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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Predicting the fate of eDNA in the environment and implications for studying biodiversity

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2019, Volume and Issue: 286(1915), P. 20191409 - 20191409

Published: Nov. 20, 2019

Environmental DNA (eDNA) applications are transforming the standard of characterizing aquatic biodiversity via presence, location and abundance collected from environmental samples. As eDNA studies use fragments as a proxy for presence organisms, ecological properties complex dynamic environments which is sampled need to be considered accurate biological interpretation. In this review, we discuss role that differing play on major processes undergoes between organism collection, including shedding, decay transport. We focus mechanistic understanding these highlight how transport models being developed towards more robust predictions fate eDNA. conclude with five recommendations researchers practitioners, advance current best practices, well support future model spatio-temporal persistence.

Language: Английский

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Non‐specific amplification compromises environmental DNA metabarcoding with COI

Methods in Ecology and Evolution, Journal Year: 2019, Volume and Issue: 10(11), P. 1985 - 2001

Published: Aug. 2, 2019

Abstract Metabarcoding extra‐organismal DNA from environmental samples is now a key technique in aquatic biomonitoring and ecosystem health assessment. Of critical consideration when designing experiments, especially so developing community standards legislative frameworks, the choice of genetic marker primer set. Mitochondrial cytochrome c oxidase subunit I (COI), standard barcode for animals, with its extensive reference library, taxonomic discriminatory power predictable sequence variation, natural many metabarcoding applications. However, targeting specific groups samples, utility COI has yet to be fully scrutinized. Here, by using case study marine freshwater fishes British Isles, we quantify silico performance twelve pairs four mitochondrial loci – COI, b , 12S 16S terms library coverage, universality. We subsequently test vitro three one their specificity, reproducibility, congruence independent datasets derived traditional survey methods at five estuarine coastal sites around English Channel North Sea. Our results show that aqueous low template concentrations, both metazoan‐targeted fish‐targeted primers perform poorly comparison 12S, exhibiting levels reproducibility due non‐specific amplification prokaryotic non‐target eukaryotic DNAs. An ideal metabarcode would have an upon which custom could designed, either broad assessments biodiversity, or taxon surveys. Such database available but specificity hinders practical application, while conversely, offer high lack adequate references. The latter, however, can mitigated expanding concept barcodes include whole genomes generated genome‐skimming existing tissue collections.

Language: Английский

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eDNA metabarcoding survey reveals fine‐scale coral reef community variation across a remote, tropical island ecosystem

Molecular Ecology, Journal Year: 2020, Volume and Issue: 29(6), P. 1069 - 1086

Published: Feb. 11, 2020

Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies from environmental samples, can detect diverse array of marine species filtered seawater samples. There is growing potential to integrate eDNA alongside existing monitoring methods in order establish or improve the assessment diversity. Remote island reefs are increasingly vulnerable climate-related threats and as such there pressing need cost-effective whole-ecosystem surveying baseline biodiversity, study assemblage changes ultimately develop sustainable management plans. We investigated utility metabarcoding high-resolution, multitrophic biomonitoring tool at Cocos (Keeling) Islands, Australia (CKI)-a remote tropical coral reef atoll situated within eastern Indian Ocean. Metabarcoding assays targeting mitochondrial 16S rRNA CO1 genes, well 18S nuclear gene, were applied 252 surface samples collected 42 sites 140 km2 area. Our successfully detected wide range bony fish elasmobranchs (244 taxa), crustaceans (88), molluscs (37) echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across ecosystem demonstrating localisation signals, despite extensive tidal oceanic movements. In addition, we document putative new occurrence records 46 taxa compare efficiency our approach visual survey techniques CKI. demonstrates multimarker capturing biodiversity an entire sets important ongoing management.

Language: Английский

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Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool?

Genes, Journal Year: 2019, Volume and Issue: 10(3), P. 192 - 192

Published: March 1, 2019

Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations contribute to effective conservation management. However, collecting samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way sample material non-invasively without requiring visual observation. While eDNA has been trialed extensively as biodiversity biosecurity monitoring tool strong taxonomic focus, it yet fully explored means for obtaining population information. Here, we review current research that employs approaches the study populations. We outline challenges facing eDNA-based methodologies, suggest avenues future developments. advocate further optimizations, this emergent field holds great potential part genetics toolkit.

Language: Английский

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Meta‐analysis shows that environmental DNA outperforms traditional surveys, but warrants better reporting standards

Ecology and Evolution, Journal Year: 2021, Volume and Issue: 11(9), P. 4803 - 4815

Published: March 18, 2021

Decades of environmental DNA (eDNA) method application, spanning a wide variety taxa and habitats, has advanced our understanding eDNA underlined its value as tool for conservation practitioners. The general consensus is that methods are more accurate cost-effective than traditional survey methods. However, they formally approved just few species globally (e.g., Bighead Carp, Silver Great Crested Newt). We conducted meta-analysis studies directly compare with surveys to evaluate the assertion consistently "better."Environmental publications multiple or single macro-organism detection were identified using Web Science, by searching "eDNA" "environmental DNA" across papers published between 1970 2020. used, focal taxa, habitats surveyed, quantitative categorical results collated analyzed determine whether under what circumstances outperforms surveys.Results show cheaper, sensitive, detect This is, however, taxa-dependent, amphibians having highest potential survey. Perhaps most strikingly, 535 reviewed 49 quantified probability both three times likely give qualitative statements performance.

Language: Английский

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Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water

Scientific Reports, Journal Year: 2019, Volume and Issue: 9(1)

Published: Aug. 9, 2019

Environmental DNA (eDNA) surveys are increasingly being used for biodiversity monitoring, principally because they sensitive and can provide high resolution community composition data. Despite considerable progress in recent years, eDNA studies examining how different environmental sample types affect species detectability remain rare. Comparisons of samples especially important providing best practice guidance on early detection subsequent mitigation non-indigenous species. Here we metabarcoding COI (cytochrome c oxidase subunit I) 18S (nuclear small ribosomal DNA) genes to compare between sediment water artificial coastal sites across the United Kingdom. We first detected markedly communities a consistently greater number distinct operational taxonomic units compared water. then our datasets with previously published rapid assessment found excellent concordance among survey techniques. Finally, many species, including several newly introduced highlighting utility both temporal / spatial monitoring conclude that careful consideration type is needed when conducting surveys, assessing change.

Language: Английский

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Environmental DNA Metabarcoding: A Novel Method for Biodiversity Monitoring of Marine Fish Communities

Annual Review of Marine Science, Journal Year: 2021, Volume and Issue: 14(1), P. 161 - 185

Published: Aug. 5, 2021

Environmental DNA (eDNA) is genetic material that has been shed from macroorganisms. It received increased attention as an indirect marker for biodiversity monitoring. This article reviews the current status of eDNA metabarcoding (simultaneous detection multiple species) a noninvasive and cost-effective approach monitoring marine fish communities discusses prospects this growing field. coamplifies short fragments across wide variety taxa and, coupled with high-throughput sequencing technologies, allows massively parallel to be performed simultaneously dozens hundreds samples. can predict species richness in given area, detect habitat segregation biogeographic patterns small large spatial scales, monitor spatiotemporal dynamics communities. In addition, it anthropogenic impact on through evaluation their functional diversity. Recognizing strengths limitations will help ensure continuous at sites useful ecosystem conservation sustainable use fishery resources, possibly contributing achieving targets United Nations' Sustainable Development Goal 14 2030.

Language: Английский

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The Essentials of Marine Biotechnology

Frontiers in Marine Science, Journal Year: 2021, Volume and Issue: 8

Published: March 16, 2021

Coastal countries have traditionally relied on the existing marine resources (e.g., fishing, food, transport, recreation, and tourism) as well tried to support new economic endeavors (ocean energy, desalination for water supply, seabed mining). Modern societies lifestyle resulted in an increased demand dietary diversity, better health well-being, biomedicines, natural cosmeceuticals, environmental conservation, sustainable energy sources. These societal needs stimulated interest of researchers diverse underexplored environments promising sources biomolecules biomass, they are addressed by emerging field (blue) biotechnology. Blue biotechnology provides opportunities a wide range initiatives commercial pharmaceutical, biomedical, cosmetic, nutraceutical, feed, agricultural, related industries. This article synthesizes essence, opportunities, responsibilities, challenges encountered outlines attainment valorization directly derived or bio-inspired products from organisms. First, concept bioeconomy is introduced. Then, diversity bioresources including overview most prominent organisms their potential biotechnological uses described. followed introducing methodologies exploration these main use case scenarios food agronomy, bioremediation climate change, materials, healthcare, well-being sectors. The key aspects fields legislation funding provided, with emphasis importance communication stakeholder engagement at all levels development. Finally, vital overarching concepts, such quadruple helix Responsible Research Innovation principle highlighted important follow within field. authors this review collaborating under European Commission-funded Cooperation Science Technology (COST) Action Ocean4Biotech – transdisciplinary networking platform focus study state affairs.

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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