Influence of accuracy, repeatability and detection probability in the reliability of species-specific eDNA based approaches
Journal article
Mauvisseau, Quentin, Burian, Alfred, Gibson, Ceri, Brys, Rein, Ramsey, Andrew and Sweet, Michael 2019. Influence of accuracy, repeatability and detection probability in the reliability of species-specific eDNA based approaches. Scientific Reports. 9 (580), pp. 1-10. https://doi.org/10.1038/s41598-018-37001-y
| Authors | Mauvisseau, Quentin, Burian, Alfred, Gibson, Ceri, Brys, Rein, Ramsey, Andrew and Sweet, Michael |
|---|---|
| Abstract | Environmental DNA (eDNA) barcoding has a high potential to increase the cost-efficiency of species detection and monitoring in aquatic habitats. However, despite vast developments in the field, many published assays often lack detailed validation and there is little to no commonly (agreed upon) standardization of protocols. In this study, we evaluated the reliability of eDNA detection and quantification using published primers and assays targeting the Freshwater Pearl Mussel as a model organism. We first assessed limits of detection for two different target genes (COI and 16S) following the MIQE guidelines, and then tested the reliability of quantification in a double-blind mesocosm experiment. Our results reveal that different methodological indicators, namely accuracy, repeatability and detection probability affected the reliability of eDNA measurement at the different levels tested. The selection of the optimal analytical method was mainly determined by detection probability. Both the COI and 16S assays were highly specific for the targeted organism and showed similar accuracy and repeatability, whilst the limit of detection was clearly lower for the COI based approach. In contrast, the reliability of eDNA quantification hinged on repeatability, reflected by the scattering (r2 = 0.87) around the relationship between eDNA and mussel density in mesocosms. A bootstrapping approach, which allowed for the assignment of measures associated with repeatability of samples, revealed that variability between natural replicates (i.e. accuracy) strongly influenced the number of replicates required for a reliable species detection and quantification in the field. |
| Keywords | Multidisciplinary; eDNA; species-specific eDNA; Environmental |
| Year | 2019 |
| Journal | Scientific Reports |
| Journal citation | 9 (580), pp. 1-10 |
| Publisher | Springer |
| ISSN | 2045-2322 |
| Digital Object Identifier (DOI) | https://doi.org/10.1038/s41598-018-37001-y |
| Web address (URL) | https://www.nature.com/articles/s41598-018-37001-y |
| hdl:10545/624394 | |
| Output status | Published |
| Publication dates | 24 Jan 2019 |
| Publication process dates | |
| Deposited | 15 Jan 2020, 12:07 |
| Accepted | 27 Oct 2018 |
| Contributors | University of Derby, Freshwater Biological Association, Cumbria and Research Institute for Nature and Forest, Belgium |
| File | File Access Level Restricted |
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Charlotte Moritz, Frédéric Ducarme, Sweet, M., Michael D. Fox, Brian Zgliczynski, Nizam Ibrahim, Ahmed Basheer, Kathryn A. Furby, Zachary R. Caldwell, Chiara Pisapia, Gabriel Grimsditch and Ameer Abdulla 2017. The “resort effect”: Can tourist islands act as refuges for coral reef species? Diversity and Distributions. https://doi.org/10.1111/ddi.12627On the importance of the microbiome and pathobiome in coral health and disease
Sweet, M. and Bulling, M. 2017. On the importance of the microbiome and pathobiome in coral health and disease. Frontiers in Marine Sciences. https://doi.org/10.3389/fmars.2017.00009'Yellow Syndrome' in scleractinian corals throughout Bintain District, Kepulauan Riau Province, Indonesia
Johan, O., Budianto, O. and Sweet, M. 2017. 'Yellow Syndrome' in scleractinian corals throughout Bintain District, Kepulauan Riau Province, Indonesia. Indonesia Aquaculture Journal. 12 (1), pp. 37-42. https://doi.org/10.15578/iaj.12.1.2017.37-42Variation in size frequency distribution of coral populations under different fishing pressures in two contrasting locations in the Indian Ocean.
Grimsditch, Gabriel, Pisapia, Chiara, Huck, M., Karisa, Juliet, Obura, David and Sweet, M. 2017. Variation in size frequency distribution of coral populations under different fishing pressures in two contrasting locations in the Indian Ocean. Marine Environmental Research. https://doi.org/10.1016/j.marenvres.2017.09.017Juvenile “black teatfish” in Maldives
Sweet, M., Ducarme, F. and Conand, C. 2016. Juvenile “black teatfish” in Maldives. SPC Beche-de-mer Information Bulletin #36. pp. 1-2.Coral responses to anthropogenic stress in the twenty-first century: an ecophysiological perspective
Sweet, M. and Brown B.E. 2016. Coral responses to anthropogenic stress in the twenty-first century: an ecophysiological perspective. in: Oceanography and Marine Biology CRC Press. pp. 271 - 314Is Acropora palmata recovering? A case study in Los Roques National Park, Venezula
Aldo Croquer, Francoise Cavada-Blanco, Ainhoa L Zubillaga, Esteban A Agudo-Adriani and Sweet, M. 2016. Is Acropora palmata recovering? A case study in Los Roques National Park, Venezula. PeerJ. (eCollection 2016). https://doi.org/10.7717/peerj.1539Baseline reef health surveys at Bangka Island (North Sulawesi, Indonesia) reveal new threats
Massimo Ponti, Francesca Fratangeli, Nicolò Dondi, Marco Segre Reinach, Clara Serra and Sweet, M. 2016. Baseline reef health surveys at Bangka Island (North Sulawesi, Indonesia) reveal new threats. PeerJ. https://doi.org/10.7717/peerj.2614The role of viruses in coral health and disease
Sweet, M. and John Bythell 2016. The role of viruses in coral health and disease. Journal of Invertebrate Biology. https://doi.org/10.1016/j.jip.2016.12.005Molecular changes in skin pigmented lesions of the coral trout Plectropomus leopardus
Adélaïde Lerebours, Emma C Chapman, Sweet, M., Jeanette M Rotchell and Michelle R Heupel 2016. Molecular changes in skin pigmented lesions of the coral trout Plectropomus leopardus. Marine Environmental Research. https://doi.org/10.1016/j.marenvres.2016.07.009Influence of Resource Availability on the Foraging Strategies of the Triangle Butterflyfish Chaetodon triangulum in the Maldives
Sweet, M. 2016. Influence of Resource Availability on the Foraging Strategies of the Triangle Butterflyfish Chaetodon triangulum in the Maldives. PLos ONE. https://doi.org/10.1371/journal.pone.0151923New disease outbreak affects two dominant sea urchin species associated with Australian temperate reefs
Sweet, M. and Bulling, M. 2016. New disease outbreak affects two dominant sea urchin species associated with Australian temperate reefs. Marine Ecological Progress Series. https://doi.org/10.3354/meps11750A review of ghost gear entanglement amongst marine mammals, reptiles and elasmobranchs
Martin Stelfox, Jillian Hudgins and Sweet, M. 2016. A review of ghost gear entanglement amongst marine mammals, reptiles and elasmobranchs. Marine Pollution Bulletin. https://doi.org/10.1016/j.marpolbul.2016.06.034Is Acropora Palmata recovering? A case study in Los Roques National Park, Venezuela
Croquer, Aldo, Cavada-Blanco, Francoise, Zubillaga, Ainhoa L., Agudo-Adriani, Esteban A. and Sweet, Michael J. 2016. Is Acropora Palmata recovering? A case study in Los Roques National Park, Venezuela. PeerJ. https://doi.org/10.7717/peerj.1539Metabolome-mediated biocryomorphic evolution promotes carbon fixation in Greenlandic cryoconite holes
Joseph M Cook, Arwyn Edwards, Bulling, M., Luis A J Mur, Sophie Cook, Jarishma K Gokul, Karen A Cameron, Sweet, M. and Tristram D L Irvine-Fynn 2016. Metabolome-mediated biocryomorphic evolution promotes carbon fixation in Greenlandic cryoconite holes. Environmental Microbiology. https://doi.org/10.1111/1462-2920.13349Coral responses to anthropogenic stress in the 21st Century – An ecophysiological perspective.
Sweet, Michael J. and Brown, Barbara E. 2016. Coral responses to anthropogenic stress in the 21st Century – An ecophysiological perspective. in: Taylor & Francis.Prevalence and Incidence of Black Band Disease of Scleractinian Corals in the Kepulauan Seribu Region of Indonesia
Johan, Ofri, Zamany, Neviaty P., Smith, David and Sweet, M. 2016. Prevalence and Incidence of Black Band Disease of Scleractinian Corals in the Kepulauan Seribu Region of Indonesia. Diversity. https://doi.org/10.3390/d8020011Microbial communities associated with healthy and white syndrome-affected Echinopora lamellose in aquaria and experimental treatment with the antibiotic ampicillin
Smith, D., Leary, P., Craggs, J., Bythell, J. and Sweet, M. 2015. Microbial communities associated with healthy and white syndrome-affected Echinopora lamellose in aquaria and experimental treatment with the antibiotic ampicillin. PLos ONE. 10 (3), pp. 1-17. https://doi.org/10.1371/journal.pone.0121780Identification of a bacterial pathogen associated with Porites white patch syndrome in the Western Indian Ocean
Mathieu G Séré, Pablo Tortosa, Pascale Chabanet, Jean-Pascal Quod, Sweet, M. and Michael H Schleyer 2015. Identification of a bacterial pathogen associated with Porites white patch syndrome in the Western Indian Ocean. Molecular Ecology. https://doi.org/10.1111/mec.13326Ciliate communities consistently associated with coral diseases
Sweet, Michael J. and Séré, Mathieu G. 2015. Ciliate communities consistently associated with coral diseases. Journal of Sea Research. https://doi.org/10.1016/j.seares.2015.06.008Fostering effective international collaboration for marine science in small island states
Hind, Edward J., Alexander, Steven M., Green, Stephanie J., Kritzer, Jacob P., Sweet, M., Johnson, Ayana Elizabeth, Amargós, Fabian P., Smith, Nicola S. and Angelie M. 2015. Fostering effective international collaboration for marine science in small island states. Frontiers in Marine Science. https://doi.org/10.3389/fmars.2015.00086Geographically conserved rates of background mortality among common reef-building corals in Lhaviyani Atoll, Maldives versus northern Great Barrier Reef, Australia
Sweet, M. 2015. Geographically conserved rates of background mortality among common reef-building corals in Lhaviyani Atoll, Maldives versus northern Great Barrier Reef, Australia. Marine Biology. 162 (8). https://doi.org/10.1007/s00227-015-2694-9Diseases in marine invertebrates associated with mariculture and commercial fisheries
Sweet, M. and Kelly S Bateman 2015. Diseases in marine invertebrates associated with mariculture and commercial fisheries. Journal of Sea Research. https://doi.org/10.1016/j.seares.2015.06.016Age-Related Shifts in Bacterial Diversity in a Reef Coral
Alex D Williams, Barbara E Brown, Lalita Putchim and Sweet, M. 2015. Age-Related Shifts in Bacterial Diversity in a Reef Coral. PLos ONE. 10 (2). https://doi.org/10.1371/journal.pone.0144902A novel sponge disease caused by a consortium of micro-organisms
Sweet, M. 2015. A novel sponge disease caused by a consortium of micro-organisms. Coral Reefs. https://doi.org/10.1007/s00338-015-1284-0Baseline coral disease surveys within three marine parks in Sabah, Borneo
Jennifer Miller, Sweet, M., Elizabeth Wood and John Bythell 2015. Baseline coral disease surveys within three marine parks in Sabah, Borneo. PeerJ. https://doi.org/10.7717/peerj.1391White Syndrome in Acropora muricata: Non-specific bacterial infection and ciliate histophagy
Sweet, M. and Bythell, J. 2015. White Syndrome in Acropora muricata: Non-specific bacterial infection and ciliate histophagy. Molecular Ecology. 24, p. 1150–1159. https://doi.org/10.1111/mec.13097The distribution and abundance of black band disease and white syndrome in Kepulauan Seribu, Indonesia
Johan, Ofri, Bengen, Dietriech Geoffrey, Zamani, Neviaty Putri, Suharsono and Sweet, M. 2015. The distribution and abundance of black band disease and white syndrome in Kepulauan Seribu, Indonesia. Journal of Biosciences. https://doi.org/10.1016/j.hjb.2015.09.001Soil contamination with silver nanoparticles reduces Bishop pine growth and ectomycorrhizal diversity on pine roots
Sweet, M. and I Singleton 2015. Soil contamination with silver nanoparticles reduces Bishop pine growth and ectomycorrhizal diversity on pine roots. Journal of Nanoparticle Research. https://doi.org/10.1007/s11051-015-3246-4A novel investigation of a blister-like syndrome in aquarium Echinopora lamellosa
David Smith, Peter Leary, Mark Bendall, Edmund Flach, Rachel Jones and Sweet, M. 2014. A novel investigation of a blister-like syndrome in aquarium Echinopora lamellosa. PLos ONE. https://doi.org/10.1371/journal.pone.0097018Experimental antibiotic treatment identifies potential pathogens of white band disease in the endangered Caribbean coral Acropora cervicornis
Sweet, M., A Croquer and J C Bythell 2014. Experimental antibiotic treatment identifies potential pathogens of white band disease in the endangered Caribbean coral Acropora cervicornis. Proc Roy Soc. https://doi.org/10.1098/rspb.2014.0094Decadal environmental ‘memory’ in a reef coral?
Brown B.E., Dunne R.P., Edwards A.J., Sweet, M. and Phongsuwan N. 2014. Decadal environmental ‘memory’ in a reef coral? Marine Biology. https://doi.org/10.1007/s00227-014-2596-2Coral diseases in aquaria and in nature
Sweet, Michael J., Jones, Rachel and Bythell, John C. 2013. Coral diseases in aquaria and in nature. https://doi.org/10.1017/S0025315411001688Development of bacterial biofilms on artificial corals in comparison to surface-associated microbes of hard corals
Sweet, Michael J., Croquer, Aldo, Bythell, John C. and Lopez-Garcia, Purification 2013. Development of bacterial biofilms on artificial corals in comparison to surface-associated microbes of hard corals. https://doi.org/10.1371/journal.pone.0021195Characterisation of the bacterial and fungal communities associated with different lesion sizes of Dark Spot Syndrome occurring in the Coral Stephanocoenia intersepta
Sweet, Michael J., Burn, Deborah, Croquer, Aldo, Leary, Peter and Bereswill, Stefan 2013. Characterisation of the bacterial and fungal communities associated with different lesion sizes of Dark Spot Syndrome occurring in the Coral Stephanocoenia intersepta. https://doi.org/10.1371/journal.pone.0062580Evidence of melanoma in wild marine fish populations
Sweet, Michael J., Kirkham, Nigel, Bendall, Mark, Currey, Leanne, Bythell, John C., Heupel, Michelle and Vartanian, Jean-Pierre 2013. Evidence of melanoma in wild marine fish populations. https://doi.org/10.1371/journal.pone.0041989