Diverse Applications of Environmental DNA Methods in Parasitology

Abstract

Nucleic acid extraction and sequencing of genes from organisms within environmental samples encompasses a variety of techniques collectively referred to as environmental DNA or 'eDNA'. The key advantages of eDNA analysis include the detection of cryptic or otherwise elusive organisms, large-scale sampling with fewer biases than specimen-based methods, and generation of data for molecular systematics. These are particularly relevant for parasitology because parasites can be difficult to locate and are morphologically intractable and genetically divergent. However, parasites have rarely been the focus of eDNA studies. Focusing on eukaryote parasites, we review the increasing diversity of the 'eDNA toolbox'. Combining eDNA methods with complementary tools offers much potential to understand parasite communities, disease risk, and parasite roles in broader ecosystem processes such as food web structuring and community assembly.

Use of qPCR-Based Cercariometry to Assess Swimmer’s Itch in Recreational Lakes

“…Molecular methods for the detection of the environmental stages of parasites have become more common in recent years and can be applied to fill crucial knowledge gaps related to the environmental transmission stages. As a review by Bass et al (2015) points out, environmental sampling for parasites coupled with molecular methods can reduce sampling bias incurred by specimen-based sampling. Additionally, molecular parasitological methods have been demonstrated to be more cost-effective, less labor intensive than specimen-based detection (Huver et al 2015).…”

“…It must be acknowledged that we tested a few factors which might affect cercariae concentrations—however, there are a number of potentially important variables which might influence cercariae concentrations, including water temperature, unpredictable cercariae shedding from snails, and shoreline bird abundance (Lo and Lee 1996; Abrous et al 1999; Byers et al 2008; Soldánová et al 2016). Furthermore, qPCR as a DNA-based molecular method will detect both live and dead cercariae in the water column and therefore may overestimate infection risk in some instances (Bass et al 2015). …”

Complementary approaches to diagnosing marine diseases: a union of the modern and the classic

“…Most sequence-independent methods target a single pathogen to detect its presence or absence (e.g. PCR and microarrays) [113,114]. Others use highly sensitive, DNA-based quantification (copy number) of a target gene or genes (i.e.…”

“…Whereas metagenomics looks at random genomic sequence from a community, amplicon analysis uses PCR to amplify a target gene that is experimentally linked to a known 'tag' sequence for sample identification. A single marker gene is amplified among target organisms such as the 16S rRNA gene in bacteria and archaea, the 18S and ITS for eukaryotic genes, and viral capsid DNA and RNA polymerases [113]. Both metagenomics and amplicon sequencing allow detection of potentially novel pathogens, and can be helpful in identification of pathogens more rapidly during an outbreak situation.…”

A new phylogeny and environmental DNA insight into paramyxids: an increasingly important but enigmatic clade of protistan parasites of marine invertebrates

“…broadly-targeted 18S sequencing surveys (Bass et al, 2015). In such cases PCR primers 114 designed specifically for the group under study can be very valuable (Hartikainen et al, 2014a,b).…”