Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA

Global Ecology and Conservation, Journal Year: 2019, Volume and Issue: 17, P. e00547 - e00547

Published: Jan. 1, 2019

Environmental DNA (eDNA) metabarcoding is a novel method of assessing biodiversity wherein samples are taken from the environment via water, sediment or air which extracted, and then amplified using general universal primers in polymerase chain reaction sequenced next-generation sequencing to generate thousands millions reads. From this data, species presence can be determined, overall assessed. It an interdisciplinary that brings together traditional field-based ecology with in-depth molecular methods advanced computational tools. As emerging monitoring method, there many pitfalls roadblocks considered avoided, but may still have ability revolutionize modern surveys for era. In paper, we review basic methodology, benefits, concerns eDNA metabarcoding, systematically cover applications global thus far, including across all habitats taxonomic groups, ancient ecosystem reconstruction, plant-pollinator interactions, diet analysis, invasive detection, pollution responses, quality monitoring. We also discuss future as well expected technological advances how they impact way used future. unique development will likely remain flux some time technology procedures become standardized. However, optimized its use becomes more widespread, it essential tool ecological conservation study.

Language: Английский

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Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects

Biodiversity and Conservation, Journal Year: 2020, Volume and Issue: 29(7), P. 2089 - 2121

Published: April 8, 2020

Language: Английский

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Persistence of environmental DNA in marine systems

Communications Biology, Journal Year: 2018, Volume and Issue: 1(1)

Published: Oct. 29, 2018

As environmental DNA (eDNA) becomes an increasingly valuable resource for marine ecosystem monitoring, understanding variation in its persistence across contrasting environments is critical. Here, we quantify the breakdown of macrobial eDNA over a spatio-temporal axis locally extreme conditions, varying from ocean-influenced offshore to urban-inshore, and between winter summer. We report that degrades 1.6 times faster inshore environment than environment, but contrary expectation find no difference season. Analysis covariables show spatial gradient salinity temporal pH, with salinity-or biotic correlates thereof-most important. Based on our estimated half-life naturally occurring concentrations, estimate may be detected around 48 h, offering potential collect ecological community data high local fidelity. conclude by placing these results context previously published decay rates.

Language: Английский

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Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds

Hydrobiologia, Journal Year: 2018, Volume and Issue: 826(1), P. 25 - 41

Published: Sept. 3, 2018

Environmental DNA (eDNA) analysis is a rapid, non-invasive, cost-efficient biodiversity monitoring tool with enormous potential to inform aquatic conservation and management. Development ongoing, strong commercial interest, new uses are continually being discovered. General applications of eDNA guidelines for best practice in freshwater systems have been established, but habitat-specific assessments lacking. Ponds highly diverse, yet understudied that could benefit from monitoring. However, ponds methodological constraints specific these environments remain unaddressed. Following stakeholder workshop 2017, researchers combined knowledge expertise review challenges must be addressed the future consistency ponds. The greatest pond surveys representative sampling, capture, PCR inhibition. We provide recommendations inhibition testing, laboratory practice, which should aid ongoing projects If implemented, will contribute towards an eventual broad standardisation research room tailor workflows optimal different applications. Such more robust, comparable, ecologically meaningful data enable effective management biodiversity.

Language: Английский

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Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus)

Ecology and Evolution, Journal Year: 2018, Volume and Issue: 8(12), P. 6330 - 6341

Published: May 29, 2018

Environmental DNA (eDNA) analysis is a rapid, cost-effective, non-invasive biodiversity monitoring tool which utilises left behind in the environment by organisms for species detection. The method used as species-specific survey rare or invasive across broad range of ecosystems. Recently, eDNA and "metabarcoding" have been combined to describe whole communities rather than focusing on single target species. However, whether metabarcoding sensitive targeted approaches detection remains be evaluated. great crested newt Triturus cristatus flagship pond international conservation concern first UK routinely monitored using eDNA. We evaluate has comparable sensitivity real-time quantitative PCR (qPCR) T. Extracted samples (N = 532) were screened qPCR analysed all vertebrate high-throughput sequencing technology. With threshold 1 12 positive replicates, newts detected 50% ponds. Detection decreased 32% when was increased 4 replicates. metabarcoding, 34% ponds without threshold, 28% (0.028%) applied. Therefore, provided greater but with no equivalent stringent threshold. proportion sequences each sample positively associated number replicates (qPCR score) suggesting may indicative concentration. holds enormous potential holistic assessment routine freshwater monitoring. advocate this community approach guide management conservation, whereby entire can initially surveyed best inform use funding time surveys.

Language: Английский

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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

Quaternary, Journal Year: 2021, Volume and Issue: 4(1), P. 6 - 6

Published: Feb. 13, 2021

The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field paleoecological research. Although largely applied nowadays, knowledge gaps remain this there therefore still research be conducted ensure reliability signal. Building on most recent literature seven original case studies, we synthesize state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation inventories from ancient (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based current best practises.

Language: Английский

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Understanding the effects of biotic and abiotic factors on sources of aquatic environmental DNA

Biodiversity and Conservation, Journal Year: 2019, Volume and Issue: 28(5), P. 983 - 1001

Published: Feb. 14, 2019

Analysis of environmental DNA (eDNA) offers an unprecedented ability to accurately survey biodiversity from aquatic ecosystems. Although eDNA methods have been applied myriad taxa, scientists are now moving away proof-of-concept work, ultimately evaluating the limits and opportunities this technology detect quantify abundance across organisms environments. Important considerations enabling such methodology be used for conservation contexts includes understanding both effects (1) amount released focal taxa—sources, (2) removal in environment—sinks. I review publications on macroorganism that evaluated or considered effect sources signal detection (or quantification) find few studies acknowledge, fewer still evaluate, impact production genomic recovery. In review, encourage readers carefully consider source dynamics, using previously published literature, dissect what roles biotic (e.g. life-history traits, species interactions including stressors) abiotic temperature, salinity) factors likely play deposition recovery, how impacts detection, abundance, biomass estimation, informed interpretation. further explore physical propose other (spatial temporal) markers assist identifying origins systems. Understanding these parameters influence variation will allow a more comprehensive tool, potentially give insights into environment-population responses.

Language: Английский

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Meta‐analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards

Ecology and Evolution, Journal Year: 2021, Volume and Issue: 11(9), P. 4803 - 4815

Published: March 18, 2021

Decades of environmental DNA (eDNA) method application, spanning a wide variety taxa and habitats, has advanced our understanding eDNA underlined its value as tool for conservation practitioners. The general consensus is that methods are more accurate cost-effective than traditional survey methods. However, they formally approved just few species globally (e.g., Bighead Carp, Silver Great Crested Newt). We conducted meta-analysis studies directly compare with surveys to evaluate the assertion consistently "better."Environmental publications multiple or single macro-organism detection were identified using Web Science, by searching "eDNA" "environmental DNA" across papers published between 1970 2020. used, focal taxa, habitats surveyed, quantitative categorical results collated analyzed determine whether under what circumstances outperforms surveys.Results show cheaper, sensitive, detect This is, however, taxa-dependent, amphibians having highest potential survey. Perhaps most strikingly, 535 reviewed 49 quantified probability both three times likely give qualitative statements performance.

Language: Английский

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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 RNA: A Revolution in Ecological Resolution?

Trends in Ecology & Evolution, Journal Year: 2021, Volume and Issue: 36(7), P. 601 - 609

Published: March 20, 2021

Language: Английский

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