Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 21(7), P. 2565 - 2579

Published: May 18, 2021

Abstract Bioinformatic analysis of eDNA metabarcoding data is a crucial step toward rigorously assessing biodiversity. Many programs are now available for each the required analyses, but their relative abilities at providing fast and accurate species lists have seldom been evaluated. We used simulated mock communities real fish to evaluate performance 13 bioinformatic pipelines retrieve occurrence read abundance using 12S mt rRNA gene marker. four indices compare outputs program with samples: sensitivity, F‐measure, root‐mean‐square error (RMSE) on abundances, execution time. found marked differences among only taxonomic assignment step, both in terms F‐measure RMSE. Running time was highly different between step. The fastest best were assembled into pipeline. compared this pipeline constructed from existing toolboxes (OBITools, Barque, QIIME 2). Our Barque obtained all appear be better alternatives analysing when complete reference database available. Analysis also indicated only. This study reveals major during choice algorithm can significant impact diversity estimates should made according objectives study.

Language: Английский

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Revisiting the effect of PCR replication and sequencing depth on biodiversity metrics in environmental DNA metabarcoding

Ecology and Evolution, Journal Year: 2021, Volume and Issue: 11(22), P. 15766 - 15779

Published: Oct. 22, 2021

Abstract Environmental DNA (eDNA) metabarcoding is an increasingly popular tool for measuring and cataloguing biodiversity. Because the environments substrates in which preserved differ considerably, eDNA research often requires bespoke approaches to generating data. Here, we explore how two experimental choices study design—the number of PCR replicates depth sequencing replicates—influence composition consistency taxa recovered from extracts. We perform 24 each six soil samples using most common metabarcodes Fungi Viridiplantae (ITS1 ITS2), sequence replicate average ~84,000 reads. find that are broadly consistent relative abundance dominant taxa, but low unique one or a few replicates. Taxa observed out make up 21–29% total detected. also observe rarefaction influences alpha diversity beta estimates. Read sampling local contribution diversity, placement ordinations, dispersion ordinations. Our results suggest that, because drive some estimates, read depths may be sufficient many biological applications metabarcoding. However, rare stochastically, never fully recover true amplifiable extract. Rare outliers lead differences at different depths. conclude researchers should consider complexity unevenness community when choosing analytical approaches, depths, filtering thresholds arrive stable

Language: Английский

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Environmental DNA Methods for Ecological Monitoring and Biodiversity Assessment in Estuaries

Estuaries and Coasts, Journal Year: 2022, Volume and Issue: 45(7), P. 2254 - 2273

Published: June 25, 2022

Abstract Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for eDNA interpretation were developed primarily freshwater environments have not been well established estuaries marine that are by nature dynamic, turbid, hydrologically complex. context species life history critical successful application of methods, challenges associated with subject a symposium held at University California Davis on January 29, 2020 ( https://marinescience.ucdavis.edu/engagement/past-events/edna ). Here, we elaborate upon topics addressed evaluate monitoring biodiversity studies estuaries. We first provide concise overview science then examine San Francisco Estuary (SFE) as case study illustrate how programs regional guidance future potential applications. Additionally, offer recommendations enhancing communication between scientists natural resource managers, which is essential integrating into existing programs. Our intent create accessible those outside field eDNA, especially without oversimplifying or advantages these methods.

Language: Английский

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Plant biodiversity assessment through soil eDNA reflects temporal and local diversity

Methods in Ecology and Evolution, Journal Year: 2022, Volume and Issue: 14(2), P. 415 - 430

Published: April 12, 2022

Abstract Several studies have shown the potential of eDNA‐based proxies for plant identification, but little is known about their spatial and temporal resolution. This limits its use biodiversity assessments monitoring vegetation responses to environmental changes. Here we calibrate signals detected with soil eDNA surveys by comparing a standard visual above‐ground survey. Our approach compares in an old‐growth boreal forest southern Norway, surveyed 100 permanent 1‐m 2 plots seven times over 30‐year period, single metabarcoding‐based survey from samples collected at same year last On average, 60% 10% vascular plants bryophytes recorded across all were eDNA. Taxa more representative local taxa pool than specific plot, corresponded those period although most closely matched current composition. Soil abundant better rare ones both unrecorded detected. study highlights broad scales. The method's ability detect makes it suitable assessment composition area broad‐scale diversity assessments.

Language: Английский

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Environmental DNA as an emerging tool in botanical research

American Journal of Botany, Journal Year: 2023, Volume and Issue: 110(2)

Published: Jan. 12, 2023

Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species communities), means of elucidating biological interaction networks, window into understanding patterns biodiversity. However, only recently potential eDNA realized in botanical world. Here we synthesize state applications systems with emphases on aquatic, ancient, contemporary sediment, airborne systems, focusing both single-species approaches multispecies community metabarcoding. Further, describe how abiotic biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, relative abundance influence utilization interpretation results. Lastly, explore several areas opportunities for further development tools plants, advancing our knowledge efficacy, utility, cost-effectiveness, ultimately facilitating increased adoption analyses systems.

Language: Английский

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An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: May 23, 2024

Abstract Anthropogenically forced changes in global freshwater biodiversity demand more efficient monitoring approaches. Consequently, environmental DNA (eDNA) analysis is enabling ecosystem-scale assessment, yet the appropriate spatio-temporal resolution of robust assessment remains ambiguous. Here, using intensive, eDNA sampling across space (five rivers Europe and North America, with an upper range 20–35 km between samples), time (19 timepoints 2017 2018) conditions (river flow, pH, conductivity, temperature rainfall), we characterise at which information on diversity animal kingdom can be gathered from eDNA. In space, beta was mainly dictated by turnover, a scale tens kilometres, highlighting that measures are not confounded upstream. Fish communities showed nested assemblages along some rivers, coinciding habitat use. Across time, seasonal life history events, including salmon eel migration, were detected. Finally, effects taxon-specific, reflecting filtering rather than molecules. We conclude riverine metabarcoding measure scales relevant to species community ecology, demonstrating its utility delivering insights into river ecology during change.

Language: Английский

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Comparing eDNA and eRNA Sampling Methodologies From Pond Environments

Aquatic Conservation Marine and Freshwater Ecosystems, Journal Year: 2025, Volume and Issue: 35(2)

Published: Feb. 1, 2025

ABSTRACT Molecular traces are increasingly being applied to assess the presence of species and communities. Studies on environmental DNA (eDNA) have, a large extent, become common practice in detection, but less studies have compared biodiversity estimations with more temporary RNA (eRNA). This study compares metabarcoding results from pond water obtained both molecule types by sequencing V4 region 18S rRNA marker. Water was collected two depths, 20 80 cm, filtered sequentially through filter porosities, 0.45 0.22 μm. Each cut half before fixation either 96% ETOH or RNAlater. The showed no differences between fixatives for molecule. Overall, estimates eDNA significantly overperformed eRNA, likely due higher concentrations terrestrial sources. Comparisons depths variation only, increasing levels found at upper layer. Both pore sizes captured distinctive compositions taxa, where about 30% diversity uniquely identified second, finer filter. Taken together, these findings imply that choice molecular marker, depth size affects pond.

Language: Английский

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Fish community shifts along a strong fluvial environmental gradient revealed by eDNA metabarcoding

Environmental DNA, Journal Year: 2021, Volume and Issue: 4(1), P. 117 - 134

Published: June 1, 2021

Abstract Large rivers and their estuaries are structurally complex comprise a diversity of habitats supporting rich biodiversity. As result, identifying monitoring fish communities using traditional methods in such systems may often be logistically challenging. Using the mitochondrial DNA 12S MiFish primers, we performed an eDNA metabarcoding analysis to assess effect spatial environmental factors on variation community structure along most St. Lawrence River/Estuary/Gulf (Québec Canada), transect spanning 1300 km across from fluviatile non‐tidal section marine environment. A total 129 species were identified including freshwater species. For sectors, 80 compared with 85 previously reported based conventional sampling. also revealed similar River. Furthermore, our study improved current knowledge about brackish sections by describing transition between association drastic shift conditions observed end fluvial estuary beginning middle (brackish) estuary. Altogether, this exemplifies how is powerful tool document shifts large temperate lotic ecosystems.

Language: Английский

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Proper environmental DNA metabarcoding data transformation reveals temporal stability of fish communities in a dendritic river system

Environmental DNA, Journal Year: 2021, Volume and Issue: 3(5), P. 1007 - 1022

Published: June 23, 2021

Abstract Protecting freshwater biodiversity is considered an ultimate challenge but depends on reliable surveys of species distribution and abundance which eDNA metabarcoding (environmental DNA metabarcoding) may offer. To do so, a better understanding the sources temporal variation among data transformation in studies needed. Here, we show that based relative critical to suitable analyses Hellinger performed slightly than other methods. Furthermore, site localities significantly explain variation, while no explained by time sampling. This indicates communities vary more spatially temporally within dendritic system composed small rivers. We then further documented community structure St. Charles River (Québec City, Canada) six its tributaries. revealed existence eight explaining 82.1% read this river network. Moreover, environmental variables sites 53.0% reads, sampling events variation. Altogether, supports claim powerful tool document monitor fish watersheds systems.

Language: Английский

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Plant–animal interactions in the era of environmental DNA (eDNA)—A review

Environmental DNA, Journal Year: 2022, Volume and Issue: 4(5), P. 987 - 999

Published: May 21, 2022

Abstract Plant–animal interactions (PAI) represent major channels of energy transfer through ecosystems, where both positive and antagonistic simultaneously contribute to ecosystem functioning. Monitoring PAI therefore increases the understanding environmental health, integrity, functioning, studying complex accurate, cost‐effective sampling can aid in management detrimental anthropogenic impacts. Environmental DNA (eDNA)‐based monitoring represents an increasingly common, nondestructive approach for biodiversity monitoring, which could help elucidate PAI. Here, we aim provide overall discussion on potential using eDNA study We assessed existing literature this subject from 2009 2021 a freely accessible web search tool. The was conducted by keywords involving PAI, including species‐specific metabarcoding approaches, recovering 43 studies. summarized advantages current limitations such outline research priorities improve future eDNA‐based methods analysis. Among studies identified measure as pollination, herbivory, mutualistic, parasitic relationships, they have often higher taxonomic diversity several direct comparisons with DNA‐based gut/bulk conventional survey methods. Research needs include following: better influencing factors detection involved (e.g., degradation, origin, types), methodological standardization (sampling primer development), more inclusive sequence reference databases. If these are addressed, it will significant impact enable eDNA. In future, implementation particularly benefit scalability biomonitoring surveys that imperative health assessments.

Language: Английский

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