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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Environmental DNA: The next chapter

Molecular Ecology, Год журнала: 2024, Номер 33(11)

Опубликована: Апрель 16, 2024

Abstract Molecular tools are an indispensable part of ecology and biodiversity sciences implemented across all biomes. About a decade ago, the use implementation environmental DNA (eDNA) to detect signals extracted from samples opened new avenues research. Initial eDNA research focused on understanding population dynamics target species. Its scope thereafter broadened, uncovering previously unrecorded via metabarcoding in both well‐studied understudied ecosystems taxonomic groups. The application rapidly became established research, field by its own. Here, we revisit key expectations made land‐mark special issue Ecology 2012 frame development six areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour environment (6) reference database development. We pinpoint success eDNA, yet also discuss shortfalls not met, highlighting areas priority identify unexpected developments. In parallel, our retrospective couples screening peer‐reviewed literature with survey users including academics, end‐users commercial providers, which address focus efforts advance eDNA. With rapid ever‐increasing pace technical advances, future looks bright, successful applications best practices must become more interdisciplinary reach full potential. Our retrospect gives towards concretely moving forward.

Язык: Английский

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Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness

Frontiers in Ecology and Evolution, Год журнала: 2020, Номер 8

Опубликована: Авг. 28, 2020

The ability to properly identify species present in a landscape is foundational ecology and essential for natural resource management conservation. However, many are often unaccounted due ineffective direct capture visual surveys, especially aquatic environments. Environmental DNA metabarcoding an approach that overcomes low detection probabilities should consequently enhance estimates of biodiversity its proxy, richness. Here, we synthesize 37 studies systems compare richness bony fish between eDNA conventional methods, such as nets, census, electrofishing. In freshwater with fewer than 100 species, found detected more methods. Using multiple genetic markers further increased metabarcoding. For diverse across marine systems, reported similar values methods; however, needed these environments better evaluate relative performance. greater biodiversity, will require populated reference databases, sampling effort, multi-marker assays ensure robust validate the approach. reliable provides path broader assessments can outperform methods estimating

Язык: Английский

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Standards for Methods Utilizing Environmental DNA for Detection of Fish Species

Genes, Год журнала: 2020, Номер 11(3), С. 296 - 296

Опубликована: Март 11, 2020

Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches used to detect specific species determine community diversity. Various protocols with methods organism detection have been reported in different studies, but there no general recommendations detection. Herein, we reviewed 168 papers supplement highlight the key criteria each step of technology provide suggestions eliminating errors. Although is unified recommendation application diverse detecting species, most cases, 1 or 2 L surface collection capture 0.7-μm glass fiber filters followed by extraction a DNeasy Blood Tissue Kit PowerWater Isolation useful obtaining high-quality eDNA. Subsequently, species-specific quantitative polymerase chain reaction (qPCR) assays based mitochondrial cytochrome b gene markers metabarcoding both 12S 16S rRNA via high-throughput sequencing can effectively target estimate richness. Furthermore, errors be minimized mitigating contamination, negative control, PCR replication, using multiple genetic markers. Our aim strategy that applied researchers, advisors, managers.

Язык: Английский

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Strategies for sample labelling and library preparation in DNA metabarcoding studies

Molecular Ecology Resources, Год журнала: 2021, Номер 22(4), С. 1231 - 1246

Опубликована: Сен. 22, 2021

Abstract Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because its targeted nature that allows sequencing genetic markers many parallel. To achieve this, PCR amplification carried out with primers designed target a taxonomically informative marker within taxonomic group, sample‐specific nucleotide identifiers are added the amplicons prior sequencing. The latter enables assignment sequences back they originated from. Nucleotide can be during metabarcoding “library preparation”, is, when prepared for Different strategies this labelling exist. All have advantages, challenges limitations, some which lead misleading results, worst case compromise fidelity data. Given range questions addressed using metabarcoding, ensuring data generation robust fit chosen purpose critically important practitioners seeking employ assessments. Here, we present an overview three main workflows library preparation studies on Illumina platforms; one‐step PCR, two‐step tagged PCR. Further, distill key considerations researchers select appropriate strategy their specific study. Ultimately, by gaining insights into consequences different workflows, hope further consolidate power as tool assess across applications.

Язык: Английский

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Comparing environmental metabarcoding and trawling survey of demersal fish communities in the Gulf of St. Lawrence, Canada

Environmental DNA, Год журнала: 2020, Номер 3(1), С. 22 - 42

Опубликована: Июль 13, 2020

Abstract Biodiversity assessment is an important part of conservation management that ideally can be accomplished with noninvasive methods without influencing the structure and functioning ecosystems. Environmental DNA (eDNA) metabarcoding has provided a promising tool to enable fast comprehensive monitoring entire ecosystems, but widespread adoption this technique requires performance evaluations compare it conventional surveys. We compared eDNA trawling data evaluate their efficiency characterize demersal fish communities in Estuary Gulf Saint‐Lawrence, Canada. Seawater bottom samples were collected parallel at 84 stations. For subset 30 these stations, water was also three different depths (15, 50, 250 m) across column. An assay based on 12S mitochondrial gene using MiFish‐U primers applied detect eDNA. detected total 88 species both combined, 72 being by eDNA, 64 trawl, 47 (53%) overlapped between methods. more efficient for quantifying richness, mainly because known less vulnerable gear. Our results indicated relative abundance estimated trawl significantly correlated methods, while relationship influenced environmental variables (temperature, depth, salinity, oxygen). Integrating surveys could provide additional information vertical distribution thus appears reliable complementary approach documenting biodiversity, including obtaining quantitative estimates marine environment.

Язык: Английский

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Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities?

Molecular Ecology, Год журнала: 2020, Номер 30(13), С. 3175 - 3188

Опубликована: Сен. 25, 2020

In the marine realm, biomonitoring using environmental DNA (eDNA) of benthic communities requires destructive direct sampling or setting-up settlement structures. Comparatively much less effort is required to sample water column, which can be accessed remotely. this study we assess feasibility obtaining information from eukaryotic by adjacent layer. We studied two different rocky-substrate with a technique based on quadrat sampling. also took replicate samples at four distances (0, 0.5, 1.5, and 20 m) habitat. Using broad range primers amplify ca. 313 bp fragment cytochrome oxidase subunit I gene, obtained total 3,543 molecular operational taxonomic units (MOTUs). The structure in environments was markedly different, Metazoa, Archaeplastida Stramenopiles being most diverse groups samples, Hacrobia, Metazoa Alveolata water. Only 265 MOTUs (7.5%) were shared between benthos and, these, 180 (5.1%) identified as taxa that left their Most them found immediately benthos, number decreased moved apart It concluded eDNA, even close vicinity poor proxy for analysis structure, methods are monitoring these complex via metabarcoding.

Язык: Английский

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Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot

Molecular Ecology Resources, Год журнала: 2021, Номер 21(5), С. 1558 - 1574

Опубликована: Март 8, 2021

Abstract Marine biodiversity can be surveyed using underwater visual censuses and recently with eDNA metabarcoding. Although a promising tool, studies have shown contrasting results related to its detection scale the number of species identified compared other survey methods. Also, accuracy relies on complete reference databases used for taxonomic assignment and, as methods, may show false‐negative false‐positive errors. Here, we from simultaneous metabarcoding fish surveys in terms observed community composition. We also assess effect custom database assignment, evaluate occupancy, capture probabilities, well error rates data. amplified 12S rRNA barcode 24 sampling sites gulf California. More were detected than UVC. Because each method largely different sets species, combined approach doubled registered. Both methods recovered known gradient biogeographic break, but captured diversity over broader geographic bathymetric scale. Furthermore, use modest‐sized significantly increased assignment. In subset occupancy models revealed provided similar or higher probabilities The value had large influence detectability, false positive negative error. Overall, these highlight potential complementing established ecological marine fishes.

Язык: Английский

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Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds

Metabarcoding and Metagenomics, Год журнала: 2020, Номер 4

Опубликована: Окт. 22, 2020

The sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the increasing number eDNA metabarcoding approaches, ability to quantify species biomass abundance natural systems still not fully understood. Previous studies have shown positive but sometimes weak correlations between estimates from data conventional capture methods. As both methods independent biases a lack concordance difficult interpret. Here we tested whether read counts provide accurate quantitative absolute fish holding ponds known individuals. Environmental samples were collected two fishery high density broad diversity. In one pond, different strategies (on-site filtration enclosed filters three preservation buffers versus lab using open filters) used evaluate their performance relation community composition biomass/abundance estimates. Fish significantly correlated abundance, this result, together information on diversity, was repeatable when or used. This research demonstrates that provides qualitative communities small ponds, results are consistent capture. method flexibility will be beneficial for future eDNA-based integration into fisheries management.

Язык: Английский

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Measuring and mitigating PCR bias in microbiota datasets

PLoS Computational Biology, Год журнала: 2021, Номер 17(7), С. e1009113 - e1009113

Опубликована: Июль 6, 2021

PCR amplification plays an integral role in the measurement of mixed microbial communities via high-throughput DNA sequencing 16S ribosomal RNA (rRNA) gene. Yet is also known to introduce multiple forms bias rRNA studies. Here we present a paired modeling and experimental approach characterize mitigate NPM-bias (PCR from non-primer-mismatch sources) microbiota surveys. We use data mock bacterial validate our human gut samples under real-world conditions. Our results suggest that can skew estimates relative abundances by factor 4 or more, but this be mitigated using log-ratio linear models.

Язык: Английский

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