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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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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A practical guide to DNA-based methods for biodiversity assessment

Pensoft Publishers eBooks, Journal Year: 2021, Volume and Issue: unknown

Published: Dec. 2, 2021

DNA-based methods for species detection and identification have revolutionised our ability to assess biodiversity in terrestrial, freshwater marine ecosystems. Starting from the seminal study that used eDNA detect invasive american bullfrogs France (Gentile Francesco Ficetola et al. 2008)), research conducted over last decade has demonstrated power of these approaches surveying a wide range groups. Early applications included use monitor Asian Carp USA (Jerde 2013). Following heavy scrutiny, method was eventually adopted, is still employed today by United States Geological Survey (USGS). A flurry followed, with tests designed many threatened including New zealand mudsnails (Goldberg 2013), crayfish (Geerts 2018), gammarids (R. Blackman 2017), great crested newts (Biggs 2015). The newt test been regulatory monitoring UK since 2014. During same time period, there proliferation studies high-throughput sequencing describe whole communities organisms mixed environmental samples, using an approach termed DNA metabarcoding (Taberlet 2012).

Language: Английский

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Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 23(4), P. 742 - 755

Published: Dec. 8, 2022

Assessment of biodiversity using metabarcoding data, such as from bulk or environmental DNA sampling, is becoming increasingly relevant in ecology, sciences and monitoring. Thereby, the taxonomic identification species their sequences relies strongly on reference databases that link genetic to names. These vary completeness availability, depending group studied region targeted. The incompleteness an important argument explain nondetection by supposedly present. However, there exist further generally overlooked problems with can lead false inaccurate inferences assignment. Here, we synthesize all possible inherent databases. In particular, identify a complete, mutually nonexclusive list seven classes challenges when it comes selecting, developing database for are: (i) mislabelling, (ii) sequencing errors, (iii) sequence conflict, (iv) (v) low resolution, (vi) missing taxa (vii) intraspecific variants. For each problem identified, provide description consequences assignment process. We illustrate respective examples taken literature obtained quantitative analyses public databases, GenBank BOLD. Finally, discuss solutions identified how navigate them. Only raising users' awareness limitations data will adequate interpretations these be achieved.

Language: Английский

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The current state of eDNA research in freshwater ecosystems: are we shifting from the developmental phase to standard application in biomonitoring?

Hydrobiologia, Journal Year: 2022, Volume and Issue: 850(6), P. 1263 - 1282

Published: May 12, 2022

Abstract Environmental DNA (eDNA) has seen a massive increase in application freshwater systems with concurrent growth protocol developments and drive to gain better understanding of the ‘ecology’ eDNA. This raises question whether we are currently still an early, developmental phase eDNA-based assessments or already transitioning into more applied stage for biomonitoring. I conducted systematic literature review on 381 eDNA-focused studies targeting macro-organisms over last 5 years, assessing study goals, methods, target taxa design aspects. The results show biomonitoring-focused throughout while fraction investigating eDNA decreased. metabarcoding significantly increased applying qPCRs tentatively declined. A geographic inequality was observed concerning numbers goals biased towards global North. Descriptive increased, but in-field conventional methods combined revealed no trend. These shift application-focused work also reveal this field be developing. In transitional phase, practitioners need ensure consistency data comparability long-term monitoring programmes.

Language: Английский

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Towards exhaustive community ecology via DNA metabarcoding

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(23), P. 6320 - 6329

Published: Feb. 10, 2023

Abstract Exhaustive biodiversity data, covering all the taxa in an environment, would be fundamental to understand how global changes influence organisms living at different trophic levels, and evaluate impacts on interspecific interactions. Molecular approaches such as DNA metabarcoding are boosting our ability perform inventories. Nevertheless, even though a few studies have recently attempted exhaustive reconstructions of communities, holistic assessments remain rare. The majority published last years used just one or two markers analysed limited number taxonomic groups. Here, we provide overview emerging that can allow all‐taxa biological by combining large specific primers, exploiting power universal primers obtain good information key while limiting overlooked biodiversity. Multiplexes shotgun sequencing capture enrichment may better coverage compared standard metabarcoding, but still require major methodological advances. identify strengths limitations approaches, suggest new development lines might improve broad scale analyses near future. More ecological communities greatly increase value studies, improving understanding consequences ongoing environmental multiple components

Language: Английский

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Environmental DNA: The next chapter

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(11)

Published: April 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.

Language: Английский

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Emerging technologies in citizen science and potential for insect monitoring

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1904)

Published: May 5, 2024

Emerging technologies are increasingly employed in environmental citizen science projects. This integration offers benefits and opportunities for scientists participants alike. Citizen can support large-scale, long-term monitoring of species occurrences, behaviour interactions. At the same time, foster participant engagement, regardless pre-existing taxonomic expertise or experience, permit new types data to be collected. Yet, may also create challenges by potentially increasing financial costs, necessitating technological demanding training participants. Technology could reduce people's direct involvement engagement with nature. In this perspective, we discuss how current have spurred an increase projects implementation emerging enhance scientific impact public engagement. We show technology act as (i) a facilitator efforts, (ii) enabler research opportunities, (iii) transformer science, policy participation, but become (iv) inhibitor equity rigour. is developing fast promises provide many exciting insect monitoring, while seize these must remain vigilant against potential risks. article part theme issue ‘Towards toolkit global biodiversity monitoring’.

Language: Английский

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Trade‐offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on “Environmental DNA: What's behind the term?” by Pawlowski et al., (2020)

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(19), P. 4601 - 4605

Published: May 25, 2021

Abstract In a recent paper, “Environmental DNA: What's behind the term? Clarifying terminology and recommendations for its future use in biomonitoring,” Pawlowski et al . argue that term eDNA should be used to refer pool of DNA isolated from environmental samples, as opposed only extra‐organismal macro‐organisms. We agree with this view. However, we are concerned their proposed two‐level specifying sampling environment targeted taxa is overly simplistic might hinder rather than improve clear communication about biomonitoring. This based on categories often difficult assign uninformative, it overlooks fundamental distinction within eDNA: type (organismal or extra‐organismal) which ecological interpretations derived.

Language: Английский

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Environmental DNA for biomonitoring

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(13), P. 2931 - 2936

Published: June 27, 2021

In 2012, Molecular Ecology published a special issue on environmental DNA, which provided an overview of the field eDNA research and presented selection papers studies (Taberlet et al., 2012). This also introduced concept Biomonitoring 2.0, advocating for use DNA-based identification taxa in biodiversity surveys ecosystem assessment (Baird & Hajibabaei, Since then, hundreds have been covering various aspects eDNA-based biomonitoring from single-species detection to community impact assessments. Numerous reviews summarized these both freshwater marine environments (Bohmann 2014; Thomsen Willerslev, 2015). The progress made during last ten years has spectacular 2018). Although basic concepts workflow DNA barcoding metabarcoding not changed, technological advances high-throughput sequencing greatly facilitated access data. It become possible monitor with unprecedented precision depth. Massive genomic datasets rapidly generated at relatively low cost. analysis using machine learning other taxonomy-free approaches opened wide doors new groups bioindicators infer ecological status (Cordier 2018, 2019; Pawlowski al. At same time, constant efforts fill gaps reference databases considerably increased effectiveness taxonomic data (Weigand 2019). Astonishingly, rapid technologies are rather timidly implemented routine (Hering 2018; Shackleton 2021). 2.0 is widely endorsed, its acceptance practice hampered reasons. There no consensus whether should only apply conventional (Renovate) or include (Rebuild) (Revolutionize) (see Figure 1). Moreover, three main steps roadmap developed equally. attention given development optimization generation analysis. standardization methods their translation into legislatory framework remain very early stage. One issues impeding application tools concerns lack congruence between results traditional molecular analyses (Aylagas 2020). expected that method "safe use" if it provides almost as one. However, obtaining such perfect often impossible because character different (e.g., abundance individuals vs reads). "ecology" can hardly be translated directly species ecology. numerous biological technical biases affect processing data, impacting interpretation. addresses some challenges by presenting latest discussing strengths limitations when applied biomonitoring. comprises 29 grouped four sections applications. accompanied opinion paper, clarifies terminology relation (Pawlowski first section series analytical (e.g. learning), types shotgun sequencing) status. followed dedicated fish eDNA, whose most advanced. third dealing methodological comparison methods. final presents few examples applications population genetics. genomics enables monitoring microbial meiofaunal communities were previously inaccessible our knowledge ecology limited therefore analytic necessary integrate them bioassessment. begins review implementation strategies diagnostics authors introduce broad categories strategies, including (1) known bioindicators, (2) discovery (3) structural metrics, (4) functional metrics. Each adapted particular type (metabarcoding, metagenomics, metatranscriptomics) rely computational order provide Among tools, seems promising way predict this issue, performance tested case benthic diatoms index used quality rivers streams (Apothéloz-Perret-Gentil study shows supervised performs better than assignment, but predictions similar those obtained assignment approach. efficiency strongly depends completeness database, highlighting need existing gaps, particularly bioindicator taxa. ability de novo prokaryotic multiple anthropogenic impacts estuarine coastal demonstrated Lanzén (2021). compare macrofauna-based indices discuss advantages they more sensitive abiotic pressures. Similar conclusions reached aquaculture (Frühe 2021) oil gas industry (Mauffrey Both demonstrate promote environments. two explore directions further ecogenomic diagnostics. Broman (2021) RNA (eRNA) analyse organic enrichment micro-eukaryotic communities. Compared majority studies, eRNA advantage overcome potential PCR amplification capture organismic response pressures targeting predominantly active cells. Ibrahim historical analyze eutrophication lake phytoplankton 20th century. demonstrates paleo-metabarcoding characterize past establish conditions future monitoring. second diversity. We focus among important perspective advanced (Pont database common regions close (Knebelsberger 2015), fish-specific markers well defined (M. Miya 2015; Valentini 2016; Zhang 2020) protocols sampling established (Masaki 2020; 2016). Currently, considerable directed solve challenging related quantitative inferring Two address proposing estimate Fukaya numerical hydrodynamic models simulate spatial temporal distribution aquatic By integrating measures concentration, estimates comparable echo sounder method. Yates improve correlation concentration allometric scaling coefficients. Such coefficients help adjust values production taking consideration density, biomass metabolic rates characteristic taxon. A understanding how shaped biotic factors, subject following papers. Littlefair seasonal variations thermal stratification influence lakes. show follows niche species, turn may certain seasons. amphibian lentic system was investigated experimentally Brys indicates high decay dispersal, reinforcing accuracy retrieving spatiotemporal occupancy patterns. survey populations section. McColl-Gausden showed generally electrofishing conducting streams, while Aglieri strong complementarity visual capture-based General requires benchmarking against morphotaxonomy-based approaches. commonly achieved samples parallel assessing fit approaches, considered ground truth. bulk morphology-based They present propose solutions outcomes processing. comparative Suter evaluate water zooplankton open ocean, currently monitored continuous plankton recorders. recover morphological analyses, however, selected marker. conclude promising, still refinement before routinely drawn sediment macrofauna salmon farms (He found coherence relative inferred observed much stronger meiofauna, usually included studies. Significant differences extracts adjacent (Antich concluded poor proxy communities, although do exclude taxon-specific could importance marker emphasized macrobenthos metabarcoding. markers, key insect orders (Ephemeroptera, Plecoptera Trichoptera) Ficetola complexity process advocate cover widest range Combining shown match macrobenthic morphotaxonomic (Meyer multimarker approach recommended macroinvertebrate preservative (Martins Despite presence heavily sclerotized exoskeleton act limiting factor reported Gleason accurately represents local stream community, being overwhelmed non-metazoan sequences. difference comparing inventories pond macroinvertebrates (Harper consider complementary suggest combined comprehensive invertebrate community. tool ecosystems highlighted van Loos Nijland affecting improvements overcoming future. five sites Brazilian Atlantic forest one site Cerrado grasslands allowed Lopes (2020) significantly improves methods, confirming frog undetected For years, invertebrate-derived (iDNA) leech blood-meal track mammalian (Schnell Here, Drinkwater assess diversity across gradient degradation Borneo. elusive mammals, iDNA complements camera trapping. optimizations aiming improving surveys. Guerrieri soil preservation richness composition. guidelines optimizing agreement objectives practical constraints project. On hand, Mächler analysis, investigating stringency filtering estimates. Hill numbers comparisons differ articles ground-breaking biodiversity. Martel clearly paired modelling uncover metapopulation dynamics drivers. information endangered distributed metapopulations quite difficult obtain via inventories. Shum Palumbi reanalyzed dataset concerning cobble within kelp ecosystems. focussed intraspecific level structure demographic trends. increases scope value opening towards metaphylogeography (Turon Finally, Sigsgaard successfully tracked insects cow dungs environments, efficient diversity, easy As collection highly diverse. Their ranges tracking surveying impact. Some bioindication systems, whereas others expand inconspicuous, overlooked All attest major done methodology every step contribute understand factors analyses. Yet, despite huge advantages, taken off. now time move transform truly science. crisis global changes call urgent modernization environment. here, top levels scientific excellence many areas. Certainly, there inherent specificity, reason technology less morpho-taxonomic actions ensure build confidence through intercalibration tests. view substantial illustrated content reasonable expect will long coming. Open Access Funding Universite Geneve. conflict interest regarding paper.

Language: Английский

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