Estimating native and invasive crayfish distributions in relation to culvert barriers with environmental DNA

Ikeda, Kazuko; Doi, Hideyuki; Terui, Shigeharu; Kato, Atsuko; Mitsuzuka, Takashi; Kawai, Tadashi; Negishi, Junjiro N.

doi:10.1086/704998

Cited by 8 publications

(6 citation statements)

References 65 publications

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“…Table 3). This is in line with results of previous studies that investigated the suitability of eDNA as monitoring tool for freshwater crayfish (Tréguier et al, 2014;Dougherty et al, 2016;Ikeda et al, 2016;Agersnap et al, 2017;Mauvisseau et al, 2017;Ikeda et al, 2019;Troth et al, 2019;Rusch et al, 2020). However, detection efficiency varied among studies.…”

Section: Discussion Primer Evaluation and Edna Detectionsupporting

confidence: 90%

“…The advantages of eDNA as monitoring tool are the high sensitivity of the method, the possibility to screen large sections of running waters with only a few sampling sites and the non-invasive nature of the sampling (Larson et al, 2017;Geerts et al, 2018). Detection by means of eDNA therefore shows considerable promise for both the early detection of new or spreading biological invasions (Jerde et al, 2011;Cowart et al, 2018), as well as the monitoring of rare or endangered species that also often occur at low abundances (Atkinson et al, 2019;Ikeda et al, 2019). Moreover, the simultaneous detection of both ICS and NICS is possible (Robinson et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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eDNA Detection of Native and Invasive Crayfish Species Allows for Year-Round Monitoring and Large-Scale Screening of Lotic Systems

Chucholl

Fiolka

Segelbacher

et al. 2021

Front. Environ. Sci.

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Effective management of both endangered native and invasive alien crayfishes requires knowledge about distribution, monitoring of existing and early detection of newly established populations. Complementary to traditional survey methods, eDNA sampling has recently emerged as a highly sensitive non-invasive detection method to monitor crayfish populations. To advance the use of eDNA as detection tool for crayfish we used a twofold approach: 1) we designed a novel set of specific eDNA-assays for all native (Austropotamobius torrentium, Austropotamobius pallipes, Astacus astacus) and the most relevant invasive crayfish species (Pacifastacus leniusculus, Faxonius limosus, Faxonius immunis) in Central Europe. To ensure specificity each primer pair was tested in silico, in vitro, and in situ; 2) we assessed the influence of spatio-temporal variables (distance to upstream population, season, stream size) on eDNA detection in seven streams using two different detection methods (qualitative endpoint PCR and quantitative droplet digital PCR, ddPCR). The newly developed eDNA assays successfully detected all crayfish species across different lotic and lentic habitats. eDNA detection rate (endpoint PCR) and eDNA-concentration (ddPCR) were significantly influenced by distance and season. eDNA detection was successful up to 7 km downstream of the source population and across all seasons, although detectability was lowest in winter. eDNA detection rate further decreased with increasing stream size. Finally, eDNA-concentration correlated positively with estimated upstream population size. Overall, we provide near operational eDNA assays for six crayfish species, enabling year-round detection, which represents a clear benefit over conventional methods. Due to its high sensitivity, eDNA detection is also suitable for the targeted search of as-yet unrecorded or newly emerging populations. Using quantitative ddPCR might further allow for a rough estimation of population size, provided that the identified spatio-temporal factors are accounted for. We therefore recommend implementing eDNA-detection as a complementary survey tool, particularly for a large-scale screening of data-deficient catchments or a year-round monitoring.

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Section: Discussion Primer Evaluation and Edna Detectionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

eDNA Detection of Native and Invasive Crayfish Species Allows for Year-Round Monitoring and Large-Scale Screening of Lotic Systems

Chucholl

Fiolka

Segelbacher

et al. 2021

Front. Environ. Sci.

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“…An increasing number of studies, including the present one, demonstrate that the eDNA approach is effective in providing presence/absence data for freshwater crayfish (Dougherty et al 2016;Ikeda et al 2016Ikeda et al , 2019Agersnap et al 2017;Mauvisseau et al 2018Mauvisseau et al , 2019Strand et al 2019). In contrast to the crayfish plague agent A. astaci, where it is possible to determine the rough quantity of spores in the water Makkonen et al 2013;Svoboda et al 2013Svoboda et al , 2014, it is not possible to quantify crayfish biomass, population density or population structure on the basis of eDNA detection (Dougherty et al 2016;Agersnap et al 2017;Laurendz 2017;Rice et al 2018).…”

Section: Environmental Dna Monitoring Of Crayfish -Pros and Consmentioning

confidence: 78%

“…This study explores the use of the eDNA methodology for the detection of the crayfish plague pathogen A. astaci and freshwater crayfish in Central and Western Europe, simultaneously covering several species and numerous habitat types. A steadily increasing number of studies use eDNA monitoring to assess the presence of native crayfish or the introduction and spread of non-native crayfish across the globe (Tréguier et al 2014;Dougherty et al 2016;Ikeda et al 2016Ikeda et al , 2019Agersnap et al 2017 Mauvisseau et al 2018). In Europe, these tend to be complemented by screening for the accompanying conservationally relevant pathogen A. astaci (Robinson et al 2018;Mauvisseau et al 2019;Strand et al 2019;Wittwer et al 2019).…”

Section: Crayfish Edna and Assays -Our Study Compared To The State Of Artmentioning

confidence: 99%

Simultaneous detection of native and invasive crayfish and Aphanomyces astaci from environmental DNA samples in a wide range of habitats in Central Europe

Rusch¹,

Mojžišová²,

Strand³

et al. 2020

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Crayfish of North American origin are amongst the most prominent high-impact invasive invertebrates in European freshwaters. They contribute to the decline of European native crayfish species by spreading the pathogen causing crayfish plague, the oomycete Aphanomyces astaci. In this study we validated the specificity of four quantitative PCR (qPCR) assays, either published or newly developed, usable for environmental DNA (eDNA) screening for widely distributed native and non-native crayfish present in Central Europe: Astacus astacus, Pacifastacus leniusculus, Faxonius limosus and Procambarus virginalis. We then conducted an eDNA monitoring survey of these crayfish as well as the crayfish plague pathogen in a wide variety of habitat types representative for Central and Western Europe. The specificity of qPCR assays was validated against an extensive collection of crayfish DNA isolates, containing most crayfish species documented from European waters. The three assays developed in this study were sufficiently species-specific, but the published assay for F. limosus displayed a weak cross-reaction with multiple other crayfish species of the family Cambaridae. In the field study, we infrequently detected eDNA of A. astaci together with the three non-native crayfish species under examination. We never detected eDNA from A. astaci together with native crayfish, but in a few locations eDNA from both native and non-native crayfish was captured, due either to passive transport of eDNA from upstream populations or co-existence in the absence of infected crayfish carriers of A. astaci. In the study, we evaluated a robust, easy-to-use and low-cost version of the eDNA sampling equipment, based mostly on items readily available in garden stores and hobby markets, for filtering relatively large (~5 l) water samples. It performed just as well as the far more expensive equipment industrially designed for eDNA water sampling, thus opening the possibility of collecting suitable eDNA samples to a wide range of stakeholders. Overall, our study confirms that eDNA-based screening for crayfish and their associated pathogen is a feasible alternative to traditional monitoring.

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“…One promising approach is using environmental DNA (eDNA). Ikeda et al (2019) proposed eDNA as an efficient and highly sensitive method to assess the distribution of aquatic organisms. The eDNA sampling approach has also been suggested to have the potential to revolutionize marine biomonitoring ( Andruszkiewicz, Sassoubre & Boehm, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Using eDNA sampling for species-specific fish detection in tropical oceanic samples: limitations and recommendations for future use

Colmenares

Montes

Harms-Tuohy³

et al. 2023

PeerJ

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Background Over the past decade, environmental DNA (eDNA) has become a resourceful tool in conservation and biomonitoring. Environmental DNA has been applied in a variety of environments, but the application to studies of marine fish, particularly at tropical latitudes, are limited. Since many commercially important Caribbean fishes are overexploited, these species are optimal candidates to explore the use of this method as a biomonitoring tool. Specifically, for many of these species, the formation of fish spawning aggregations (FSAs) marks a critical life history event where fishes will gather in large numbers for reproduction. These FSAs are ephemeral in nature, lasting only a few days, but are predictable in time and space which makes them susceptible to overfishing. Methods In this study, we test the feasibility of using an eDNA sampling approach (water and sediment collection) to detect the presence of known FSAs off the west coast of Puerto Rico, with cytochrome c oxidase subunit 1 (CO1) and 12S rRNA (12S) primers designed to target specific species. A total of 290 eDNA samples were collected and, of those, 206 eDNA samples were processed. All eDNA samples varied in DNA concentration, both between replicates and collection methods. A total of 12 primer sets were developed and tested using traditional PCR and qPCR. Results Despite validation of primer accuracy and sample collection during known peak spawning times, the use of traditional PCR and qPCR with both molecular markers failed to produce species-specific amplification. Thus, a trial test was conducted using the CO1 primers in which target fish DNA was ‘spiked’ at various concentrations into the respective eDNA samples to determine the target species DNA concentration limit of detection. Upon successful amplification of the trial, results indicated that eDNA samples were below the detection threshold of our methods, suggesting that the number of fish present at the spawning aggregations was inadequate for single-species detection methods. In addition, elements such as the unavoidable presence of non-target DNA, oceanic environmental conditions, shedding rates of target fish, among other biotic and abiotic factors could have affected DNA persistence and degradation rates at the sites. Conclusion We provide recommendations for species-specific fish detection in lower latitudes, and suggestions for studies aiming to monitor or detect fish spawning aggregations using eDNA sampling.

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Estimating native and invasive crayfish distributions in relation to culvert barriers with environmental DNA

Cited by 8 publications

References 65 publications

eDNA Detection of Native and Invasive Crayfish Species Allows for Year-Round Monitoring and Large-Scale Screening of Lotic Systems

eDNA Detection of Native and Invasive Crayfish Species Allows for Year-Round Monitoring and Large-Scale Screening of Lotic Systems

Simultaneous detection of native and invasive crayfish and Aphanomyces astaci from environmental DNA samples in a wide range of habitats in Central Europe

Using eDNA sampling for species-specific fish detection in tropical oceanic samples: limitations and recommendations for future use

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