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

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.

Molecular identification and environmental DNA detection of gill lice ectoparasites associated with Brook Trout declines

“…2015, 2023; Thomas et al. 2022). However, PCR bias and other factors may limit eDNA metabarcoding's sensitivity (Harper et al.…”

“…Highly sensitive single-species qPCR-based approaches are clearly effective for detecting small and cryptic freshwater parasites, but multispecies approaches, such as eDNA metabarcoding, may offer additional management utility in host-parasite systems. Environmental DNA metabarcoding can generate vast amounts of ecological data that can be used to explore host-parasite dynamics and reveal potential ecological factors influencing their distributions (Bass et al 2015(Bass et al , 2023Thomas et al 2022). However, PCR bias and other factors may limit eDNA metabarcoding's sensitivity (Harper et al 2018), suggesting that future research is needed to verify whether this multispecies approach can match qPCR's sensitivity for detecting low-concentration gill lice eDNA.…”

Snail hosts abundance mediates the effects of antagonist interactions between trematodes on the transmission of human schistosomes.

“…Huge works remain to be done to characterise both the fauna involved in supplying trematodes that interact with species of the genus Schistosoma in their intermediate hosts, and the fauna involved in maintaining the local life cycles of these trematodes. We believe that the newly available metabarcoding tools such as used in the present study (19,34,40), combined with the implementation of large and well documented sequence datasets, provide a promising avenue to characterise trematode life cycles.…”

Working towards a conservation plan for fish parasites: Cyprinid parasites from the south African cape fold freshwater ecoregion as a case study

“…In South Africa, similar to many other developing countries, we are currently facing a deficit in knowledge on biodiversity, with a great shortfall in past knowledge to guide the policy on the management and protection of parasitic species along with their application in the conservation of ecological units (parasites and hosts) for the future. Currently, the application of non-lethal tools, such as eDNA, to assess parasitic communities is still in the developing and refinement stages, and these are not yet accepted as default tools for detection ( Thomas et al, 2022 ). In addition, comparative libraries for the datasets obtained using non-lethal tools first need to be populated prior to its consideration as the primary method of assessment, and in South Africa, there is much to be done before such tools can be utilised effectively.…”