EnvironmentalDNA(eDNA) detects the invasive rusty crayfishOrconectes rusticusat low abundances

Abstract

Summary Early detection is invaluable for the cost‐effective control and eradication of invasive species, yet many traditional sampling techniques are ineffective at the low population abundances found at the onset of the invasion process. Environmental DNA (eDNA) is a promising and sensitive tool for early detection of some invasive species, but its efficacy has not yet been evaluated for many taxonomic groups and habitat types.We evaluated the ability of eDNA to detect the invasive rusty crayfish Orconectes rusticus and to reflect patterns of its relative abundance, in upper Midwest, USA, inland lakes. We paired conventional baited trapping as a measure of crayfish relative abundance with water samples for eDNA, which were analysed in the laboratory with a qPCR assay. We modelled detection probability for O. rusticus eDNA using relative abundance and site characteristics as covariates and also tested the relationship between eDNA copy number and O. rusticus relative abundance.We detected O. rusticus eDNA in all lakes where this species was collected by trapping, down to low relative abundances, as well as in two lakes where trap catch was zero. Detection probability of O. rusticus eDNA was well predicted by relative abundance of this species and lake water clarity. However, there was poor correspondence between eDNA copy number and O. rusticus relative abundance estimated by trap catches. Synthesis and applications. Our study demonstrates a field and laboratory protocol for eDNA monitoring of crayfish invasions, with results of statistical models that provide guidance of sampling effort and detection probabilities for researchers in other regions and systems. We propose eDNA be included as a tool in surveillance for invasive or imperilled crayfishes and other benthic arthropods.

Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America

“…We used a primer pair designed for the O. rusticus cytochrome c oxidase subunit I (COI) mitochondrial DNA gene previously published by Dougherty et al (2016) that was tested for specificity against tissue samples from all other known Great Lakes region sympatric crayfishes (11 species), and that was also found effective at detecting this invasive crayfish from inland lakes of Wisconsin and Michigan, US. We refer readers to Dougherty et al (2016) for more details on primer design, testing, and previous performance, but report here that the primer pair used was Orusticus_COI_5F (5 0 -CAGGGGCGTCAGTAGATTTAG GTAT-3 0 ) and Orusticus_COI_5R (5 0 -CATTCGATC TATAGTCATTCCCGTAG-3 0 ), which produces a 128 base pair (bp) amplicon.…”

“…We refer readers to Dougherty et al (2016) for more details on primer design, testing, and previous performance, but report here that the primer pair used was Orusticus_COI_5F (5 0 -CAGGGGCGTCAGTAGATTTAG GTAT-3 0 ) and Orusticus_COI_5R (5 0 -CATTCGATC TATAGTCATTCCCGTAG-3 0 ), which produces a 128 base pair (bp) amplicon.…”

“…Among the most promising advances in invasive species surveillance to emerge recently has been environmental DNA (eDNA), or DNA of macrobiota collected and identified from environmental samples (Ficetola et al, 2008;Lodge et al, 2012b). Research to date has consistently found eDNA to be highly sensitive to detection of potentially harmful species at the low population abundances associated with early stages of invasion (e.g., Egan et al, 2015;Smart et al, 2015;Dougherty et al, 2016;Matsuhashi et al, 2016). However, a number of questions related to the application and interpretation of eDNA methods persist and require ongoing research attention (Roussel et al, 2015;Barnes & Turner, 2016).…”

“…As examples, the performance of eDNA for benthic arthropods like freshwater crayfish has been equivocal between initial studies (e.g., Tréguier et al, 2014;Figiel & Bohn, 2015;Dougherty et al, 2016), and tests of eDNA in the largest of freshwater habitats like the Laurentian Great Lakes of the United States (US) and Canada (hereafter Great Lakes) have been relatively rare (but see Tucker et al, 2016). Given that organisms like crayfish have invaded and negatively affected large freshwater habitats including the Great Lakes (Peters et al, 2014), we ask: is it feasible to provide early detection of invasive benthic arthropods in massive freshwater lakes using eDNA?…”

“…We used a quantitative PCR (qPCR) eDNA assay that was recently found effective at detecting O. rusticus in smaller inland lakes (Dougherty et al, 2016), and developed a new qPCR eDNA assay for P. leniusculus using a recently published, comprehensive molecular dataset on the phylogenetics of the Pacifastacus genus . We collected water samples for eDNA from locations across all five of the Great Lakes and several associated waters, including Lake Champlain (133,100 ha) and the St. Lawrence Seaway, as well as from the two largest natural lakes in California (Lake Tahoe at 49,000 ha, Clear Lake at 18,000 ha) and a number of nearby, smaller lakes and reservoirs.…”