Future potential
@Zerina Rahic
Rare and invasive species
eDNA analysis can complement conventional methods, act as an early warning system for invasive species (Goldberg et al., 2013; Piaggio et al., 2014; Smart et al., 2015; Blackman et al., 2017), and improve distribution mapping and occupancy modelling for rare species (Thomsen et al., 2012; Biggs et al., 2015; Doi et al., 2017; Niemiller et al., 2017; Torresdal et al., 2017).However, substantial variation exists in design, validation, and application of species-specific assays, even for the same target species. False positives and negatives remain pertinent issues in eDNA monitoring and intuitive counter-strategies are required for their mitigation. For purposes of eventual standardisation and consistency of eDNA research independent of target species or environment, researchers must ensure they familiarise themselves with existing guidelines for assay development, such as the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines (Bustin et al., 2009) and the eDNA minimum reporting guidelines established by Goldberg et al. (2016).
Disease Management
Detection and management of disease in freshwater environments is crucial to preventing spread and further infection. Crayfish plague Aphanomyces astaci (Schikora, 1906) and chytrid fungi Batrachochytrium dendrobatidis (Longcore et al., 1999) and B. salamandrivorans (Martel et al., 2013) pose major threats to pond biodiversity. Chytrid fungi have decimated amphibian populations and contributed to global decline and extinction risk of species (Walker et al., 2007; Mosher et al., 2018). Microscopy or molecular techniques were once used to detect zoosporangium in host individuals but swabs were required from the host’s skin or mouth (Mosher et al., 2018). eDNA presented an alternative avenue of diagnosis: water is sampled and filtered, followed by detection of chytrid zoospores using qPCR (Walker et al., 2007; Schmidt et al., 2013; Mosher et al., 2018). A similar procedure was developed to detect crayfish plague spores, carried by invasive North American crayfish but lethal to European crayfish species (Strand et al., 2014), and has since been multiplexed to allow simultaneous qPCR detection of host, vector, and pathogen using eDNA (Robinson et al., 2018). eDNA metabarcoding may be the next logical step to screen for multiple freshwater diseases that threaten biodiversity, or to monitor host, threatened species, and pathogens simultaneously. Microbiome research is another field that has been pivotal to understanding chytrid fungus resistance and immunity in amphibian species, and cure development. Obtaining microbiome data has been dependent on whole body or ventral swabbing, but eDNA metabarcoding of bacterial communities may be an option where tissues samples are not available
References