EnvironmentalDNAsurveillance for invertebrate species: advantages and technical limitations to detect invasive crayfishProcambarus clarkiiin freshwater ponds

Abstract

SummaryThe introduction of non‐native species is a major threat to biodiversity. While eradication programs of well‐established invaders are costly and hazardous for non‐target species, the early detection of a non‐native species at low density is critical for preventing biological invasions in recipient ecosystems. Recent studies reveal that environmentalDNA(eDNA) is a powerful tool for detecting target species in aquatic ecosystems, but these studies focus mostly on fish and amphibians.We examine the reliability of using eDNAto detect the presence of an invasive freshwater crustacean species, the red swamp crayfishProcambarus clarkii. Species‐specific primers and probes were designed; their specificity was tested usingin silicoPCRsimulations and against tissues of other crayfish species. Limits of detection and quantification were specified for the targetDNAsequence by means of quantitativePCRamplifications on dilution series of known amount ofP. clarkiiDNA.The method was applied to water samples collected in 158 ponds in aFrenchNaturePark, and results were compared to a traditional method using food‐baited funnel traps. EnvironmentalDNAhad a better detection efficiency but predominantly led to divergent results compared with the trapping method. While habitat features partly explained the failure of crayfish detection by trapping, detection by eDNAwas problematic at low crayfish abundances. WhenP. clarkiiwas detected, the estimated concentrations of crayfishDNAin water samples were always below the limit of quantification for the targetDNAsequence.Synthesis and applications. The combination of environmentalDNA(eDNA) and conventional trapping methods is recommended to monitor the invasion byP. clarkiiin small waterbodies such as ponds. However, the risk of mortality for non‐target species, notably amphibians, has to be carefully evaluated before large‐scale deployment of traps. Contrary to fish and amphibians, a low amount of extracellularDNAin water is suspected to be the major limitation for crayfish detection by molecular approaches. Current advancements inPCRtechnology, together with optimization of the water sampling method, promise upcoming developments of eDNAdetection for aquatic invertebrate species.