Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

Molecular Ecology, Journal Year: 2017, Volume and Issue: 26(21), P. 5872 - 5895

Published: Sept. 18, 2017

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid of DNA from diverse kinds environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences eDNA a taxonomic name is called "eDNA metabarcoding" and offers powerful molecular tool capable noninvasively surveying species richness many ecosystems. Here, review use metabarcoding for animal plant richness, challenges in using approaches estimate relative abundance. We highlight applications freshwater, marine terrestrial environments, this broad context, distill what known about different sample types approximate space across time. provide guiding questions study design discuss workflow focus primers library preparation methods. additionally important criteria consideration bioinformatic filtering data sets, recommendations increasing transparency. Finally, looking future, emerging ecology, conservation, invasion biology, biomonitoring, can empower citizen science education.

Language: Английский

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Environmental DNA

Oxford University Press eBooks, Journal Year: 2018, Volume and Issue: unknown

Published: Feb. 15, 2018

Abstract Environmental DNA (eDNA), i.e. released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on distribution or feeding habits of species. It has therefore great potential for applications ecology biodiversity management. However, this research field is fast-moving, involves different areas expertise currently lacks approaches, which calls an up-to-date comprehensive synthesis. monitoring covers current methods based eDNA, with particular focus “eDNA metabarcoding”. Intended scientists managers, it provides background allow design sound experiments. revisits all steps necessary produce high-quality metabarcoding data such as sampling, metabarcode design, optimization PCR sequencing protocols, well analysis large datasets. All these are presented discussing challenges eDNA-based approaches infer parameters ecological processes. The last chapters book review how been used so far unravel novel patterns diversity space time, detect species, answer new questions various ecosystems organisms. constitutes essential reading graduate students, researchers practitioners who do not have strong molecular genetics willing use eDNA biomonitoring.

Language: Английский

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Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

Molecular Ecology, Journal Year: 2018, Volume and Issue: 28(2), P. 391 - 406

Published: June 2, 2018

Abstract Advances in DNA sequencing technology have revolutionized the field of molecular analysis trophic interactions, and it is now possible to recover counts food sequences from a wide range dietary samples. But what do these mean? To obtain an accurate estimate consumer's diet should we work strictly with data sets summarizing frequency occurrence different taxa, or use relative number sequences? Both approaches are applied semi‐quantitative summaries, but often promoted as more conservative reliable option due taxa‐specific biases recovery sequences. We explore representative metabarcoding point out that summaries based on overestimate importance consumed small quantities (potentially including low‐level contaminants) sensitive count threshold used define occurrence. Our simulations indicate using read abundance ( RRA ) information provides view population‐level even moderate incorporated; however, impacting common taxa. when mean taxa samples small. The ideas presented here highlight need consider all sources bias justify methods interpret studies. encourage researchers continue addressing methodological challenges acknowledge unanswered questions help spur future investigations this rapidly developing area research.

Language: Английский

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The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

The Science of The Total Environment, Journal Year: 2018, Volume and Issue: 637-638, P. 1295 - 1310

Published: May 22, 2018

The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance selected taxonomic groups to define ecological status. These conventional have some limitations, often related difficulties in morphological identification bioindicator taxa. Recent development DNA barcoding and metabarcoding could potentially alleviate these by using sequences instead morphology identify organisms characterize a given ecosystem. In this paper, we review structure indices, present results pilot studies environmental infer indices. We discuss main advantages pitfalls approaches assess parameters such as richness, abundance, composition species values, be used for calculation future developments fully exploit potential data improve accuracy precision their analysis. also propose recommendations integration routine biomonitoring programs.

Language: Английский

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Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive

Water Research, Journal Year: 2018, Volume and Issue: 138, P. 192 - 205

Published: March 20, 2018

Language: Английский

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Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation

Scientific Reports, Journal Year: 2018, Volume and Issue: 8(1)

Published: July 3, 2018

Abstract Despite the ecological and societal importance of large rivers, fish sampling remains costly limited to specific habitats (e.g., river banks). Using an eDNA metabarcoding approach, we regularly sampled 500 km a (Rhône River). Comparisons with long-term electrofishing surveys demonstrated ability qualitatively quantitatively reveal assemblage structures (relative species abundance) but integrated larger space than classical location. Combination literature review field data showed that behaves in water column like fine particulate organic matter. Its detection distance varied from few small stream more 100 river. To our knowledge, results are first demonstration capacity describe longitudinal patterns river, appears be reliable, cost-effective method for future monitoring.

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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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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Non‐specific amplification compromises environmental DNA metabarcoding with COI

Methods in Ecology and Evolution, Journal Year: 2019, Volume and Issue: 10(11), P. 1985 - 2001

Published: Aug. 2, 2019

Abstract Metabarcoding extra‐organismal DNA from environmental samples is now a key technique in aquatic biomonitoring and ecosystem health assessment. Of critical consideration when designing experiments, especially so developing community standards legislative frameworks, the choice of genetic marker primer set. Mitochondrial cytochrome c oxidase subunit I (COI), standard barcode for animals, with its extensive reference library, taxonomic discriminatory power predictable sequence variation, natural many metabarcoding applications. However, targeting specific groups samples, utility COI has yet to be fully scrutinized. Here, by using case study marine freshwater fishes British Isles, we quantify silico performance twelve pairs four mitochondrial loci – COI, b , 12S 16S terms library coverage, universality. We subsequently test vitro three one their specificity, reproducibility, congruence independent datasets derived traditional survey methods at five estuarine coastal sites around English Channel North Sea. Our results show that aqueous low template concentrations, both metazoan‐targeted fish‐targeted primers perform poorly comparison 12S, exhibiting levels reproducibility due non‐specific amplification prokaryotic non‐target eukaryotic DNAs. An ideal metabarcode would have an upon which custom could designed, either broad assessments biodiversity, or taxon surveys. Such database available but specificity hinders practical application, while conversely, offer high lack adequate references. The latter, however, can mitigated expanding concept barcodes include whole genomes generated genome‐skimming existing tissue collections.

Language: Английский

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Sequestration of macroalgal carbon: the elephant in the Blue Carbon room

Biology Letters, Journal Year: 2018, Volume and Issue: 14(6), P. 20180236 - 20180236

Published: June 1, 2018

Macroalgae form the most extensive and productive benthic marine vegetated habitats globally but their inclusion in Blue Carbon (BC) strategies remains controversial. We review arguments offered to reject or include macroalgae BC framework, identify challenges that have precluded from being incorporated so far. Evidence support significant carbon burial is compelling. The they supply sediment stocks angiosperm already included current assessments, are de facto recognized as important donors of BC. key (i) documenting macroalgal sequestered beyond habitat, (ii) tracing it back source habitats, (iii) showing management actions at habitat lead increased sequestration sink site. These apply equally exported coastal habitats. Because large support, incorporation into accounting an imperative. This requires a paradigm shift procedures well developing methods enable capacity trace donor ocean.

Language: Английский

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