Hostname: page-component-f554764f5-246sw Total loading time: 0 Render date: 2025-04-11T13:05:22.788Z Has data issue: false hasContentIssue false
  • English
  • Français

Lurking in the water: testing eDNA metabarcoding as a tool for ecosystem-wide parasite detection

Published online by Cambridge University Press:  28 October 2021

Leighton J. Thomas Open the ORCID record for Leighton J. Thomas [Opens in a new window] ,
Marin Milotic ,
Felix Vaux  and
Robert Poulin Open the ORCID record for Robert Poulin [Opens in a new window]
Leighton J. Thomas*
Affiliation:
Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
Marin Milotic
Affiliation:
Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
Felix Vaux
Affiliation:
Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
Robert Poulin
Affiliation:
Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
*
Author for correspondence: Leighton J. Thomas, E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

In the light of global biodiversity change and emerging disease, there is an urgent need to establish efficient monitoring programmes of parasites in aquatic ecosystems. However, parasite identification is time-consuming, requires a high degree of taxonomic expertize and in general requires lethal sampling. The use of environmental DNA methodology to identify parasites has the potential to circumvent these limitations. This study evaluates the use of eDNA metabarcoding to detect the presence of all species of nematode and platyhelminth parasites in two New Zealand lakes. We developed two novel metabarcoding primer pairs targeting a region of cytochrome oxidase I gene (COI) specific to platyhelminths and nematodes. We successfully detected parasite DNA in both lakes. Platyhelminth DNA yield was in general greater than nematode DNA yield. This most likely results from the larger biomass of the former quantified using traditional methods, or the presence of free-swimming life stages in the life cycle of many platyhelminths. By using eDNA, we did not detect all expected parasite families revealed through traditional methods, likely due to a lack of sequencing data available from public databases such as GenBank. As such, genetic resources need to include full reference sequences if parasitology is to truly harness eDNA to characterize and monitor parasite biodiversity in natural systems.

Keywords

Biodiversity monitoringeDNAfreshwatermetabarcodingNematodaplatyhelminthes
Type
Research Article
Information
Parasitology , Volume 149 , Issue 2 , February 2022 , pp. 261 - 269
Check for updates
Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Article purchase

Temporarily unavailable

References

Altizer, S, Ostfeld, RS, Johnson, PTJ, Kutz, S and Harvell, CD (2013) Climate change and infectious diseases: from evidence to a predictive framework. Science (New York, N.Y.) 341, 514–519.CrossRefGoogle ScholarPubMed
Altschul, SF, Gish, W, Miller, W, Myers, EW and Lipman, DJ (1990) Basic local alignment search tool. Journal of Molecular Biology 215, 403–410.CrossRefGoogle ScholarPubMed
Bastos Gomes, G, Hutson, KS, Domingos, JA, Chung, C, Hayward, S, Miller, TL and Jerry, DR (2017) Use of environmental DNA (eDNA) and water quality data to predict protozoan parasites outbreaks in fish farms. Aquaculture 479, 467–473.10.1016/j.aquaculture.2017.06.021CrossRefGoogle Scholar
Beveridge, I and Gasser, RB (2014) Diversity in parasitic helminths of Australasian marsupials and monotremes: a molecular perspective. International Journal for Parasitology 44, 859–864.10.1016/j.ijpara.2014.06.001CrossRefGoogle ScholarPubMed
Collins, RA, Bakker, J, Wangensteen, OS, Soto, AZ, Corrigan, L, Sims, DW, Genner, MJ and Mariani, S (2019) Non-specific amplification compromises environmental DNA metabarcoding with COI. Methods in Ecology and Evolution 10, 1985–2001.10.1111/2041-210X.13276CrossRefGoogle Scholar
Cox, MP, Peterson, DA and Biggs, PJ (2010) SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11, 485.CrossRefGoogle ScholarPubMed
Dario, MA, Moratelli, R, Schwabl, P, Jansen, AM and Llewellyn, MS (2017) Small subunit ribosomal metabarcoding reveals extraordinary trypanosomatid diversity in Brazilian bats. PLOS Neglected Tropical Diseases 11, e0005790.CrossRefGoogle ScholarPubMed
Elbrecht, V and Leese, F (2017) PrimerMiner: an R package for development and in silico validation of DNA metabarcoding primers. Methods in Ecology and Evolution 8, 622–626.CrossRefGoogle Scholar
Gogarten, JF, Calvignac-Spencer, S, Nunn, CL, Ulrich, M, Saiepour, N, Nielsen, HV, Deschner, T, Fichtel, C, Kappeler, PM, Knauf, S, Müller-Klein, N, Ostner, J, Robbins, MM, Sangmaneedet, S, Schülke, O, Surbeck, M, Wittig, RM, Sliwa, A, Strube, C, Leendertz, FH, Roos, C and Noll, A (2020) Metabarcoding of eukaryotic parasite communities describes diverse parasite assemblages spanning the primate phylogeny. Molecular Ecology Resources 20, 204–215.10.1111/1755-0998.13101CrossRefGoogle ScholarPubMed
Harper, LR, Handley, LL, Hahn, C, Boonham, N, Rees, HC, Gough, KC, Lewis, E, Adams, IP, Brotherton, P, Phillips, S and Hänfling, B (2018) Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus). Ecology and Evolution 8, 6330–6341.CrossRefGoogle Scholar
Harper, LR, Buxton, AS, Rees, HC, Bruce, K, Brys, R, Halfmaerten, D, Read, DS, Watson, HV, Sayer, CD, Jones, EP, Priestley, V, Mächler, E, Múrria, C, Garcés-Pastor, S, Medupin, C, Burgess, K, Benson, G, Boonham, N, Griffiths, RA, Lawson Handley, L and Hänfling, B (2019) Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds. Hydrobiologia 826, 25–41.CrossRefGoogle Scholar
Huver, JR, Koprivnikar, J, Johnson, PTJ and Whyard, S (2015) Development and application of an eDNA method to detect and quantify a pathogenic parasite in aquatic ecosystems. Ecological Applications 25, 991–1002.10.1890/14-1530.1CrossRefGoogle ScholarPubMed
Jeunen, G-J, Knapp, M, Spencer, HG, Taylor, HR, Lamare, MD, Stat, M, Bunce, M and Gemmell, NJ (2019) Species-level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization. Ecology and Evolution 9, 1323–1335.CrossRefGoogle ScholarPubMed
Katoh, K and Standley, DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30, 772–780.CrossRefGoogle ScholarPubMed
Koboldt, DC, Chen, K, Wylie, T, Larson, DE, McLellan, MD, Mardis, ER, Weinstock, GM, Wilson, RK and Ding, L (2009) VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics (Oxford, England) 25, 2283–2285.CrossRefGoogle ScholarPubMed
Lagrue, C and Poulin, R (2016) The scaling of parasite biomass with host biomass in lake ecosystems: are parasites limited by host resources? Ecography 39, 507–514.CrossRefGoogle Scholar
Lehnert, K, Poulin, R and Presswell, B (2019) Checklist of marine mammal parasites in New Zealand and Australian waters. Journal of Helminthology 93, 649–676.CrossRefGoogle ScholarPubMed
Li, H and Durbin, R (2010) Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics (Oxford, England) 26, 589–595.CrossRefGoogle ScholarPubMed
Li, H, Handsaker, B, Wysoker, A, Fennell, T, Ruan, J, Homer, N, Marth, G, Abecasis, G and Durbin, R and 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinformatics (Oxford, England) 25, 2078–2079.CrossRefGoogle ScholarPubMed
Mitsi, K, Arroyo, AS and Ruiz-Trillo, I (2019) A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades. Biology Letters 15, 20190182.10.1098/rsbl.2019.0182CrossRefGoogle ScholarPubMed
Norris, L, Lawler, N, Hunkapiller, A, Mulrooney, DM, Kent, ML and Sanders, JL (2020) Detection of the parasitic nematode, Pseudocapillaria tomentosa, in zebrafish tissues and environmental DNA in research aquaria. Journal of Fish Diseases 43, 1087–1095.10.1111/jfd.13220CrossRefGoogle ScholarPubMed
Poulin, R and Presswell, B (2016) Taxonomic quality of species descriptions varies over time and with the number of authors, but unevenly among parasitic taxa. Systematic Biology 65, 1107–1116.10.1093/sysbio/syw053CrossRefGoogle ScholarPubMed
Rohland, N and Reich, D (2012) Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Research 22, 939–946.CrossRefGoogle ScholarPubMed
Sepulveda, AJ, Hutchins, PR, Forstchen, M, Mckeefry, MN and Swigris, AM (2020) The elephant in the lab (and field): contamination in aquatic environmental DNA studies. Frontiers in Ecology and Evolution 8, 440.10.3389/fevo.2020.609973CrossRefGoogle Scholar
Shamsi, S (2019) Parasite loss or parasite gain? Story of Contracaecum nematodes in antipodean waters. Parasite Epidemiology and Control 4, e00087.CrossRefGoogle ScholarPubMed
Wingett, SW and Andrews, S (2018) FastQ screen: a tool for multi-genome mapping and quality control. F1000Research 7. doi: 10.12688/f1000research.15931.2CrossRefGoogle ScholarPubMed
Zhang, J, Kobert, K, Flouri, T and Stamatakis, A (2014) PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics (Oxford, England) 30, 614–620.CrossRefGoogle ScholarPubMed
Supplementary material: File

Thomas et al. supplementary material

Thomas et al. supplementary material

Download Thomas et al. supplementary material(File)
File 663.5 KB