The update and optimization of an eDNA assay to detect the invasive rusty crayfish (Faxonius rusticus)

• Published in: PloS one Vol. 16; no. 10; p. e0259084
• Main Authors: Coster, Stephanie S, Dillon, Megan N, Moore, William, Merovich, Jr, George T
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 29.10.2021; Public Library of Science (PLoS)
• Subjects: Analysis; Animals; Aquatic environment; Assaying; Astacoidea - genetics; Biology; Biology and Life Sciences; Buffer storage; Buffers (chemistry); Crayfish; Deoxyribonucleic acid; DNA; DNA, Environmental - isolation & purification; Ecology and Environmental Sciences; Ecosystem biology; Ecosystems; Engineering and Technology; Environmental DNA; Environmental Monitoring - methods; Ethanol; Faxonius rusticus; Fisheries; Fishing; Genetic aspects; Introduced Species; Invasive species; Medicine and Health Sciences; Mitochondrial DNA; Mollusks; Native species; Optimization; Orconectes rusticus; Pennsylvania; Physical Sciences; Polymerase chain reaction; Polymerase Chain Reaction - methods; Research and analysis methods; Rivers - chemistry; Streams; Watersheds; Pennsylvania; United States; Juniata River; United States > US; Virginia
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0259084

Environmental DNA (eDNA) is nuclear or mitochondrial DNA shed into the environment, and amplifying this DNA can serve as a reliable, noninvasive way to monitor aquatic systems for the presence of an invasive species. Assays based on the collection of eDNA are becoming increasingly popular, and, when optimized, can aid in effectively and efficiently tracking invasion fronts. We set out to update an eDNA assay to detect the invasive rusty crayfish, Faxonius rusticus. We tested for species specificity compared to other stream crayfish and field tested the assay at sites with known presence (N = 3) and absence (N = 4) in the Juniata River watershed in central Pennsylvania, USA. To maximize sensitivity, we field tested different storage buffers (Longmire's buffer and ethanol), DNA extraction methods (Qiagen's DNEasy and PowerWater kits), and quantitative polymerase chain reaction (qPCR) chemistries (TaqMan and SYBR green). Our assay confirmed the presence data and performed optimally when filter samples were stored in Longmire's buffer, DNA was extracted with DNeasy Blood and Tissue Kit, and TaqMan qPCR chemistry was utilized. With proper sample processing, our assay allows for accurate, noninvasive detection of F. rusticus in streams.