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

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 873, P. 162322 - 162322

Published: Feb. 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.

Language: Английский

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Environmental DNA metabarcoding from flowers reveals arthropod pollinators, plant pests, parasites, and potential predator–prey interactions while revealing more arthropod diversity than camera traps

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(3), P. 551 - 569

Published: March 29, 2023

Abstract Arthropods can strongly impact ecosystems through pollination, herbivory, predation, and parasitism. As such, characterizing arthropod biodiversity is vital to understanding ecosystem health, functions, services. Emerging environmental DNA (eDNA) methods targeting trace eDNA left behind on flowers have the potential track interactions. The goal of this study was determine extent which metabarcoding identify plant‐arthropod arthropod‐arthropod interactions assess compared conventional sampling. We deployed camera traps document activity specific flowers, sampled from those same then performed a analysis that targets partial fragment cytochrome c oxidase subunit I gene (COI) all present. found our detected small pollinators, plant pests, parasites, shed light predator–prey while detecting 55 species just 21 trapping. trapping survey, however, larger, more conspicuous nectarivores successfully. also explored ecology residual eDNA, finding rainfall had significant negative effect ability detect eDNA. Preliminary evidence indicates flower may amount be detected. provide clues highlights insights gained future studies. show valuable tool for not only pollinator communities but revealing among plants, predators. Future research should focus how improve detection large pollinators/nectivores studying further explore method's utility.

Language: Английский

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Environmental RNA can distinguish life stages in amphibian populations

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 24(4)

Published: Aug. 18, 2023

Abstract Applications of environmental DNA (eDNA) analysis methods for biomonitoring have grown exponentially over the last decade and provide a wealth new information on distribution species. However, eDNA limited application estimating population‐level metrics. Environmental RNA (eRNA) has potential to address ecological questions by gathering population demographic from media but may be challenging detect analyze. We developed gene‐specific eRNA assays targeting keratin‐associated genes in two focal species, American bullfrogs ( Lithobates catesbeianus ) tiger salamanders Ambystoma mavortium answer an important question amphibian management: whether species detections represent breeding populations versus transitory adults. performed extensive laboratory validation with amphibians housed across development stages, where we collected 95 127 samples salamanders, respectively. Both were highly specific larval stage amplified high sensitivity (90% bullfrog 88.4% salamander samples). then applied our validated multiple natural systems. When larvae present, found 74.1% overall detection field 70.8% 48.5% ponds A. macrodactylum californiense larvae, correlating rates. only adults did not larvae‐specific ponds, despite Although much work is ahead optimizing assay design, sampling filtering methods, demonstrate that can successfully used discern life stages direct ecology conservation management.

Language: Английский

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Current status and topical issues on the use of eDNA-based targeted detection of rare animal species

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 904, P. 166675 - 166675

Published: Aug. 29, 2023

Language: Английский

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Comparing cost, effort, and performance of environmental DNA sampling and trapping for detecting an elusive freshwater turtle

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(2)

Published: March 1, 2024

Abstract Environmental DNA (eDNA) analysis is an effective and non‐invasive technique for surveying monitoring rare, threatened, or endangered (RTE) species. Compared to conventional capture‐based sampling, eDNA may offer a more cost‐effective approach RTE species, yet few studies have compared their cost‐efficiency—a critical consideration conservation planning. We the costs, effort, relative performance of aquatic sampling trapping detecting Alligator Snapping Turtle, Macrochelys temminckii Troost, 1835, in southwest Louisiana, United States. was sampled quarterly over 1 year (2018–2019) at 19 streams, including three streams where M. presence had been previously confirmed via efforts (2012–2013). Water samples from each stream were analyzed using quantitative polymerase chain reaction (qPCR) assess presence/absence. Time costs (i.e., labor, travel, wages, supplies) per detection calculated compared. documented two individuals trapped yielded detections (qPCR amplifications) 16 additional not sampled, expanding 's distribution our study sites by 84%. returned rate (per site) 5.55 times higher than 18.7% less expensive. Our results provide evidence that strategically deployed surveys be cost‐efficient freshwater With analysis, resources can invested toward survey coverage increasing frequency, allowing managers effectively target subsequent intensive efforts.

Language: Английский

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Phenological mismatches mitigate the ecological impact of a biological invader on amphibian communities

Ecological Applications, Journal Year: 2024, Volume and Issue: 34(6)

Published: Aug. 8, 2024

Horizon scans have emerged as a valuable tool to anticipate the incoming invasive alien species (IAS) by judging on their potential impacts. However, little research has been conducted quantifying actual impacts and assessing causes of species-specific vulnerabilities particular IAS due persistent methodological challenges. The underlying interspecific mechanisms driving therefore remain poorly understood, even though they can substantially improve accuracy risk assessments. Given that interactions ecological are often shaped phenological synchrony, we tested hypothesis temporal mismatches in breeding phenology between native mitigate Focusing American bullfrog (Lithobates catesbeianus), combined an environmental DNA (eDNA) quantitative barcoding metabarcoding survey Belgium with global meta-analysis, integrated citizen-science data phenology. We examined whether presence amphibian was negatively related or abundance bullfrogs this relationship affected mismatches. field study revealed significant negative effect increasing eDNA concentrations richness community structure. These observations were bullfrogs, late spring- summer-breeding being strongly affected, while winter-breeding remained unaffected. This trend confirmed meta-analysis. A observed mismatch impact bullfrogs. Specifically, differing 6 weeks less from more likely be absent than whose differed Taken together, present novel method based combination aqueous quantify biological invaders at level. show strong predictor invasion regardless context. Therefore, advocate for integration alignment IAS's phenologies into frameworks.

Language: Английский

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Monitoring terrestrial rewilding with environmental DNA metabarcoding: a systematic review of current trends and recommendations

Frontiers in Conservation Science, Journal Year: 2025, Volume and Issue: 5

Published: Jan. 2, 2025

Introduction Rewilding, the facilitation of self-sustaining and resilient ecosystems by restoring natural processes, is an increasingly popular conservation approach potential solution to biodiversity climate crises. Outcomes rewilding can be unpredictable, monitoring essential determine whether are recovering. Metabarcoding, particularly environmental DNA (eDNA), revolutionizing could play important role in understanding impacts but has mostly been applied within aquatic systems. Methods This systematic review focuses on applications eDNA metabarcoding terrestrial monitoring, with additional insights from bulk ingested DNA. We examine publication trends, choice sampling substrate focal taxa, investigate how well performs compared other methods (e.g. camera trapping). Results Terrestrial represented a small proportion total papers, forests most studied system, soil water substrates, vertebrates targeted taxa. Most studies focused measuring species richness, few included analyzes functional diversity. Greater richness was found when using multiple took this approach. Metabarcoding did not consistently outperform terms number vertebrate taxa detected, likely influenced marker, habitat. Discussion Our findings indicate that metabarcoding, eDNA, key rewilding, further ground- truthing needed establish appropriate experimental pipelines for target system interest. Systematic Review Registration https://osf.io/38w9q/?view_only=47fdab224a7a43d298eccbe578f1fcf0 , identifier 38w9q.

Language: Английский

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Vertical distribution of free and multi-fraction environmental DNA in a controlled aquatic system: insights into dispersal dynamics and sampling implications

Hydrobiologia, Journal Year: 2025, Volume and Issue: unknown

Published: April 10, 2025

Language: Английский

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Life history traits influence method-specific detection of native and invasive amphibians

Frontiers in Amphibian and Reptile Science, Journal Year: 2025, Volume and Issue: 3

Published: April 24, 2025

Introduction Efficient and effective monitoring is essential for informing conservation efforts determining where to focus management actions. Newly arriving invasive declining native taxa are often the of programs, but these species inherently difficult monitor detect. A key challenge when a present at location goes undetected, creating uncertainty about whether truly absent or unobserved. Estimating detection improves efficacy methods accurately informs efforts. Methods In this study, we applied occupancy modeling estimate method-specific probabilities two focal amphibian species: northern leopard frog ( Lithobates pipiens ) American bullfrog catesbeianus ). We evaluated three techniques: automated acoustic recorders, eDNA, visual encounter surveys 38 breeding sites in Colorado’s South Platte River Basin, USA, an area frogs declining, bullfrogs expanding. investigated how local environmental conditions (temperature pH) survey-specific choices (survey date, number observers, search time, liters filtered water) influenced each method. Results Our results showed that probability increased slightly with longer times eDNA was highest neutral pH conditions. Acoustic calls peaked early spring. For bullfrogs, improved water both temperature. Bullfrog call mid late summer. Discussion Northern distinct life history traits related habitat preferences, behaviors, seasonal emergence explained differences their probabilities.

Language: Английский

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BeeDNA: Microfluidic environmental DNA metabarcoding as a tool for connecting plant and pollinator communities

Environmental DNA, Journal Year: 2022, Volume and Issue: 5(1), P. 191 - 211

Published: Oct. 19, 2022

Abstract Pollinators are declining globally, and this loss can reduce plant reproduction, erode critical ecosystem services resilience, drive economic losses. Monitoring pollinator biodiversity trends is essential for adaptive conservation management, but conventional surveys often costly, time‐consuming, requires considerable taxonomic expertise. Environmental DNA (eDNA) metabarcoding booming due to their rapidity, nondestructiveness, cost efficiency. Microfluidic technology allows multiple primer sets from different markers be used in eDNA more comprehensive inventories, minimizing associated bias. We evaluated microfluidic community monitoring both controlled greenhouse natural field settings. Using a variety of sampling, preservation, extraction methods, we assessed communities with number using metabarcoding. In experiments, detected the target bumblebee two four focal flower species as well insects all species. field, numerous common regional arthropods, including some directly observed, were detected. Pollinator detection was maximized whole heads preserved ATL buffer extracted modified Qiagen® DNeasy protocol amplification COI primers. surveillance could enhance assessment by detecting protected endangered being applicable remote, inaccessible locations, whilst reducing survey time, effort, expense. optimization address remaining efficacy concerns, approach shows potential revealing complex networks underpinning functions services, enabling accurate assessments resilience.

Language: Английский

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