Environmental DNA (eDNA) metabarcoding surveys show evidence of non-indigenous freshwater species invasion to new parts of Eastern Europe

Abstract

Active environmental DNA (eDNA) surveillance through species-specific amplification has shown increased sensitivity in the detection of non-indigenous species (NIS) compared to traditional approaches. When many NIS are of interest, however, active surveillance decreases in cost- and time-efficiency. Passive surveillance through eDNA metabarcoding takes advantage of the complex DNA signal in environmental samples and facilitates the simultaneous detection of multiple species. While passive eDNA surveillance has previously detected NIS, comparative studies are essential to determine the ability of eDNA metabarcoding to accurately describe the range of invasion for multiple NIS versus alternative approaches. Here, we surveyed twelve sites, covering nine rivers across Belarus for NIS with three different techniques, i.e. an ichthyological, hydrobiological and eDNA survey, whereby DNA was extracted from 500 ml surface water samples and amplified with two 16S rDNA primer assays targeting the fish and macroinvertebrate biodiversity. Nine non-indigenous fish and ten non-indigenous benthic macroinvertebrates were detected by traditional surveys, while seven NISeDNA signals were picked up, including four fish, one aquatic and two benthic macroinvertebrates. Passive eDNA surveillance extended the range of invasion further north for two invasive fish and identified a new NIS for Belarus, the freshwater jellyfish Craspedacusta sowerbii. False-negative detections for the eDNA survey might be attributed to: (i) preferential amplification of aquatic over benthic macroinvertebrates from surface water samples and (ii) an incomplete reference database. The evidence provided in this study recommends the implementation of both molecular-based and traditional approaches to maximise the probability of early detection of non-native organisms.

The status of COI and 12S rRNA DNA barcode reference libraries for freshwater fish in South Africa: Implications for future eDNA projects

“…Environmental DNA methods have also been used successfully for the detection and monitoring of invasive fish (Takahara et al 2013; Keskin 2014; Bylemans et al 2016; Keskin et al 2016; Hinlo et al 2017; Clusa and García-Vázquez 2018; Jo et al 2021; Minett et al 2021; Dubreuil et al 2022; Jeunen et al 2022). Considerable efforts have been made to barcode introduced freshwater fish species in South Africa (van der Walt et al 2017).…”

“…This further highlights the importance of using multi-marker approaches, which include the use of genes such as Cytb that have more complete reference libraries, for eDNA studies in South Africa. Environmental DNA methods have also been used successfully for the detection and monitoring of invasive fish (Takahara et al 2013;Keskin 2014;Bylemans et al 2016;Keskin et al 2016;Hinlo et al 2017;Clusa and García-Vázquez 2018;Jo et al 2021;Minett et al 2021;Dubreuil et al 2022;Jeunen et al 2022). Considerable efforts have been made to barcode introduced freshwater fish species in South Africa (van der Walt et al 2017).…”

The Application of eDNA for Monitoring Aquatic Non-Indigenous Species: Practical and Policy Considerations

“…DNA-based methods using eDNA allow the identification of organisms present in water, sediment, or air samples, where DNA is released into the environment (e.g., via mucus, skin, scales, fur, urine, and cell debris) [17]. In contrast to traditional detection methods, environmental DNA is known to be sensitive enough to monitor difficult-to-detect aquatic species at low densities [26,27], with an order of magnitude more sensitive than the former [18,28]. For example, monitoring studies of the invasive non-native quagga mussel Dreissena bugensis tested three DNA-based approaches, and all proved to be more sensitive than traditional kick-net sampling for its detection in flowing water [18].…”

“…Some studies suggest that eDNA is a more sensitive method for species detection than traditional survey methods [22,33], whereas others advocate that, despite the higher sensitivity of eDNA, both methods offer similar ecological results [34]. Further combining morphologybased taxonomy with molecular approaches would benefit not only curating existing databases [17,35,36], as this would offer an extended taxa confirmation, but many studies also suggest complementarity when using both approaches [27,[36][37][38][39]. Both methods have their own advantages and limitations, and there is no one-size-fits-all approach that can be used for all NIS detection and monitoring efforts.…”

“…For example, freshwater monitoring studies on redfin perch, Perca fluviatilis, using eDNA metabarcoding and qPCR, found that the latter was more sensitive [66]. Passive monitoring through eDNA metabarcoding can be more costly for monitoring purposes if the number of target NIS is small [67], but conversely, it will provide additional information on a wider set of species, some of which might even be of unknown existence in that specific habitat [27,59]. Another advantage of using eDNA metabarcoding is the opportunity to apply nanopore-based sequencing technologies (Oxford Nanopore Technologies, ONT), which can sequence longer reads and thus offer a higher species resolution power [68].…”