Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

Molecular Ecology, Journal Year: 2017, Volume and Issue: 26(21), P. 5872 - 5895

Published: Sept. 18, 2017

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid of DNA from diverse kinds environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences eDNA a taxonomic name is called "eDNA metabarcoding" and offers powerful molecular tool capable noninvasively surveying species richness many ecosystems. Here, review use metabarcoding for animal plant richness, challenges in using approaches estimate relative abundance. We highlight applications freshwater, marine terrestrial environments, this broad context, distill what known about different sample types approximate space across time. provide guiding questions study design discuss workflow focus primers library preparation methods. additionally important criteria consideration bioinformatic filtering data sets, recommendations increasing transparency. Finally, looking future, emerging ecology, conservation, invasion biology, biomonitoring, can empower citizen science education.

Language: Английский

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Environmental DNA

Oxford University Press eBooks, Journal Year: 2018, Volume and Issue: unknown

Published: Feb. 15, 2018

Abstract Environmental DNA (eDNA), i.e. released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on distribution or feeding habits of species. It has therefore great potential for applications ecology biodiversity management. However, this research field is fast-moving, involves different areas expertise currently lacks approaches, which calls an up-to-date comprehensive synthesis. monitoring covers current methods based eDNA, with particular focus “eDNA metabarcoding”. Intended scientists managers, it provides background allow design sound experiments. revisits all steps necessary produce high-quality metabarcoding data such as sampling, metabarcode design, optimization PCR sequencing protocols, well analysis large datasets. All these are presented discussing challenges eDNA-based approaches infer parameters ecological processes. The last chapters book review how been used so far unravel novel patterns diversity space time, detect species, answer new questions various ecosystems organisms. constitutes essential reading graduate students, researchers practitioners who do not have strong molecular genetics willing use eDNA biomonitoring.

Language: Английский

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Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects

Biodiversity and Conservation, Journal Year: 2020, Volume and Issue: 29(7), P. 2089 - 2121

Published: April 8, 2020

Language: Английский

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Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment

Scientific Reports, Journal Year: 2017, Volume and Issue: 7(1)

Published: Sept. 19, 2017

Abstract Effective marine management requires comprehensive data on the status of biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating biota ecosystems. Here, we investigated potential eDNA to inform breadth present tropical environment. Directly sequencing using shotgun approach resulted only 0.34% 22.3 million reads assigning eukaryotes, highlighting inefficiency this method assessing eukaryotic diversity. In contrast, ‘tree life’ (ToL) metabarcoding and 20-fold fewer reads, could detect 287 families across major divisions eukaryotes. Our also show best performing ‘universal’ PCR assay recovered 44% eukaryotes identified all assays, need multiple assays catalogue Lastly, focusing fish genus Lethrinus , intra- inter-specific haplotypes samples, illustrating be used explore diversity beyond taxon identifications. Given sensitivity low cost advocate rapidly integrated into biomonitoring programs.

Language: Английский

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Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive

Water Research, Journal Year: 2018, Volume and Issue: 138, P. 192 - 205

Published: March 20, 2018

Language: Английский

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Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment

Frontiers in Environmental Science, Journal Year: 2017, Volume and Issue: 5

Published: April 9, 2017

A central challenge in the present era of biodiversity loss is to assess and manage human impacts on freshwater ecosystems. Macroinvertebrates are an important group for bioassessment as many taxa show specific responses environmental conditions. However, generating accurate macroinvertebrate inventories based larval morphology difficult error-prone. Here, DNA metabarcoding provides new opportunities. Its potential accurately identify invertebrates bulk samples species level, has been demonstrated several case studies. identification often limited by primer bias, potentially leading sample remaining undetected. Thus, success emerging technique critically relies carefully evaluating primers. We used R package PrimerMiner obtain process cytochrome c oxidase I (COI) sequence data 15 most globally relevant invertebrate groups stream assessment. Using these alignments, we developed four combinations optimized macrozoobenthos. All primers were evaluated sequencing ten mock community samples, each consisting 52 taxa. Additionally, popular from literature tested silico against groups. The varied amplification efficiency number detected taxa, yet all more than standard 'Folmer' barcoding Two showed consistent a previously ribosomal marker (16S) 42 insect samples. In evaluation revealed critical design flaws some commonly literature. demonstrate reliable strategy develop using tool PrimerMiner. almost argue that high base degeneracy necessary decrease bias confirmed experimental results evaluation. further currently studies may not be suitable macroinvertebrates. Therefore, careful region / ecosystem needed before can routine

Language: Английский

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Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement

Molecular Ecology Resources, Journal Year: 2018, Volume and Issue: 19(2), P. 426 - 438

Published: Dec. 21, 2018

While in recent years environmental DNA (eDNA) metabarcoding surveys have shown great promise as an alternative monitoring method, the integration into existing marine programs may be confounded by dispersal of eDNA signal. Currents and tidal influences could transport over distances, inducing false-positive species detection, leading to inaccurate biodiversity assessments and, ultimately, mismanagement environments. In this study, we determined ability distinguish localized signals obtained from four habitats within a small spatial scale (<5 km) subject significant along-shore water flow. Our survey detected 86 genera, 77 families across 11 phyla using three established assays targeting fish (16S rRNA gene), crustacean gene) eukaryotic (cytochrome oxidase subunit 1) diversity. Ordination cluster analyses for both taxonomic OTU data sets show distinct between sampled habitats, suggesting among was limited. Individual taxa with strong habitat preferences displayed accordance their respective habitat, whereas known less habitat-specific generated more ubiquitous signals. add evidence that environments detect broad range are spatially discrete. work also highlights refinement assay choice is essential realize full potential programs.

Language: Английский

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Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms

Communications Biology, Journal Year: 2018, Volume and Issue: 1(1)

Published: Jan. 15, 2018

Accurate quantification of biodiversity is fundamental to understanding ecosystem function and for environmental assessment. Molecular methods using DNA (eDNA) offer a non-invasive, rapid, cost-effective alternative traditional assessments, which require high levels expertise. While eDNA analyses are increasingly being utilized, there remains considerable uncertainty regarding the dynamics multispecies eDNA, especially in variable systems such as rivers. Here, we utilize four sets upland stream mesocosms, across an acid-base gradient, assess temporal degradation eDNA. Sampling included water column biofilm sampling over time with quantified qPCR. Our findings show that persistence lotic sampled from biofilm, decays non-detectable within 2 days acidic environments accelerate process. Collectively, results provide basis predictive framework relationship between spatio-temporally dynamic river ecosystems.

Language: Английский

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Effect of water temperature and fish biomass on environmental DNA shedding, degradation, and size distribution

Ecology and Evolution, Journal Year: 2019, Volume and Issue: 9(3), P. 1135 - 1146

Published: Jan. 21, 2019

Environmental DNA (eDNA) analysis has successfully detected organisms in various aquatic environments. However, there is little basic information on eDNA, including the eDNA shedding and degradation processes. This study focused water temperature fish biomass showed that shedding, degradation, size distribution varied depending biomass. The tank experiments consisted of four levels three levels. total size-fractioned from Japanese Jack Mackerels (Trachurus japonicus) were quantified before after removing fish. results rate increased at higher larger biomass, decay also In addition, small-sized fractions proportionally temperatures, these proportions among After tanks, percentage temporally decreased when fraction was >10 µm, while smaller increased. These have potential to make use more widespread future.

Language: Английский

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Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds

Hydrobiologia, Journal Year: 2018, Volume and Issue: 826(1), P. 25 - 41

Published: Sept. 3, 2018

Environmental DNA (eDNA) analysis is a rapid, non-invasive, cost-efficient biodiversity monitoring tool with enormous potential to inform aquatic conservation and management. Development ongoing, strong commercial interest, new uses are continually being discovered. General applications of eDNA guidelines for best practice in freshwater systems have been established, but habitat-specific assessments lacking. Ponds highly diverse, yet understudied that could benefit from monitoring. However, ponds methodological constraints specific these environments remain unaddressed. Following stakeholder workshop 2017, researchers combined knowledge expertise review challenges must be addressed the future consistency ponds. The greatest pond surveys representative sampling, capture, PCR inhibition. We provide recommendations inhibition testing, laboratory practice, which should aid ongoing projects If implemented, will contribute towards an eventual broad standardisation research room tailor workflows optimal different applications. Such more robust, comparable, ecologically meaningful data enable effective management biodiversity.

Language: Английский

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