Combining multiple markers significantly increases the sensitivity and precision of eDNA‐based single‐species analyses DOI Creative Commons
Rein Brys, David Halfmaerten, Teun Everts

et al.

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(5), P. 1065 - 1077

Published: April 24, 2023

Abstract The analysis of environmental DNA (eDNA) is becoming integrated as an established biomonitoring tool, often characterized by detection limits exceeding those conventional counterparts. However, further improving the sensitivity these methods may be invaluable for early invasive species, or locating remnant populations endangered and adequate quantification their abundances. In this study, we provide empirical evidence showing that implementation multiple genetic markers targeting different loci a surprisingly overlooked strategy to increase single‐species detections abundance, particularly at lower end species abundance range. We analyzed 45 natural eDNA samples obtained from wide range water bodies in Belgium, which either American bullfrog ( Lithobates catesbeianus ) rare European weather loach Misgurnus fossilis occurred under variable abundances, compared success precision simplex (single locus) versus multiplex (multilocus) droplet digital PCR (ddPCR) analyses. Multiplexing primer/probe assays independent resulted significantly enhanced probability analyses, gaining twofold reduction limit (LOD). Also improved reactions, especially low concentration samples. This was reflected significant coefficient variation (CV) among technical replicates, resulting associated decrease (LOQ). conclude use can improve analytical eDNA‐based absolute quantifications.

Language: Английский

Exploitation of environmental DNA (eDNA) for ecotoxicological research: A critical review on eDNA metabarcoding in assessing marine pollution DOI
Sakib Tahmid Rishan, Richard J. Kline, Md Saydur Rahman

et al.

Chemosphere, Journal Year: 2024, Volume and Issue: 351, P. 141238 - 141238

Published: Jan. 21, 2024

Language: Английский

Citations

8
Effectiveness of eDNA for monitoring riverine macroinvertebrates DOI Creative Commons

Imogen P. Poyntz-Wright,

Xavier A. Harrison,

Siffreya Pedersen

et al.

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 941, P. 173621 - 173621

Published: May 28, 2024

Environmental DNA (eDNA) is a technique increasingly used for monitoring organisms in the natural environment including riverine macroinvertebrates. However, effectiveness of eDNA macroinvertebrates compared with more traditional method sampling directly and identifying them via morphological analysis, has not been well established. Furthermore, ability various gene markers PCR primer sets to detect full range invertebrate taxa quantified. Here we conducted meta-analysis available literature, assess detecting applying analysis. We found, on average, sampling, irrespective marker used, detected fewer invertebrates than sampling. The most effective set was mlCOIintF/jgHCO2198, (mlCOIintF- forward primer, jgHCO2198, - reverse primer). Regardless or however, many were by metabarcoding that these invertebrates, over 100 members Arthropoda. failed any species belonging Nematoda, Platyhelminthes, Cnidaria Nematomorpha applied terrestrial systems also do Nematoda. In addition issues, uncertainties relating false positives from upstream sources, stability different species, differences propensity release into organisms, lack sequence information numerous illustrates use yet applicable as robust stand-alone invertebrates. As primary consideration, further methodological developments are needed ensure captures some key freshwater taxa, notably phyla Arthropoda, Nematomorpha.

Language: Английский

Citations

8
Mapping differences in mammalian distributions and diversity using environmental DNA from rivers DOI
Holly A. Broadhurst, Luke M. Gregory,

Emma K. Bleakley

et al.

The Science of The Total Environment, Journal Year: 2021, Volume and Issue: 801, P. 149724 - 149724

Published: Aug. 18, 2021

Language: Английский

Citations

36
Monitoring of environmental DNA from nonindigenous species of algae, dinoflagellates and animals in the North East Atlantic DOI Creative Commons
Steen Wilhelm Knudsen, Martin Hesselsøe, Jens Thaulow

et al.

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 821, P. 153093 - 153093

Published: Jan. 14, 2022

Monitoring the distribution of marine nonindigenous species is a challenging task. To support this monitoring, we developed and validated specificity 12 primer-probe assays for detection environmental DNA (eDNA) from species, all to Europe. The include sturgeons, Pacific red algae, oyster thief, freshwater hydroid Black Sea, Chinese mitten crab, oyster, warty comb jelly, sand gaper, round goby, pink salmon, rainbow trout North American mud crab. We tested in laboratory, on extracted both target non-target ensure that they only amplified intended species. Subsequently, were used analyse water samples collected at 16 different harbours across two seasons during 2017. also included six previously published targeting eDNA goldfish, European carp, dinoflagellates genera Karenia Prorocentrum, heterokont flagellate genus Pseudochattonella. Conventional monitoring was carried out alongside sampling but with one event over year. Because relatively fast easy collect compared conventional sampling, sampled twice 2017, which showed seasonal changes Comparing levels salinity gradients did not show any correlation. A significant correlation observed between number detected methods found using each location. This supports use surveillance where speed relative field combined molecular analysis may provide advantages methods. Prior validation increases taxonomic precision, laboratorial setup facilitates multiple simultaneously. specific presented here can be implemented directly programmes Europe potentially worldwide infer more precise picture dynamics

Language: Английский

Citations

25
Combining multiple markers significantly increases the sensitivity and precision of eDNA‐based single‐species analyses DOI Creative Commons
Rein Brys, David Halfmaerten, Teun Everts

et al.

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(5), P. 1065 - 1077

Published: April 24, 2023

Abstract The analysis of environmental DNA (eDNA) is becoming integrated as an established biomonitoring tool, often characterized by detection limits exceeding those conventional counterparts. However, further improving the sensitivity these methods may be invaluable for early invasive species, or locating remnant populations endangered and adequate quantification their abundances. In this study, we provide empirical evidence showing that implementation multiple genetic markers targeting different loci a surprisingly overlooked strategy to increase single‐species detections abundance, particularly at lower end species abundance range. We analyzed 45 natural eDNA samples obtained from wide range water bodies in Belgium, which either American bullfrog ( Lithobates catesbeianus ) rare European weather loach Misgurnus fossilis occurred under variable abundances, compared success precision simplex (single locus) versus multiplex (multilocus) droplet digital PCR (ddPCR) analyses. Multiplexing primer/probe assays independent resulted significantly enhanced probability analyses, gaining twofold reduction limit (LOD). Also improved reactions, especially low concentration samples. This was reflected significant coefficient variation (CV) among technical replicates, resulting associated decrease (LOQ). conclude use can improve analytical eDNA‐based absolute quantifications.

Language: Английский

Citations

15