Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution

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

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Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities

Annual Review of Marine Science, Год журнала: 2021, Номер 14(1), С. 161 - 185

Опубликована: Авг. 5, 2021

Environmental DNA (eDNA) is genetic material that has been shed from macroorganisms. It received increased attention as an indirect marker for biodiversity monitoring. This article reviews the current status of eDNA metabarcoding (simultaneous detection multiple species) a noninvasive and cost-effective approach monitoring marine fish communities discusses prospects this growing field. coamplifies short fragments across wide variety taxa and, coupled with high-throughput sequencing technologies, allows massively parallel to be performed simultaneously dozens hundreds samples. can predict species richness in given area, detect habitat segregation biogeographic patterns small large spatial scales, monitor spatiotemporal dynamics communities. In addition, it anthropogenic impact on through evaluation their functional diversity. Recognizing strengths limitations will help ensure continuous at sites useful ecosystem conservation sustainable use fishery resources, possibly contributing achieving targets United Nations' Sustainable Development Goal 14 2030.

Язык: Английский

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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, 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

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eDNA metabarcoding detection of nearshore juvenile white sharks (Carcharodon carcharias) and prey fish communities

Journal of Experimental Marine Biology and Ecology, Год журнала: 2025, Номер 583, С. 152084 - 152084

Опубликована: Янв. 31, 2025

Язык: Английский

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Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem

Molecular Ecology Resources, Год журнала: 2021, Номер 21(7), С. 2546 - 2564

Опубликована: Июль 8, 2021

Abstract DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate performance MiFish 12S taxonomic assignments using a case study California Current Large Marine Ecosystem fishes to determine best practices metabarcoding. Specifically, use taxonomy cross‐validation by identity framework compare between global database comprised all available sequences curated that only includes from Ecosystem. We demonstrate regional provides higher assignment accuracy than comprehensive database. also document tradeoff misclassification across range cutoff scores, highlighting importance parameter selection classification. Furthermore, compared with without inclusion additionally generated sequences. To this end, sequenced tissue 597 species primers, adding 252 GenBank's existing 550 fish then reads identified seawater environmental samples our references, The addition new references allowed identification 16 additional native taxa representing 17.0% total eDNA samples, including vast ecological economic value. Together these results effective need locus‐specific validation efforts.

Язык: Английский

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Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems

Environmental DNA, Год журнала: 2021, Номер 3(6), С. 1113 - 1127

Опубликована: Июль 6, 2021

Abstract Through the development of environmental DNA (eDNA) metabarcoding, in situ monitoring organisms is becoming easier and promises a revolution our approaches to detect changes biodiversity over space time. A cornerstone eDNA approach primer pairs that allow amplifying specific taxonomic groups, which then used link sequence identification. Here, we propose framework for comparing regarding (a) their capacity bind amplify broad coverage species within target clade using silico PCR, (b) not only discriminate between but also genera or families, (c) specificity efficiency across variety environments. As case study, focus on two mitochondrial 12S pairs, MiFish‐U teleo, were designed fishes. We found performance PCRs high both teleo amplified more Actinopterygii, Chondrichthyes, Petromyzontomorphi than MiFish‐U. In contrast, discriminatory power species, genera, families higher likely associated with greater length fragments. The evaluation showed recovered richness compared tropical temperate freshwater environments, generally primers perform well monitor fish species. Since detected when together, those are best combination increase ability detection.

Язык: Английский

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Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary

PLoS ONE, Год журнала: 2022, Номер 17(6), С. e0266720 - e0266720

Опубликована: Июнь 17, 2022

Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome these efforts are dependent upon either de novo primer design or selecting an appropriate set from the dozens that have already been published. Unfortunately, there a lack studies directly compared efficacy different metabarcoding primers marine estuarine systems. Here we evaluate five commonly sets designed to amplify rRNA barcoding genes fishes compare their performance using water samples collected sites highly biodiverse Indian River Lagoon Florida. Three portion mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp 16S (Berry_16S), other 271 nuclear 18S (MacDonald_18S). vast majority reads (> 99%) generated assigned non-target (non-fish) taxa therefore this was omitted most analyses. Using conservative 99% similarity threshold species level assignments, detected comparable number (55 49, respectively) similarly high Shannon's diversity values Riaz_12S Berry_16S sets. Meanwhile, just 34 32 were MiFish_12S Valentini_12S sets, respectively. We able both bony cartilaginous four with (>99%) former. greatest elasmobranchs (six species) suggesting it may be suitable candidate detection sharks rays. Of total 76 fish identified across all datasets, combined three 85.5% (65 while combination 93.4% (71 species). These results highlight importance employing multiple as well target genomic regions. Moreover, our suggest widely adopted not best choice, rather found effective eDNA-based surveys system.

Язык: Английский

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A National Scale “BioBlitz” Using Citizen Science and eDNA Metabarcoding for Monitoring Coastal Marine Fish

Frontiers in Marine Science, Год журнала: 2022, Номер 9

Опубликована: Март 28, 2022

Marine biodiversity is threatened by human activities. To understand the changes happening in aquatic ecosystems and to inform management, detailed, synoptic monitoring of across large spatial extents needed. Such challenging due time, cost, specialized skills that this typically requires. In an unprecedented study, we combined citizen science with eDNA metabarcoding map coastal fish at a national scale. We engaged 360 scientists collect filtered seawater samples from 100 sites Denmark over two seasons (1 p.m. on September 29th 2019 May 10th 2020), sampling nearly exact same time all sites, obtained overview largely unaffected temporal variation. This would have been logistically impossible for involved without help volunteers. high return rate 94% samples, total richness 52 species, representing approximately 80% Danish species 25% marine species. retrieved distribution patterns matching known occurrence both invasive, endangered, cryptic detected seasonal variation accordance phenology. Dissimilarity community compositions increased distance between sites. Importantly, comparing our data National Fish Atlas (the latter compiled century observations) found positive correlation values congruent pattern compositions. These findings support use eDNA-based detect biodiversity, approach readily scalable other countries, or even regional global scales. argue future large-scale biomonitoring will benefit using emerging technology, such be important data-driven management conservation.

Язык: Английский

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Systematic review of marine environmental DNA metabarcoding studies: toward best practices for data usability and accessibility

PeerJ, Год журнала: 2023, Номер 11, С. e14993 - e14993

Опубликована: Март 24, 2023

The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR–findable, accessible, interoperable, and reusable–despite growing awareness the importance such practices. In order to better understand these usability challenges, we systematically reviewed 60 peer articles conducting a specific subset eDNA research: metabarcoding studies in marine environments. For each article, characterized approximately 90 features across several categories: general article attributes topics, methodological choices, types metadata included, availability storage sequence data. Analyzing characteristics, identified barriers accessibility, including lack common context vocabulary articles, missing metadata, supplementary information limitations, concentration both sample collection analysis United States. While some require significant effort address, also found many instances where small choices made by authors journals could have an outsized influence on discoverability reusability Promisingly, showed consistency creativity as well strong trend toward open access publishing. Our underscores need think critically about accessibility studies, projects more broadly, continue proliferate.

Язык: Английский

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Skimming genomes for systematics and DNA barcodes of corals

Ecology and Evolution, Год журнала: 2024, Номер 14(5)

Опубликована: Май 1, 2024

Numerous genomic methods developed over the past two decades have enabled discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa scales. Genome skimming (or low-coverage genome sequencing) is a promising method not only extract high-copy but also 100s 1000s phylogenetically informative nuclear (e.g., ultraconserved elements [UCEs] exons) from contemporary museum samples. The subphylum Anthozoa, including important ecosystem engineers stony corals, black anemones, octocorals) in marine environment, critical need resolution thus might benefit genome-skimming approach. We conducted on 242 anthozoan corals collected 1886 2022. Using existing target-capture baitsets, we bioinformatically obtained UCEs exons data incorporated them with previously published studies. mean number UCE exon extracted was 1837 ± 662 SD for octocorals 1379 476 hexacorals. Phylogenetic were well resolved within each class. A 1422 720 historical specimens, 1253 recovered oldest specimen 1886. partial whole mitogenomes rRNA genes >95% Bioinformatically pulling UCEs, exons, mitochondrial genomes, viable low-cost option This approach can be used review support taxonomic revisions reconstruct evolutionary histories, type specimens.

Язык: Английский

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