Journal of Environmental Management, Год журнала: 2025, Номер 376, С. 124531 - 124531
Опубликована: Фев. 16, 2025
Язык: Английский
The Science of The Total Environment, Год журнала: 2023, Номер 873, С. 162322 - 162322
Опубликована: Фев. 18, 2023
Environmental DNA (eDNA) is the fastest growing biomonitoring tool fuelled by two key features: time efficiency and sensitivity. Technological advancements allow rapid biodiversity detection at both species community levels with increasing accuracy. Concurrently, there has been a global demand to standardise eDNA methods, but this only possible an in-depth overview of technological discussion pros cons available methods. We therefore conducted systematic literature review 407 peer-reviewed papers on aquatic published between 2012 2021. observed gradual increase in annual number publications from four (2012) 28 (2018), followed growth 124 This was mirrored tremendous diversification methods all aspects workflow. For example, freezing applied preserve filter samples, whereas we recorded 12 different preservation 2021 literature. Despite ongoing standardisation debate community, field seemingly moving fast opposite direction discuss reasons implications. Moreover, compiling largest PCR-primer database date, provide information 522 141 species-specific metabarcoding primers targeting wide range organisms. works as user-friendly 'distillation' primer that hitherto scattered across hundreds papers, list also reflects which taxa are commonly studied technology environments such fish amphibians, reveals groups corals, plankton algae under-studied. Efforts improve sampling extraction specificity reference databases crucial capture these ecologically important future surveys. In rapidly diversifying field, synthetises procedures can guide users towards best practice.
Язык: Английский
Процитировано
154
Molecular Biology and Evolution, Год журнала: 2023, Номер 40(3)
Опубликована: Фев. 28, 2023
Abstract MitoFish, MitoAnnotator, and MiFish Pipeline are comprehensive databases of fish mitochondrial genomes (mitogenomes), accurate annotation software mitogenomes, a web platform for metabarcoding analysis environmental DNA (eDNA), respectively. The MitoFish Suite currently receives over 48,000 visits worldwide every year; however, the performance usefulness online platforms can still be improved. Here, we present essential updates on these platforms, including an enrichment reference data sets, enhanced searching function, substantially faster genome eDNA with denoising sequencing errors, multisample comparative function. These have made our more intuitive, effective, reliable. updated freely available at http://mitofish.aori.u-tokyo.ac.jp/.
Язык: Английский
Процитировано
75
Environmental Advances, Год журнала: 2023, Номер 12, С. 100370 - 100370
Опубликована: Апрель 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.
Язык: Английский
Процитировано
42
Molecular Ecology, Год журнала: 2023, Номер 32(15), С. 4118 - 4132
Опубликована: Май 30, 2023
Abstract Advancements in environmental DNA (eDNA) approaches have allowed for rapid and efficient species detections diverse environments. Although most eDNA research is focused on leveraging genetic diversity to identify taxa, some recent studies explored the potential these detect within‐species variation, allowing population assessments abundance estimates from samples. However, we currently lack a framework outlining key considerations specific generating, analysing applying data two purposes. Here, discuss how various markers differ with regard information detectability samples analysis of differs common tissue‐based analyses. We then outline it may be possible obtain absolute by detecting intraspecific variation mixtures under multiple scenarios. also major causes contributing allele detection frequency errors data, their consequences population‐level analyses bioinformatic remove erroneous sequences. This review summarizes advances required harness full eDNA‐based inform questions ecology, evolutionary biology conservation management.
Язык: Английский
Процитировано
25
Diversity, Год журнала: 2025, Номер 17(1), С. 35 - 35
Опубликована: Янв. 2, 2025
Fish in the Yong River basin have been significantly impacted by pollution, habitat modification and overfishing. In order to facilitate recovery of freshwater biodiversity, a fishing ban has implemented since 2022. However, high level human activity along waterways poses significant challenge monitoring fish biodiversity using established methods. It is essential, therefore, effective tools assess effectiveness policy. this study, environmental DNA (eDNA) metabarcoding was employed species across five river sections October Additionally, we checked results against gear (drift gillnets ground cages) surveys historical records. A total twenty-two were found from eDNA metabarcoding, fourteen via fishing, only two both The most dominant identified Alburnus mossulensis, present all sections. decline observed whole basin, with difference community composition Upper Yao (UYAR) (YOR). Moreover, detected potentially invasive consistent their geographic distribution. Overall, study provide snapshot current offering baseline data for future evaluations policies ecosystem.
Язык: Английский
Процитировано
1
Journal of Ocean University of China, Год журнала: 2025, Номер 24(1), С. 217 - 228
Опубликована: Янв. 16, 2025
Язык: Английский
Процитировано
1
Molecular Ecology Resources, Год журнала: 2025, Номер unknown
Опубликована: Апрель 1, 2025
Environmental DNA (eDNA) metabarcoding technologies promise significant advances in biodiversity monitoring, yet their application requires extensive optimisation and standardisation. Recent research demonstrated that increased sampling analytical efforts are needed to improve estimates, though fully optimising study designs is often hindered by resource constraints. Consequently, researchers must carefully navigate methodological trade-offs design effective eDNA monitoring studies. We conducted a water survey of vertebrates Mediterranean watershed identify key factors influencing species richness composition estimates. examined the impacts using high- versus low-capacity filtration capsules, varying levels biological technical replication, pooling PCR replicates before indexing. The primary sources variation identified were capsule capacity site replication across watershed. While within sites also improved effects comparatively smaller. Pooling indexing performed more poorly than analysing them independently. Methodological stronger on terrestrial aquatic species. Based these results, we recommend priority should be given high-capacity multiple sites. Site-level deserves lower priority, especially when filtering large volumes. crucial for detecting rare but balanced with eventually site-level replication. Avoiding important enhance sensitivity Overall, stress importance balancing choices constraints goals, emphasise need assessing different systems.
Язык: Английский
Процитировано
1
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
Процитировано
22
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
Процитировано
17
Molecular Ecology Resources, Год журнала: 2024, Номер 24(4)
Опубликована: Фев. 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.
Язык: Английский
Процитировано
7