Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels,Dreissena rostriformis bugensisin flowing water

Abstract

The early detection of invasive non-native species (INNS) is important to allow for informed management actions. Established monitoring methods require the collection or observation of specimens, which is unlikely at the beginning of an invasion when densities are likely to be low. Environmental DNA (eDNA) analysis is a highly promising technique for the detection of INNS – particularly during the early stages of an invasion.Here, we compared the use of traditional kick-net sampling with two eDNA approaches (targeted detection using both conventional and quantitative PCR, and passive detection via metabarcoding) for detection of quagga mussel, Dreissena rostriformis bugensis; a high priority INNS, along a density gradient on the River Wraysbury, UK.All three molecular tools outperformed traditional sampling in terms of detection. Conventional PCR and qPCR both had 100% detection rate in all samples, and outperformed metabarcoding when the target species was at low densities. Additionally, quagga mussel DNA copy number (qPCR) and read count (metabarcoding) had a significant negative relationship with distance from source population.Synthesis and application. All three molecular approaches were more sensitive than traditional kick-net sampling for the detection of the quagga mussel in flowing water, and both qPCR and metabarcoding enabled estimates of relative abundance. Targeted approaches were more sensitive than metabarcoding, but metabarcoding has the advantage of providing information on the wider community, and consequently impacts of INNS.

Advanced molecular-based surveillance of quagga and zebra mussels: A review of environmental DNA/RNA (eDNA/eRNA) studies and considerations for future directions

“…The observation that HTS was less sensitive than species-specific qPCR is consistent with other studies (Lacoursière-Roussel et al 2016b;Harper et al 2018;Bylemans et al 2019). Nevertheless, the relatively low performance of HTS in Blackman et al (2020a) may be due to the use of a universal primer that presumably targets most animal groups (metazoans), but was not specifically designed for molluscs and, as a result, may preferentially amplify DNA from other, more abundant species and/or other species whose DNA exhibits better matches to the primer sequence. Thus, in the following paragraphs, we detail the development and use of more-specific HTS metabarcodes (e.g.…”

“…Metabarcoding HTS methods have been successfully applied to QM-ZM eDNA surveillance efforts, where several surveillance objectives have been met using a variety of primers (Table 3). For example, COI metabarcoding primers, designed to generically target metazoans (Leray et al 2013) and/or marine invertebrates (Geller et al 2013), have been used to specifically detect ZM (Ardura et al 2017) or QM eDNA (Blackman et al 2020a) and to detect QM-ZM eDNA in community-wide surveys (Mychek-Londer et al 2020). Metabarcoding primers targeting 18S and designed to detect crustaceans, molluscs and tunicates (Zhan et al 2013), have also been used alongside HTS to detect AIS at freshwater ports, revealing the presence of QM (Brown et al 2016).…”

“…Metabarcoding primers targeting 18S and designed to detect crustaceans, molluscs and tunicates (Zhan et al 2013), have also been used alongside HTS to detect AIS at freshwater ports, revealing the presence of QM (Brown et al 2016). Blackman et al (2020a) report two important HTS findings from knowninfested waters: 1) an increase in distance between sampling (i.e. the point of eDNA collection) and the source population negatively influenced QM eDNA concentrations and 2) HTS underperformed in comparison to simultaneously employed speciesspecific cPCR and qPCR (Table 3), where QM detection was 86% and 100% successful, respectively.…”

“…Since then, eDNA sampling has been widely adopted as an AIS monitoring tool, often outperforming traditional survey methods for hard-to-detect aquatic species, including QM-ZM (e.g. De Ventura et al 2017;Gingera et al 2017;Sepulveda et al 2019;Blackman et al 2020a).…”

How does eDNA decay affect metabarcoding experiments?

“…An unexplored question is to what extent the results of the above single-species studies (qPCR-based) also apply to metabarcoding experiments. Some work has directly compared the sensitivity of qPCR and metabarcoding using non-specific primers (Blackman et al, 2020;Bylemans et al, 2019;Harper et al, 2018;Simmons et al, 2016;Wood et al, 2019). In all these studies, the qPCR assays were shown to be more sensitive for the detection of the study species.…”