Improving the reliability of eDNA data interpretation

Journal article


Burian, Alfred, Mauvisseau, Quentin, Bulling, Mark, Domisch, Sami, Qian, Song and Sweet, Michael 2021. Improving the reliability of eDNA data interpretation. Molecular Ecology Resources. 21, p. 1422–1433.. https://doi.org/10.1111/1755-0998.13367
AuthorsBurian, Alfred, Mauvisseau, Quentin, Bulling, Mark, Domisch, Sami, Qian, Song and Sweet, Michael
Abstract

Global declines in biodiversity highlight the need to effectively monitor the density and distribution of threatened species. In recent years, molecular survey methods detecting DNA released by target‐species into their environment (eDNA) have been rapidly on the rise. Despite providing new, cost‐effective tools for conservation, eDNA‐based methods are prone to errors. Best field and laboratory practices can mitigate some, but the risks of errors cannot be eliminated and need to be accounted for. Here, we synthesize recent advances in data processing tools that increase the reliability of interpretations drawn from eDNA data. We review advances in occupancy models to consider spatial data‐structures and simultaneously assess rates of false positive and negative results. Further, we introduce process‐based models and the integration of metabarcoding data as complementing approaches to increase the reliability of target‐species assessments. These tools will be most effective when capitalizing on multi‐source data sets collating eDNA with classical survey and citizen‐science approaches, paving the way for more robust decision‐making processes in conservation planning.

KeywordsBiotechnology; Genetics; Ecology, Evolution, Behavior and Systematics; eDNA
Year2021
JournalMolecular Ecology Resources
Journal citation21, p. 1422–1433.
PublisherWiley
ISSN1755-098X
1755-0998
Digital Object Identifier (DOI)https://doi.org/10.1111/1755-0998.13367
Web address (URL)https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.13367
hdl:10545/625716
Output statusPublished
Publication dates02 Mar 2021
Publication process dates
Deposited16 Apr 2021, 09:15
Accepted24 Feb 2021
ContributorsUniversity of Derby, Marine Ecology Department, Lurio University, Nampula, Mozambique, Helmholtz Centre for Environmental Research, Leipzig, Germany, Natural History Museum, University of Oslo, Oslo, Norway, Leibniz‐Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany and University of Toledo, Toledo, OH, USA
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Crooks, Esther R., Bulling, Mark T. and Barnes, Kate M. 2016. Microbial effects on the development of forensically important blow fly species. Forensic Science International. https://doi.org/10.1016/j.forsciint.2016.05.026
Symbiotic microbes from marine invertebrates: Driving a new era of natural product drug discovery.
Blockley, Alix, Elliott, D., Roberts, Adam and Sweet, Michael J. 2017. Symbiotic microbes from marine invertebrates: Driving a new era of natural product drug discovery. Diversity. 9 (4), pp. 1-13. https://doi.org/10.3390/d9040049
Designer reefs and coral probiotics; great concepts but are they good practice?
Sweet, M., Ramsey, A. and Bulling, M. 2017. Designer reefs and coral probiotics; great concepts but are they good practice? Biodiversity. https://doi.org/10.1080/14888386.2017.1307786
Inducing broadcast coral spawning ex situ: Closed system mesocosm design and husbandry protocol.
Craggs, Jamie, Guest, James R., Davis, Michelle, Simmons, Jeremy, Dashti, Ehsan and Sweet, Michael J. 2017. Inducing broadcast coral spawning ex situ: Closed system mesocosm design and husbandry protocol. Ecology and Evolution. https://doi.org/10.1002/ece3.3538
Evidence for rapid, tide-related shifts in the microbiome of the coral Coelastrea aspera
Sweet, Michael J., Brown, Barbara E., Dunne, Richard P., Singleton, Ian and Bulling, Mark T. 2017. Evidence for rapid, tide-related shifts in the microbiome of the coral Coelastrea aspera. Coral Reefs. https://doi.org/10.1007/s00338-017-1572-y
The “resort effect”: Can tourist islands act as refuges for coral reef species?
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.12627
On 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.12.1.2017.37-42
Variation 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.2017.09.017
Juvenile “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 - 314
Is 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.1539
Baseline 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.2614
The 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.2016.12.005
Molecular 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.2016.07.009
Influence 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.0151923
New 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/meps11750
A 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.2016.06.034
Is 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.1539
Metabolome-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/10.1111/1462-2920.13349
Coral 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/d8020011
Microbial 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.0121780
Identification 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.13326
Ciliate 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.2015.06.008
Fostering 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.2015.00086
Geographically 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/s00227-015-2694-9
Diseases 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.2015.06.016
Age-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.0144902
A 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/s00338-015-1284-0
Baseline 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.1391
White 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.13097
The 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.2015.09.001
Soil 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/s11051-015-3246-4
A 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.0097018
Experimental 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.2014.0094
Decadal 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/s00227-014-2596-2
Coral 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/S0025315411001688
Development 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.0021195
Characterisation 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.0062580
Evidence 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
Metal-based nanoparticles; size, function and areas for advancement
Sweet, Michael J. 2013. Metal-based nanoparticles; size, function and areas for advancement. in:
Using model systems to address the biodiversity-ecosystem functioning process
Bulling, Mark T., White, Piran C. L., Raffaelli, D. and Pierce, Graham J. 2013. Using model systems to address the biodiversity-ecosystem functioning process.
How biodiversity affects ecosystem processes: implications for ecological revolutions and benthic ecosystem function
Solan, Martin, Batty, P., Bulling, Mark T. and Godbold, J. A. 2013. How biodiversity affects ecosystem processes: implications for ecological revolutions and benthic ecosystem function. Aquatic Biology. https://doi.org/10.3354/ab00058
Global patterns of bioturbation intensity and mixed depth of marine soft sediments
Teal, L. R., Bulling, Mark T., Parker, E. R. and Solan, Martin 2013. Global patterns of bioturbation intensity and mixed depth of marine soft sediments. Aquatic Biology. https://doi.org/10.3354/ab00052
Bacterial biodiversity-ecosystem functioning relations are modified by environmental complexity
Langenheder, Silke, Bulling, Mark T., Solan, Martin, Prosser, James I. and Bell, Thomas 2013. Bacterial biodiversity-ecosystem functioning relations are modified by environmental complexity. PLos ONE. https://doi.org/10.1371/journal.pone.0010834
Impact of biodiversity-climate futures on primary production and metabolism in a model benthic estuarine system
Hicks, Natalie, Bulling, Mark T., Solan, Martin, Raffaelli, D., White, Piran C. L. and Paterson, David M. 2013. Impact of biodiversity-climate futures on primary production and metabolism in a model benthic estuarine system. BMC Ecology. https://doi.org/10.1186/1472-6785-11-7
Role of functionally dominant species in varying environmental regimes: evidence for the performance-enhancing effect of biodiversity
Langenheder, Silke, Bulling, Mark T., Prosser, James I. and Solan, Martin 2013. Role of functionally dominant species in varying environmental regimes: evidence for the performance-enhancing effect of biodiversity. BMC Ecology. https://doi.org/10.1186/1472-6785-12-14
Funding begets biodiversity
Ahrends, Antje, Burgess, Neil D., Gereau, Roy E., Marchant, Rob, Bulling, Mark T., Lovett, Jon C., Platts, Philip J., Kindemba, Victoria Wilkins, Owen, Nisha, Fanning, Eibleis and Rahbek, Carsten 2013. Funding begets biodiversity. Diversity and Distributions. https://doi.org/10.1111/j.1472-4642.2010.00737.x
Conservation and the botanist effect
Ahrends, Antje, Rahbek, Carsten, Bulling, Mark T., Burgess, Neil D., Platts, Philip J., Lovett, Jon C., Kindemba, Victoria Wilkins, Owen, Nisha, Sallu, Albert Ntemi and Marshall, Andrew R. 2013. Conservation and the botanist effect. Biological Conservation. https://doi.org/10.1016/j.biocon.2010.08.008
Habitat structure mediates biodiversity effects on ecosystem properties
Godbold, J. A., Bulling, Mark T. and Solan, Martin 2013. Habitat structure mediates biodiversity effects on ecosystem properties. Proceedings of the Royal Society B: Biological Sciences. https://doi.org/10.1098/rspb.2010.2414
Permeability of intertidal sandflats: impact of temporal variability on sediment metabolism
Zetzche, E., Bulling, Mark T. and Witte, U. 2013. Permeability of intertidal sandflats: impact of temporal variability on sediment metabolism.
Modelling the impact of vaccination on tuberculosis in badgers.
Hardstaff, Joanne L., Bulling, Mark T., Marion, Glenn, Hutchings, Michael R. and White, Piran C. L. 2013. Modelling the impact of vaccination on tuberculosis in badgers. Epidemiology and infection. https://doi.org/10.1017/S0950268813000642
Indirect effects of non-lethal predation on bivalve activity and sediment reworking
Maire, O., Merchant, J. N., Bulling, Mark T., Teal, L. R., Grémare, A., Duchêne, J. C. and Solan, Martin 2013. Indirect effects of non-lethal predation on bivalve activity and sediment reworking. Journal of Experimental Marine Biology and Ecology. https://doi.org/10.1016/j.jembe.2010.08.004
Predictable waves of sequential forest degradation and biodiversity loss spreading from an African city
Ahrends, Antje, Burgess, Neil D., Milledge, Simon A. H., Bulling, Mark T., Fisher, Brendan, Smart, James C. R., Clarke, G. P., Mhoro, Boniface E. and Lewis, Simon L. 2013. Predictable waves of sequential forest degradation and biodiversity loss spreading from an African city. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0914471107
Geographical variation in the response to nitrogen deposition in Arabidopsis lyrata petraea.
Vergeer, Philippine, van den Berg, Leon L. J., Bulling, Mark T., Ashmore, Mike R. and Kunin, William E. 2008. Geographical variation in the response to nitrogen deposition in Arabidopsis lyrata petraea. The new phytologist. https://doi.org/10.1111/j.1469-8137.2008.02445.x
Marine biodiversity-ecosystem functions under uncertain environmental futures
Bulling, Mark T., Hicks, Natalie, Murray, L., Paterson, David M., Raffaelli, D., White, Piran C. L. and Solan, Martin 2013. Marine biodiversity-ecosystem functions under uncertain environmental futures. Philosophical Transactions of the Royal Society B: Biological Sciences. https://doi.org/10.1098/rstb.2010.0022
Species effects on ecosystem processes are modified by faunal responses to habitat composition.
Bulling, Mark T., Solan, Martin, Dyson, Kirstie E., Hernandez-Milian, Gema, Luque, Patricia, Pierce, Graham J., Raffaelli, D., Paterson, David M. and White, Piran C. L. 2008. Species effects on ecosystem processes are modified by faunal responses to habitat composition. Oecologia. https://doi.org/10.1007/s00442-008-1160-5
Influence of macrofaunal assemblages and environmental heterogeneity on microphytobenthic production in experimental systems
Dyson, Kirstie E., Bulling, Mark T., Solan, Martin, Hernandez-Milian, Gema, Raffaelli, D., White, Piran C. L. and Paterson, David M. 2013. Influence of macrofaunal assemblages and environmental heterogeneity on microphytobenthic production in experimental systems. Proceedings of the Royal Society B: Biological Sciences. https://doi.org/10.1098/rspb.2007.0922
Quantifying individual feeding variability: implications for mollusc feeding experiments
Hanley, M. E., Bulling, Mark T. and Fenner, M. 2013. Quantifying individual feeding variability: implications for mollusc feeding experiments.
Dirichlet neighbours: revisiting Dirichlet tessellation for neighbourhood analysis
Halls, P. J., Bulling, Mark T., White, Piran C. L., Garland, Lynette and Harris, S. 2013. Dirichlet neighbours: revisiting Dirichlet tessellation for neighbourhood analysis.
Impact of external sources of infection on the dynamics of bovine tuberculosis in modelled badger populations
Hardstaff, Joanne L., Bulling, Mark T., Marion, Glenn, Hutchings, Michael R. and White, Piran C. L. 2013. Impact of external sources of infection on the dynamics of bovine tuberculosis in modelled badger populations. BMC Veterinary Research. https://doi.org/10.1186/1746-6148-8-92
Diseases in coral aquaculture: causes, implications and preventions
Kramarsky-Winter, Esti, Sweet, Michael J., Leal, Miguel Costa, Sheridan, Christopher and Kushmaro, Ariel 2013. Diseases in coral aquaculture: causes, implications and preventions. Aquaculture. https://doi.org/10.1016/j.aquaculture.2013.02.037
Assessment of the microbial communities associated with white syndrome and brown jelly syndrome in aquarium corals
Sweet, Michael J., Craggs, J., Robson, J. and Bythell, John C. 2013. Assessment of the microbial communities associated with white syndrome and brown jelly syndrome in aquarium corals.
Microsatellites for microbiologists
Sweet, Michael J., Scriven, Lucinda A. and Singleton, Ian 2012. Microsatellites for microbiologists. Advances in Applied Microbiology. https://doi.org/10.1016/B978-0-12-394382-8.00005-8