Development of a TaqMan qPCR protocol for detecting Acipenser ruthenus in the Volga headwaters from eDNA samples

Schenekar, Tamara; Schletterer, Martin; Weiss, Steven

doi:10.1007/s12686-020-01128-w

Cited by 9 publications

(8 citation statements)

References 17 publications

(19 reference statements)

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“…These results are concordant with previous studies that showed a higher sensitivity of targeted qPCR compared to metabarcoding (Bylemans et al, ; Harper et al, ), indicating a better performance of targeted approaches particularly for species of low abundance. However, a recently developed TaqMan qPCR assay did not detect sterlet ( Acipenser ruthenus ) in the same system, despite recent reports of its presence at individual sites (Schenekar, Schletterer, & Weiss, ), potentially indicating the border of sensitivity of such assays for a species occurring at very low densities. The sensitivity of eDNA assays will always be influenced by the filtered water volume, storage and extraction methods, and the number of PCR replicates performed, as well as both metabarcoding thresholds or qPCR detection thresholds (as also discussed by Goldberg et al, ; Harper et al, ).…”

Section: Discussionmentioning

confidence: 75%

Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

Schenekar

Schletterer

Lecaudey

et al. 2020

River Research & Apps

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Biodiversity monitoring via environmental DNA, particularly metabarcoding, is evolving into a powerful assessment tool for riverine systems. However, for metabarcoding to be fully integrated into standardized monitoring programmes, some current challenges concerning sampling design, laboratory workflow, and data analysis need to be overcome. Here, we review some of these major challenges and potential solutions. We further illustrate three potential pitfalls, namely the choice of suitable metabarcoding primers, the necessity of complete reference databases, and varying assay sensitivities, by a reappraisal of our‐own recently carried out metabarcoding study in the Volga headwaters. TaqMan qPCRs had detected catfish (Silurus glanis) and European eel (Anguilla anguilla), whereas metabarcoding had not, in the same samples. Furthermore, after extending the genetic reference database by 12 additional species and re‐analysing the metabarcoding data, we additionally detected the Siberian spiny loach (Cobitis sibirica) and Ukrainian brook lamprey (Eudontomyzon mariae) and reassigned the operational taxonomic units previously assigned to Misgurnus fossilis to Cobitis sibirica. In silico analysis of metabarcoding primer efficiencies revealed considerable variability among primer pairs and among target species, which could lead to strong primer bias and potential false‐negatives in metabarcoding studies if not properly compensated for. These results highlight some of the pitfalls of eDNA‐metabarcoding as a means of monitoring fish biodiversity in large rivers, which need to be considered in order to fully unleash the full potential of these approaches for freshwater biodiversity monitoring.

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Section: Discussionmentioning

confidence: 75%

Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

Schenekar

Schletterer

Lecaudey

et al. 2020

River Research & Apps

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“…trammel‐nets). Recent advances in environmental DNA (eDNA) suggest that this method can be used in future for monitoring the sturgeon populations in large rivers (Pfleger et al, 2016; Schenekar, Schletterer & Weiss, 2020) such as the Danube.…”

Section: Discussionmentioning

confidence: 99%

Bayesian modelling suggests that the sterlet (Acipenser ruthenus, Linnaeus 1758) population is ageing in the middle Danube River

Kubala

Farský²,

Krajč³

et al. 2021

Aquatic Conservation

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In the past, sturgeons played an important role in commercial and recreational fisheries in the Danube River and its tributaries. Human impacts in the Danube River Basin coupled with exploitation of sturgeon stocks led to all species being either locally extinct, critically endangered or of unknown status. Sterlet (Acipenser ruthenus, Linnaeus 1758) is the last known sturgeon species occurring in the upper and middle Danube; however, the population of this species is considered unbalanced and decreasing since the beginning of the twenty‐first century. The decline of sturgeon stocks has been noted before owing to their economic importance. With commercial fisheries being forbidden in the Slovak section of the Danube River, there is generally no information available about the status of what is considered a local population. Databases containing recreational catch of sterlet (2003–2018) and historical records of commercial harvest (1961–1990) were used to describe the trend in the weight and number of sterlet caught over the following years. Modelling indicated that the number of fish caught each year appears to be lower, while the average weight of each individual is increasing. This might suggest that the population is ageing. Although older individuals can contribute a great deal more to spawning because they produce a greater number of eggs, several problems are apparent. The number of spawners might be decreasing as a result of bycatch or fishing, their ability to spawn might be obstructed, or annual recruitment may fail owing to unpredictable events. Although restocking programmes are in place to help maintain the sterlet population in the Danube River, their efficiency seems to be drastically low. In fact, restocking could be of little value unless studies on the availability of key habitats are conducted and their protection and restoration are ensured.

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“…However, these primers are not able to distinguish among Ponto-Caspian species, namely the Siberian and Russian sturgeons, and sterlet (Knudsen et al, 2022). Schenekar et al (2020) developed an assay for A. ruthenus and possibly Huso, but this also amplified other non-target sturgeons. According to the approach proposed by Farrington and Lance (2014), positive detection of North American species using common markers, in combination with the absence of positive detection by species-specific markers, makes it possible to determine the occurrence of other sturgeon species with an overlapping range.…”

Section: Status In Kazakhstanmentioning

confidence: 99%

Environmental DNA reveals the ecology and seasonal migration of a rare sturgeon species in the Ural River

Abileva,

Turzhanova,

Zhamangara

et al. 2024

Environmental DNA

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Environmental DNA (eDNA) technology is an essential tool for monitoring living organisms in ecological research. The combination of eDNA methods with traditional methods of ecological observation can significantly improve the study of the ecology of rare species. Here, we present the development and application of an eDNA approach to identify rare sturgeons in the lower reaches of the Ural River (Zhaiyk) (~1084 km). The presence of representatives of the genus Sturgeon was detected at all sites in spring (nine sites) and autumn (ten sites) while they were absent during the summer period, consistent with their semi‐anadromous ecology. Detection in spring and autumn indicates the passage of spring and winter forms to the lower and upper spawning grounds, respectively. This study confirms the difficulties of species‐specific identification of Eurasian sturgeon and provides the first documented eDNA detection of specimens of the genus Sturgeon in the Ural River. It also provides a biogeographic snapshot of their distribution, experimentally confirming their seasonal migrations in the lower reaches of the river. The successful detection of sturgeon motivates further eDNA surveys of this and other fish species for accurate species identification and population assessment, opening up prospects for the management of these threatened species.

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Development of a TaqMan qPCR protocol for detecting Acipenser ruthenus in the Volga headwaters from eDNA samples

Cited by 9 publications

References 17 publications

Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

Reference databases, primer choice, and assay sensitivity for environmental metabarcoding: Lessons learnt from a re‐evaluation of an eDNA fish assessment in the Volga headwaters

Bayesian modelling suggests that the sterlet (Acipenser ruthenus, Linnaeus 1758) population is ageing in the middle Danube River

Environmental DNA reveals the ecology and seasonal migration of a rare sturgeon species in the Ural River

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