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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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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The Multiple States of Environmental DNA and What Is Known about Their Persistence in Aquatic Environments

Environmental Science & Technology, Journal Year: 2022, Volume and Issue: 56(9), P. 5322 - 5333

Published: April 18, 2022

Increased use of environmental DNA (eDNA) analysis for indirect species detection has spurred the need to understand eDNA persistence in environment. Understanding is complex because it exists a mixture different states (e.g., dissolved, particle adsorbed, intracellular, and intraorganellar), each state expected have specific decay rate that depends on parameters. Thus, improving knowledge about conversion rates between reactions degrade needed. Here, we focus eukaryotic extraorganismal eDNA, outline how water chemistry suspended mineral particles likely affect among state, indicate parameters column. On basis deducing these controlling parameters, synthesized literature assess whether could already derive general understanding persisting However, found are often not being measured or reported when measured, many cases very few experimental data exist from which draw conclusions. Therefore, further study aquatic environments We recommend analytic controls can be used during processing potential losses if all were present sample, future work would help determine dominant water.

Language: Английский

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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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MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences

Environmental DNA, Journal Year: 2022, Volume and Issue: 4(4), P. 894 - 907

Published: April 11, 2022

Abstract Analysis of environmental DNA is increasingly used to characterize ecological communities, but the effectiveness this approach depends on accuracy taxonomic reference databases. The MIDORI databases, first released in 2017, were built improve for mitochondrial metazoan (animal) sequences. has now been significantly improved and renamed MIDORI2 (available at http://www.reference‐midori.info ). Like MIDORI, from GenBank contains curated sequences thirteen protein‐coding two ribosomal RNA genes. Coverage substantially expanded cover all eukaryotes, including fungi, green algae land plants, other multicellular algal groups, diverse protist lineages. also includes not only species with full binomials, taxa referred by genus left unspecified (“sp.”). Another new feature updating databases approximately every months version numbers corresponding each release. Additional potentially erroneously annotated have removed. Finally, ability export data files BLAST+ added original preformatted five assignment programs, amino acid are made available As a technical validation, we conducted preliminary comparison performance programs. Results suggest that top hits performed better assigning CO1 than alignment‐free methods based compositional features. Comparing commonly sequences, CO‐ARBitrator BOLD, show broader range non‐metazoan taxa. Overall, many contexts, offers clear advantages: higher diversity variety user‐friendly features, regular updates. particularly well‐suited studies target genes broad primers.

Language: Английский

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Environmental DNA/RNA for pathogen and parasite detection, surveillance, and ecology

Trends in Parasitology, Journal Year: 2023, Volume and Issue: 39(4), P. 285 - 304

Published: Feb. 8, 2023

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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Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 23(2), P. 396 - 409

Published: Sept. 24, 2022

Environmental DNA (eDNA) metabarcoding is an effective method for studying fish communities but allows only estimation of relative species abundance (density/biomass). Here, we combine with the total eDNA amplified by our universal marker (teleo) using a quantitative (q)PCR approach to infer absolute species. We carried out 2850-km survey within Danube catchment spatial integrative sampling protocol coupled traditional electrofishing biomass and density estimation. Total concentrations were highly correlated. The correlation between per taxon specific was comparable strength when all sites pooled remained significant considered separately. Furthermore, nonlinear mixed model showed that richness underestimated amount teleo-DNA extracted from sample below threshold 0.65 × 10

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

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(4), P. 671 - 682

Published: May 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.

Language: Английский

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