention, the potential of RNA as a biomonitoring tool remains under‐explored. Several recent studies using paired metabarcoding bulk samples suggest that might better reflect “metabolically active” parts community. However, such mainly capture organismal eDNA eRNA. For larger eukaryotes, isolation extra‐organismal will be important, but viability needs to examined in field‐based setting. In this study we evaluate (a) whether eRNA release macroeukaryotes can detected given its supposedly rapid degradation, (b) if same field collection methods applied We collected water lakes where fish community composition is well documented, enabling comparison between two nucleic different seasons with monitoring conventional methods. found filtered metabarcoded similar manner reliably provide species information. had small significantly greater true positive rate than eDNA, indicating it correctly detects more known exist lakes. Given relatively differences molecules describing composition, conclude provides significant advantages terms lability, strong candidate add suite tools.

Язык: Английский

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

Environmental Science and Ecotechnology, Год журнала: 2024, Номер 21, С. 100441 - 100441

Опубликована: Июнь 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.

Язык: Английский

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Environmental DNA and RNA in aquatic community ecology: Toward methodological standardization

Environmental DNA, Год журнала: 2023, Номер 5(6), С. 1133 - 1147

Опубликована: Сен. 28, 2023

Abstract Molecular technologies have facilitated the expansion of biodiversity assessments across a broad range organisms and aquatic systems. Environmental DNA (eDNA) environmental RNA (eRNA), collectively referred to as nucleic acids (eNAs), revolutionized monitoring due their noninvasive nature high‐resolution capabilities when compared traditional survey methods. While eNA applications grown exponentially over past decade, methodological inconsistencies hinder reproducibility comparability. To assess current state methodologies in ecology, we conducted systematic review 300 peer‐reviewed studies that ecological communities diverse Of these papers, 291 examine eDNA, four eRNA, five consider both eDNA eRNA. The small number eRNA highlights field is its infancy. looked at, found clear geographic bias, with approximately 50% all occurring six high‐income countries, while less than 10% occur South America Africa. Further, report lack standardization studies, showing high variability water filtration volume, filter material, pore size, extraction method, marker choice, bioinformatic pipelines. We further highlight incomplete reference sequence databases for limit taxonomic assignment inferences. Finally, identify issue community ecology: missing details, which compromise reproducibility, especially newly emerging applications. facilitate systems permit integration monitoring, recommend improvement alongside guidelines encourage transparency.

Язык: 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, Год журнала: 2023, Номер 57(34), С. 12654 - 12662

Опубликована: Авг. 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.

Язык: Английский

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