Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution

The Science of The Total Environment, Год журнала: 2023, Номер 873, С. 162322 - 162322

Опубликована: Фев. 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.

Язык: 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, Год журнала: 2022, Номер 31(6), С. 1820 - 1835

Опубликована: Янв. 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.

Язык: Английский

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Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Molecular Ecology, Год журнала: 2022, Номер 31(20), С. 5132 - 5164

Опубликована: Авг. 16, 2022

Abstract Vast global declines of freshwater and marine fish diversity population abundance pose serious threats to both ecosystem sustainability human livelihoods. Environmental DNA (eDNA)‐based biomonitoring provides robust, efficient, cost‐effective assessment species occurrences trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks facilitate conservation fisheries management. However, the many technical considerations rapid developments underway eDNA arena can overwhelm researchers practitioners new field. Here, we systematically analysed 416 studies summarize research terms investigated targets, aims, study systems, reviewed applications, rationales, methodological considerations, limitations methods with an emphasis on research. We highlighted how technology may advance our knowledge behaviour, distributions, genetics, community structures, ecological interactions. also synthesized current several important concerns, including qualitative quantitative power has recover biodiversity abundance, spatial temporal representations respect its sources. To applications implementing techniques, recent literature was summarized generate guidelines effective sampling lentic, lotic, habitats. Finally, identified gaps limitations, pointed out newly emerging avenues eDNA. As optimization standardization improve, should revolutionize monitoring promote management that transcends geographic boundaries.

Язык: Английский

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Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses

Molecular Ecology Resources, Год журнала: 2022, Номер 23(4), С. 742 - 755

Опубликована: Дек. 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.

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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Assemblage-based biomonitoring of freshwater ecosystem health via multimetric indices: A critical review and suggestions for improving their applicability

Water Biology and Security, Год журнала: 2022, Номер 1(3), С. 100054 - 100054

Опубликована: Май 29, 2022

Freshwater biota are more comprehensive and direct indicators of biological impacts, meaningful to the public than water quality or physical habitat surrogates. biotic data multiple developed from them offer a much richer array for assessing impacts pollution controls limited set chemical measures. In recent decades, assemblage-based assessments by ecologists, environmental scientists, agencies have been employed globally determining condition of, threats to, freshwater ecosystems. A key step in this advance has development multimetric indices (MMIs) integrity (IBIs) based on quantitative algae, macrophyte, macroinvertebrate, fish riparian bird assemblages. Europe, where assemblages mandated ecosystem health, many multimetric. However, proliferation MMIs not always occurred through application rigorous study designs monitoring protocols, nor they effectively incorporated functional metrics, stressor assessments, statistical analyses. Therefore, review, we discuss eleven major concerns with (including logistical limitations) encourage widely applicable (transferable) MMI use implementation. Specifically, our focus reference conditions; sampling effort, methods, season; trophic guild definition; metric comprehensiveness, options, screening scoring; validation. could also benefit increased attention ecological mechanisms development, further improve understanding anthropogenic as well rehabilitation effects ecosystems globally. Paying closer designs, should better facilitate degraded ecosystems, aiding conservation healthy

Язык: Английский

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Environmental DNA metabarcoding read numbers and their variability predict species abundance, but weakly in non‐dominant species

Environmental DNA, Год журнала: 2022, Номер 5(5), С. 1092 - 1104

Опубликована: Сен. 30, 2022

Abstract Metabarcoding of environmental DNA (eDNA) provides more comprehensive, efficient, and non‐invasive sampling biological communities than conventional methods. However, limitations metabarcoding include taxon‐specific biases in amplification sequencing that distort assessments community composition. Further, hyper‐abundant species may disproportionately affect composition impair the detection rare (i.e., “species masking”). In this study, we examine methodological approaches to improve eDNA structure using fish diversity a pond south Florida MiFish primers modified cichlid detection. Mitochondrial 12S amplicon via Illumina NovaSeq was analyzed DADA2 model‐based exact sequence inference. The abundances system were recorded during piscicide treatment subsequent native restocking. Our results demonstrate (1) ultra‐high‐throughput on newer patterned flow cell provided reliable very taxa—with detections single individual. (2) Read numbers significantly correlated total surface area population, numerical abundance lesser degree; however, dominant taxa largely drove those correlations, simulations showed most abundant will have disproportionate effects strength correlation. (3) read number coefficient variation for each across spatially separated replicate samples provide less biased estimates compared with based average counts. Finally, (4) inference detected multiple haplotypes population genetic within species. real‐world capacity reveal reliably detect unique shows can, limited degree, be used infer size populations. Careful examination among spatial are required rigorous eDNA‐based structure. freshwater haplotypes. species' populations, allowing conditional inferences sizes. indicated toward

Язык: Английский

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Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs

Environmental DNA, Год журнала: 2023, Номер 5(4), С. 671 - 682

Опубликована: Май 16, 2023

Abstract Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems informing policy decision‐making, especially in an era massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at forefront technological advances monitoring, last few years have seen major progress solutions to technical challenges from laboratory bioinformatics. Water eDNA has been shown allow fast efficient recovery signals, but rapid pace development meant that some important principles regarding sampling design, which well established traditional inventories, neglected. Using a spatially explicit river flow model, we illustrate how must be adjusted size watercourse increase quality signal recovered. We additionally investigate effect parameters (volume, number sites, sequencing depth) detection probability empirical data set. Based principles, propose aquatic replication volume scaled match organisms' ecosystems' properties provide reliable estimates. present generalizable conceptual equation describing features as function ecosystem monitored, abundance target organisms, procedure. The aim this formalization enhance standardization critical steps design inventory studies using eDNA. More robust standards will generate more eDNA, necessary method's long‐term plausibility comparability.

Язык: Английский

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Systematic review of marine environmental DNA metabarcoding studies: toward best practices for data usability and accessibility

PeerJ, Год журнала: 2023, Номер 11, С. e14993 - e14993

Опубликована: Март 24, 2023

The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR–findable, accessible, interoperable, and reusable–despite growing awareness the importance such practices. In order to better understand these usability challenges, we systematically reviewed 60 peer articles conducting a specific subset eDNA research: metabarcoding studies in marine environments. For each article, characterized approximately 90 features across several categories: general article attributes topics, methodological choices, types metadata included, availability storage sequence data. Analyzing characteristics, identified barriers accessibility, including lack common context vocabulary articles, missing metadata, supplementary information limitations, concentration both sample collection analysis United States. While some require significant effort address, also found many instances where small choices made by authors journals could have an outsized influence on discoverability reusability Promisingly, showed consistency creativity as well strong trend toward open access publishing. Our underscores need think critically about accessibility studies, projects more broadly, continue proliferate.

Язык: Английский

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A spatial fingerprint of land-water linkage of biodiversity uncovered by remote sensing and environmental DNA

The Science of The Total Environment, Год журнала: 2023, Номер 867, С. 161365 - 161365

Опубликована: Янв. 10, 2023

Aquatic and terrestrial ecosystems are tightly connected via spatial flows of organisms resources. Such land-water linkages integrate biodiversity across suggest a association aquatic biodiversity. However, knowledge about the extent this is limited. By combining satellite remote sensing (RS) environmental DNA (eDNA) extraction from river water 740-km2 mountainous catchment, we identify characteristic fingerprint. Specifically, find riverine eDNA diversity with RS spectral upstream, peaking at 400 m distance yet still detectable up to 2.0 km radius. Our findings show that patterns in rivers can be linked functional surrounding provide dominant scale which these strongest. spatially explicit information necessary for understanding linkages.

Язык: Английский

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