Utility of environmental DNA analysis for effective monitoring of invasive fish species in reservoirs

Abstract

Dam-mediated biological invasions are a serious problem all over the world. Once established in reservoirs, the invasive species have catastrophic impacts on the river ecosystems downstream, and thus, rapid monitoring of invasive species is an urgent issue for the effective removal of them and the conservation management of native ecosystems. Here, we verified the utility of environmental DNA (eDNA) analysis as a tool to effectively monitor three invasive fish species (bluegill, largemouth bass, and smallmouth bass) in reservoirs using multiplex real-time PCR. First, to determine the optimal sampling location and season to detect eDNA from these species, we analyzed the eDNA in water samples from shore and offshore sites in three reservoirs all year around. We found that eDNA detection rates either did not differ between sampling locations or were higher for shore than offshore sites. In addition, eDNA detection rates were higher in spring (breeding season of target species) and/or summer than winter. Second, we extensively surveyed the distribution of the three species in 30 reservoirs in Japan using eDNA analysis. Consequently, a single eDNA-based surveillance in summer allowed to match approximately 90% of the presence/absence of the invasive fish species known from 27 yr of administrative capture-based surveillances. Given these results, we recommend collecting the replicated water samples from shore sites in summer or the breeding season for the effective detection of invasive fish eDNA in reservoirs. Our eDNA assays with multiplex real-time PCR enable the rapid and sensitive monitoring of invasive fish distribution in reservoirs.

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).…”

Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis

“…However, these methods are usually invasive for individuals and their habitats, require high morphological expertise for species identification and substantial survey effort and costs, or produce variable results depending on researchers' ability [8][9][10][11]. Recent blossoming of environmental DNA (eDNA) analysis has overcome these limitations and allowed cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial and aquatic environments [12][13][14][15][16][17]. Environmental DNA is basically defined as the total pool of DNA fragments isolated from environmental samples, including water, soil and air [18,19].…”

Tracking an invasion front with environmental DNA

“…Historically, cost‐effective management strategies have had to balance high survey costs for small populations and high eradication costs if the survey fails to detect an incipient population in the initial stages of invasion (Lodge et al, 2006). Genetic approaches may better detect rare individuals, and thereby lower costs and improve the sensitivity of surveys for small populations, such as those at invasion fronts (Beauclerc et al, 2019; Harper et al, 2018; Jo et al, 2021; Kuehne et al, 2020; Schütz et al, 2020). However, traditional monitoring methods outperform some eDNA assays (Rose et al, 2019; Ulibarri et al, 2017), underscoring the importance of side‐by‐side comparisons of detection efficiency.…”