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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DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions

Molecular Ecology, Journal Year: 2019, Volume and Issue: 28(8), P. 1857 - 1862

Published: April 1, 2019

DNA metabarcoding, especially when coupled with high-throughput sequencing, is currently revolutionizing our capacity to assess biodiversity across a full range of taxa and habitats, from soil microbes (e.g., Thompson et al., 2017) large marine fish Thomsen 2016), contemporary tens thousands year-old biological communities Willerslev 2003). The breadth potential applications immense spans surveys on the diversity or diet species native specific ecosystems bioindication (Pawlowski 2018). approach also cost-effective easy implement, which makes metabarcoding one tools choice 21st century for fundamental research future large-scale monitoring programs (reviewed in Bohan 2017; Creer 2016; Taberlet, Bonin, Zinger, & Coissac, 2018; Willerslev, 2015). However, as often case any emerging technology, we feel that rise occurring at pace manner loses sight challenges producing high-quality reproducible data (Baker, 2016). by essence multidisciplinary building upon many complementary expertises, including field theoretical knowledge, taxonomic expertise, molecular biology, bioinformatics, computational statistics. Combining all these within single studies necessary, not so much analyzing per se, but rather minimizing controlling possible biases can be introduced step experimental workflow—i.e., sampling analysis—and lead spurious ecological conclusions Bálint Nilsson 2019; Dickie Taberlet Whether starting material consists bulk samples (community DNA) and/or environmental (eDNA), rely deceptively simple succession core steps: (a) preservation material, (b), extraction, (c) PCR amplification taxonomically-informative genomic region, (d) sequencing amplicons, (e) sequence analysis using bioinformatic pipelines. Despite this apparent simplicity, each potentially introduce its own sources artifacts (Figure 1). For example, design might effective capturing processes under study, an undesired bias based detection. availability governed production rate, transport persistence, are largely dependent targeted organisms, their biomass, ecosystem considered. A correct assessment phenomenon require only implementation standardized standardized, randomized repeatable designs procedures (Dickie 2018), consideration dynamics underlying matrix (i.e., gut, faeces, water matrices tropical boreal organisms/ecosystems; Barnes Turner, Likewise, community study enriched purpose depending how sample collected filter size samples, removal roots soils), it transported/preserved, extracted (differential extraction efficiencies). well known important source biases, now fully revealed techniques. preferential certain over other ones due inappropriate primers provides such example (Clarke, Soubrier, Weyrich, Cooper, 2014; Deagle, Jarman, Pompanon, 2014). Primer both skew abundance profiles false negatives. produce negatives too through presence e.g., inhibitors, positives introduction replication errors polymerase formation chimeric fragments False workflow reagent contaminants (Salter 2014), extractions cross-contaminations. An even more insidious pertains occurrence "tag jumps", sometimes referred "mistagging", "tag-switching", "cross-talks" (Carlsen 2012; Edgar, Esling, Lejzerowicz, Pawlowski, 2015; Schnell, Bohmann, Gilbert, amplicons indeed tagged unique short nucleotide sequences added 5'-end "tags"), allow pooling PCRs run reducing costs. Each obtained then bioinformatically assigned back origin basis tags (Schnell preparation libraries tag particular fact recombined belonging another (Taberlet This introduces additional, non-negligible levels cross-contaminations, primarily involve most abundant have disproportionate impact low concentrations (Esling Murray, Coghlan, Bunce, Schnell Similarly, Illumina index located P5 adaptor subjected "index resulting cross-contaminations happens several individual pooled loaded same lane (Kircher, Sawyer, Meyer, 2012). Finally, instruments error rates (Schirmer above list problems clearly exhaustive, interested reader will find complete reviews elsewhere (e.g. Still, illustrates must considered carefully designing protocol interpreting results. crucial limit downstream analyses, ensure conclusion drawn authentic. There increasingly diverse field, laboratory Caporaso 2011; Valentini 2009) bioinformatics Boyer 2010; Dumbrell, Ferguson, Clark, 2016) aiming amount partial sampling, bias) contaminations, "tag/index errors) experiments. protocols does necessarily guarantee problem completely control. These continuously reconsidered, alongside emergence novel technologies provide new opportunities, challenges. Additionally, marker comes specificities, requires customization protocols. clustering threshold used form Molecular Operational Taxonomic Units relevant question addressed removing intraspecific variability level desired) critically depend specificities PCR/sequencing rates. Bioinformatics further fail exclude filtering thresholds relaxed, inflates estimates. they generate negatives, genuine metabarcode falsely flagged chimera, incorrect taxon incomplete reference databases (Alsos Riaz, Puillandre, problematic investigated strongly relies It therefore include types controls facilitate exclusion signal support reliability Amongst controls, conducting pilot experiments particularly helpful appropriate We recommend replicates multiple independent samples) technical extractions/PCR extract) included disentangle effect variances (Ficetola replications necessary because stochastic manner, concentration target low. essential analyze sufficient number negative PCR, steps, positive consisting mock communities, synthetic reflecting attributes products All sequenced along detection sporadic contaminations jumps while helping adjusting thresholds. Ultimately, token whole curation process (De Barba encourage careful itself, since steps curate study. Typically, given may deriving tag/index jumps. retained thus artifacts, depth. As different direct measurements better tuning considerations should precisely reported publications together illustrations statistics characterizing workflow, relevance quality underpinning conclusions. last, obvious control assessing plausibility composition priori knowledge system studied. Such derived sensing approaches visual observations. In case, exhaustive local specimens secure assignment Alsos When information unavailable, typically studying microorganisms, remains whether composed clades expected occur surveyed not, soils, sediments, gut environments harbour highly bacterial phyla 2017). users, readers, referees editors, realize mentioned issues remain overlooked. stance unsubstantiated claims undermine scientific advances if resolved. Inappropriate practices estimating richness fingerprint (Bent 2007), absence (Prosser, 2010), contaminant (Perez-Muñoz, Arrieta, Ramer-Tait, Walter, been repeatedly criticized microbial ecology, latter contribute rising debate about existence womb microbiota. Ancient has developed rigorous standards tackle related contamination, errors, reproducibility (Poinar 2000). believe users come age learnt past errors. At time guides best subject (Knight Pollock, Glendinning, Wisedchanwet, Watson, where costs rapidly decreasing, always mindful adage "better safe than sorry". note mean imply systematic use highest analytical reasonable nor universal remedy associated metabarcoding. Rather, researchers end-users adopt reflective decision-making experiment appraise results, ultimate aim prove robustness

Language: Английский

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A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA

Nature, Journal Year: 2022, Volume and Issue: 612(7939), P. 283 - 291

Published: Dec. 7, 2022

Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago

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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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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Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

Molecular Ecology, Journal Year: 2022, Volume and Issue: 31(6), P. 1820 - 1835

Published: Jan. 25, 2022

Abstract DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated consistency this technique with traditional morpho‐taxonomic approaches. These individual to assess diversity community structure organisms both in marine freshwater systems globally over last decade. However, a systematic analysis comparability effectiveness DNA‐based across all these has hitherto been lacking. Here, we performed first meta‐analysis available comparing methods measure biological key groups, including plankton, microphytobentos, macroinvertebrates, fish. Across 215 data sets, found that provides richness estimates are consistent those obtained using methods, at local regional scale. also generates species inventories highly congruent Contrastingly, microphytobenthos macroinvertebrates by showed pronounced differences missing some taxa but same time detecting otherwise overseen diversity. The method generally sufficiently advanced study composition fish communities replace more invasive methods. For smaller organisms, like plankton microphytobenthos, may continue give complementary rather than identical compared Systematic comparable collection will increase understanding different aspects complementarity, adequate interpretation results.

Language: Английский

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Quantitative and qualitative assessment of pollen DNA metabarcoding using constructed species mixtures

Molecular Ecology, Journal Year: 2018, Volume and Issue: 28(2), P. 431 - 455

Published: Aug. 17, 2018

Pollen DNA metabarcoding-marker-based genetic identification of potentially mixed-species pollen samples-has applications across a variety fields. While basic species-level using standard barcode markers is established, the extent to which metabarcoding (a) correctly assigns species identities mixes (qualitative matching) and (b) generates sequence reads proportionally their relative abundance in sample (quantitative unclear, as these have not been assessed known standards. We tested quantitative qualitative robustness constructed mixtures varying richness (1-9 species), taxonomic relatedness (within genera class) rarity (5%-100% grains), Illumina MiSeq with rbcL ITS2. Qualitatively, composition determinations were largely correct, but false positives negatives occurred. False typically driven by lack gap or sample. Species relatedness, however, did strongly impact correct determinations. likely contamination, chimeric sequences and/or misidentification bioinformatics pipeline. Quantitatively, proportion for each was only weakly correlated its abundance, contrast suggestions from some other studies. Quantitative mismatches are correctable consistent scaling factors, instead context-dependent on present Together, our results show that robust determining presence/absence should be used infer grains.

Language: Английский

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PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding

Database, Journal Year: 2020, Volume and Issue: 2020

Published: Jan. 1, 2020

Abstract DNA metabarcoding combines barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated accurate reference dataset of plant sequences not available so far. Here, we constructed datasets Viridiplantae ITS1, ITS2 entire including both Chlorophyta Streptophyta. were retrieved from NCBI, the region was extracted. underwent identity check remove misidentified records clustered at 99% reduce redundancy computational effort. For this step, developed script called ‘better clustering QIIME’ (bc4q) ensure that representative are chosen according composition cluster taxonomic level. three obtained bc4q PLANiTS1 (100 224 sequences), PLANiTS2 (96 771 sequences) PLANiTS (97 550 all pre-formatted QIIME, being most bioinformatic pipeline analysis. Being curated databases, PLANiTS1, reliable, pivotal first step general standardization studies. is presented new tool useful in each research dealing clustering. Database URL: https://github.com/apallavicini/bc4q; https://github.com/apallavicini/PLANiTS.

Language: Английский

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Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

Frontiers in Ecology and Evolution, Journal Year: 2019, Volume and Issue: 7

Published: June 20, 2019

The lake sediments of Hässeldala Port in south-east Sweden provide an archive local and regional environmental conditions ~14.5-9.5 ka BP (thousand years before present) allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun with plant micro- macrofossil analyses investigate dating the Allerød (14.1-12.7 BP), Younger Dryas (12.7-11.7 BP) Preboreal (<11.7 BP). Number reads taxa were not associated sample age or organic content. This suggests that, beyond initial rapid degradation, is well preserved. proportion recovered was low, but allowed identifying important number taxa, thus adding valid information on composition vegetation. Importantly, provides a stronger signal community changes than alone, since larger new recorded samples. A comparison between three proxies highlights differences similarities supports earlier findings that plants growing close within are by DNA. Plant remains moreover show tree birch present ancient Allerød; together results, this indicates boreal subarctic climatic also prevailed during cold interval. Increasing reference libraries enrichment strategies prior necessary improve potential accuracy identification using metagenomic approach.

Language: Английский

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A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples

Scientific Data, Journal Year: 2019, Volume and Issue: 6(1)

Published: Dec. 6, 2019

Abstract The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library curated reference sequences. However, it is estimated that just 15% described animal species are represented in public repositories. To begin to address this deficiency, we provide barcodes for 1,500,003 specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, nation comprises 7% the planet’s land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, 64,264 Barcode Index Numbers (BINs; proxy species) represented. Species-level taxonomy was available 38% specimens, but higher proportions were assigned genus (69.5%) family (99.9%). Voucher extracts archived Centre Biodiversity Genomics where they further research. corresponding can be accessed Life Data System, GenBank, Global Information Facility, Genome Network Portal.

Language: Английский

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