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

Rosetta C Blackman,Lynsey R Harper,Bernd Hänfling,Peter Shum,Kar Keun Sean Ling,Lori Lawson-Handley

doi:10.1002/ece3.6921

Abstract

The early detection of invasive non‐native species (INNS) is important for informing 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 with conserved primers) 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 relative read count (metabarcoding) were significantly influenced by both mussel density and distance from source population, with distance being the most significant predictor. 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 the impacts of INNS.

Highlights

Invasive non-native species (INNS) have wide ranging effects on ecosystems, from biodiversity loss (Doherty et al, 2016; Gallardo et al, 2016) to economic impacts, including damage to infrastructure (Connelly et al, 2007; Pimentel et al, 2005)
We compared the use of traditional kick-net sampling with two Environmental DNA (eDNA) approaches for detection of quagga mussel, Dreissena rostriformis bugensis, a high priority INNS, along a density gradient on the River Wraysbury, UK. 3
We hypothesized that: (1) The probability of detecting quagga mussels will be higher for eDNA methods than traditional methods, (2) targeted methods will have a higher probability of detecting quagga mussel than the passive method, (3) quantitative PCR (qPCR) will be more sensitive than conventional PCR (cPCR) for quagga mussel detection, and (4) both read count and DNA copy number will decline with distance downstream of the main population

Summary

| INTRODUCTION

Invasive non-native species (INNS) have wide ranging effects on ecosystems, from biodiversity loss (Doherty et al, 2016; Gallardo et al, 2016) to economic impacts, including damage to infrastructure (Connelly et al, 2007; Pimentel et al, 2005). The potential of eDNA metabarcoding for INNS monitoring has already been shown as an effective tool (Simmons et al, 2015; Brown et al, 2016; Blackman et al, 2017; Borrell et al, 2017; Holman et al, 2019 ) These studies include the detection of new INNS, which had been previously overlooked by traditional methods. Possible causes of this include primer choice and PCR bias, that is, species successfully amplifying and masking others in the PCR reaction during metabarcoding (Harper et al, 2018) Further comparisons of these methods covering different target taxa are required to better inform management strategies. We hypothesized that: (1) The probability of detecting quagga mussels will be higher for eDNA methods than traditional methods, (2) targeted methods will have a higher probability of detecting quagga mussel than the passive method, (3) qPCR will be more sensitive than cPCR for quagga mussel detection, and (4) both read count and DNA copy number will decline with distance downstream of the main population

| METHODS

Findings

| DISCUSSION