To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography

BMC Bioinformatics, Journal Year: 2021, Volume and Issue: 22(1)

Published: April 5, 2021

The recent blooming of metabarcoding applications to biodiversity studies comes with some relevant methodological debates. One such issue concerns the treatment reads by denoising or clustering methods, which have been wrongly presented as alternatives. It has also suggested that denoised sequence variants should replace clusters basic unit analyses, missing fact are a proxy for species-level entities, in studies. We argue here methods developed and tested ribosomal markers uncritically applied highly variable cytochrome oxidase I (COI) without conceptual operational (e.g., parameter setting) adjustment. COI naturally high intraspecies variability be assessed reported, it is source valuable information. contend not Rather, they complementary both used together pipelines.Using dataset from benthic marine communities, we compared two procedures (based on UNOISE3 DADA2 algorithms), set suitable parameters clustering, these steps different orders. Our results indicated algorithm preserved higher intra-cluster variability. introduce program DnoisE implement taking into account natural (measured entropy) each codon position protein-coding genes. This correction increased number sequences retained 88%. order (denoising clustering) had little influence final outcome.We highlight need combining adequate choice stringency parameters, metabarcoding. present uses coding properties this marker improve step. recommend researchers report their terms (a haplotypes) formed species), avoid collapsing latter single representative. will allow at cluster (ideally equating diversity) level, ease additivity comparability between

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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Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance

Water, Journal Year: 2021, Volume and Issue: 13(8), P. 1113 - 1113

Published: April 18, 2021

The field of eDNA is growing exponentially in response to the need for detecting rare and invasive species management conservation decisions. Developing technologies standard protocols within biosecurity sector must address myriad challenges associated with marine environments, including salinity, temperature, advective deposition processes, hydrochemistry pH, contaminating agents. These approaches also provide a robust framework that meets decisions regarding threats human health, environmental resources, economic interests, especially areas limited clean-laboratory resources experienced personnel. This contribution aims facilitate dialogue innovation this by reviewing current sample collection, post-sampling capture concentration eDNA, preservation, extraction, all through monitoring lens.

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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Metabarcoding as a quantitative tool for estimating biodiversity and relative biomass of marine zooplankton

ICES Journal of Marine Science, Journal Year: 2021, Volume and Issue: 78(9), P. 3342 - 3355

Published: Aug. 17, 2021

Abstract Although metabarcoding is a well-established tool for describing diversity of pelagic communities, its quantitative value still controversial, with poor correlations previously reported between organism abundance/biomass and sequence reads. In this study, we explored an enhanced approach by whole zooplankton communities using highly degenerate primer set the mitochondrial marker cytochrome oxidase I compared results to biomass estimates obtained traditional morphological processing samples. As expected, detected species richness was 3–4 times higher processing, highest differences found in meroplankton fraction. About 75% identified microscopy were also recovered run. Within taxa both approaches, relative numbers counts showed strong relationship their biomass, estimated from length-weight regressions, wide range metazoan taxa. The crustaceans lowest meroplanktonic larvae. Our show that improved taxonomic resolution, universal coverage metazoans, reduced bias, availability comprehensive reference database, allow rapid relatively inexpensive hundreds samples at resolution than sorting. described can therefore be widely applied monitoring or ecological studies.

Language: Английский

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Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates

Water, Journal Year: 2021, Volume and Issue: 13(3), P. 331 - 331

Published: Jan. 29, 2021

Benthic macroinvertebrates are among the most used biological quality elements for assessing condition of all types aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review 90 publications on use DNA metabarcoding benthic in bioassessments. Metabarcoding bulk macrozoobenthos has been preferentially waters, whereas marine environmental (eDNA) from sediment communities deployed artificial structures favored. extraction done predominantly through commercial kits, cytochrome c oxidase subunit I (COI) been, far, marker, occasionally combined with others, namely, 18S rRNA gene. include lack standardized protocols broad-coverage primers, incompleteness reference libraries, inability to reliably extrapolate abundance data. In addition, morphology versus benchmarking ecological status biotic indexes required allow general implementation higher end-user confidence. The increased sensitivity, high throughput, faster execution can provide much spatial temporal data resolution status, thereby being more responsive immediate management needs.

Language: Английский

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Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

Scientific Reports, Journal Year: 2021, Volume and Issue: 11(1)

Published: April 12, 2021

Abstract Despite representing one of the largest biomes on earth, biodiversity deep seafloor is still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories and surveys, yet requires standardized sampling approaches careful choice environmental substrate. Here, we aimed to optimize genetic assessment prokaryote (16S), protistan (18S V4), metazoan V1–V2, COI) communities, by evaluating strategies sediment aboveground water, deployed simultaneously at deep-sea site. For sediment, while size-class sorting through sieving had no significant effect total detected alpha diversity resolved similar taxonomic compositions phylum level all markers studied, it effectively increased detection meiofauna phyla. large volumes obtained from an in situ pump (~ 6000 L) significantly more than 7.5 L collected boxes. However, being limited larger mesh sizes (> 20 µm), only captured a fraction microbial diversity, boxes allowed access pico- nanoplankton. More importantly, communities characterized water samples differed those whatever volume used, both sample types shared between 3 8% molecular units. Together, these results underline that may be recommended when targeting metazoans, does not represent alternative benthic diversity.

Language: Английский

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Environmental RNA as a Tool for Marine Community Biodiversity Assessments

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: Oct. 22, 2022

Abstract Microscopic organisms are often overlooked in traditional diversity assessments due to the difficulty of identifying them based on morphology. Metabarcoding is a method for rapidly where Environmental DNA (eDNA) used as template. However, legacy problematically detected from no longer environment during sampling. RNA (eRNA), which only produced by living organisms, can also be collected environmental samples and metabarcoding. The aim this study was determine differences community composition between eRNA eDNA templates Using mesocosms containing field-collected communities an estuary, were co-extracted sediment, libraries prepared two loci (18S COI), sequenced using Illumina MiSeq. Results show higher number unique sequences both markers α-diversity compared eDNA. Significant all β-diversity metrics detected. This first demonstrate with estuarine system illustrates broad applications tool assessing benthic diversity, particularly conservation management applications.

Language: Английский

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EnvironmentalDNAsurveys of African biodiversity: State of knowledge, challenges, and opportunities

Environmental DNA, Journal Year: 2022, Volume and Issue: 5(1), P. 12 - 17

Published: Sept. 23, 2022

Abstract Environmental DNA surveys have become a well‐established tool for detecting natural communities, showing excellent promise supporting biodiversity monitoring, conservation, and management efforts. Africa is continent of exceptional biodiversity, threatened not only by anthropogenic pressures but also general lack research capacity infrastructure, limiting evaluation monitoring ecosystems. This commentary explores the use environmental in surveying diversity, rapidly moving field, within context capturing Africa's capital. Through an extensive literature search filtering, 65 papers from 22 countries were identified, with Madagascar forming bulk (~38%), many represented one to three papers. There was diverse range studies, more than half reporting on communities or diet analyses; freshwater marine are underrepresented, accounting ~5% studies. some disease particularly freshwater. Disturbingly, representation authors highly skewed highlights ongoing inequality scientific publishing extent parachute science; one‐third ( n = 21) reported no African representation, contrast 18 that had either first senior affiliated institution Africa. The remainder 27) at least author institution. In addition, less appropriate sampling permits. Importantly concerted global effort, building long‐term capacity, through meaningful equitable relationships will help increase self‐sustaining science around technologies based eDNA, thus ensuring humanitarian benefits across

Language: Английский

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Framing Cutting-Edge Integrative Deep-Sea Biodiversity Monitoring via Environmental DNA and Optoacoustic Augmented Infrastructures

Frontiers in Marine Science, Journal Year: 2022, Volume and Issue: 8

Published: Jan. 12, 2022

Deep-sea ecosystems are reservoirs of biodiversity that largely unexplored, but their exploration and biodiscovery becoming a reality thanks to biotechnological advances (e.g., omics technologies) integration in an expanding network marine infrastructures for the seas, such as cabled observatories. While still its infancy, application environmental DNA (eDNA) metabarcoding approaches is revolutionizing monitoring capability. Indeed, analysis eDNA conjunction with collection multidisciplinary optoacoustic data, can provide more comprehensive deep-sea biodiversity. Here, we describe potential acquiring core component ecological capabilities through observatories docked Internet Operated Vehicles (IOVs), crawlers. Furthermore, critical overview four areas development: (i) Integrating imaging; (ii) Development repositories cross-linking other databases; (iii) Artificial Intelligence analyses imaging data; (iv) Benefits augmented conservation sustainable management Finally, discuss technical limitations recommendations future deep-sea. It hoped this review will frame direction exciting journey remote yet vulnerable our planet, overall aim understand hence manage protect vital resources.

Language: Английский

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