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

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 impacts of INNS.