TY  - JOUR
AU  - Pont, Didier
AU  - Meulenbroek, Paul
AU  - Bammer, Vincenz
AU  - Dejean, Tony
AU  - Erős, Tibor
AU  - Jean, Pauline
AU  - Lenhardt, Mirjana
AU  - Nagel, Christoffer
AU  - Pekarik, Ladislav
AU  - Schabuss, Michael
AU  - Stoeckle, Bernhard C
AU  - Stoica, Elena
AU  - Zornig, Horst
AU  - Weigand, Alexander
AU  - Valentini, Alice
PY  - 2022
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5163
AB  - Environmental DNA (eDNA) metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density/biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a quantitative (q)PCR approach to infer the absolute abundance of fish species. We carried out a 2850-km eDNA survey within the Danube catchment using a spatial integrative sampling protocol coupled with traditional electrofishing for fish biomass and density estimation. Total fish eDNA concentrations and total fish abundance were highly correlated. The correlation between eDNA concentrations per taxon and absolute specific abundance was of comparable strength when all sites were pooled and remained significant when the sites were considered separately. Furthermore, a nonlinear mixed model showed that species richness was underestimated when the amount of teleo-DNA extracted from a sample was below a threshold of 0.65 × 106 copies of eDNA. This result, combined with the decrease in teleo-DNA concentration by several orders of magnitude with river size, highlights the need to increase sampling effort in large rivers. Our results provide a comprehensive description of longitudinal changes in fish communities and underline our combined metabarcoding/qPCR approach for biomonitoring and bioassessment surveys when a rough estimate of absolute species abundance is sufficient.
PB  - Hoboken: Wiley
T2  - Molecular Ecology Resources
T1  - Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR.
DO  - 10.1111/1755-0998.13715
ER  - 

@article{
author = "Pont, Didier and Meulenbroek, Paul and Bammer, Vincenz and Dejean, Tony and Erős, Tibor and Jean, Pauline and Lenhardt, Mirjana and Nagel, Christoffer and Pekarik, Ladislav and Schabuss, Michael and Stoeckle, Bernhard C and Stoica, Elena and Zornig, Horst and Weigand, Alexander and Valentini, Alice",
year = "2022",
abstract = "Environmental DNA (eDNA) metabarcoding is an effective method for studying fish communities but allows only an estimation of relative species abundance (density/biomass). Here, we combine metabarcoding with an estimation of the total abundance of eDNA amplified by our universal marker (teleo) using a quantitative (q)PCR approach to infer the absolute abundance of fish species. We carried out a 2850-km eDNA survey within the Danube catchment using a spatial integrative sampling protocol coupled with traditional electrofishing for fish biomass and density estimation. Total fish eDNA concentrations and total fish abundance were highly correlated. The correlation between eDNA concentrations per taxon and absolute specific abundance was of comparable strength when all sites were pooled and remained significant when the sites were considered separately. Furthermore, a nonlinear mixed model showed that species richness was underestimated when the amount of teleo-DNA extracted from a sample was below a threshold of 0.65 × 106 copies of eDNA. This result, combined with the decrease in teleo-DNA concentration by several orders of magnitude with river size, highlights the need to increase sampling effort in large rivers. Our results provide a comprehensive description of longitudinal changes in fish communities and underline our combined metabarcoding/qPCR approach for biomonitoring and bioassessment surveys when a rough estimate of absolute species abundance is sufficient.",
publisher = "Hoboken: Wiley",
journal = "Molecular Ecology Resources",
title = "Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR.",
doi = "10.1111/1755-0998.13715"
}

Pont, D., Meulenbroek, P., Bammer, V., Dejean, T., Erős, T., Jean, P., Lenhardt, M., Nagel, C., Pekarik, L., Schabuss, M., Stoeckle, B. C., Stoica, E., Zornig, H., Weigand, A.,& Valentini, A.. (2022). Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR.. in Molecular Ecology Resources
Hoboken: Wiley..
https://doi.org/10.1111/1755-0998.13715

Pont D, Meulenbroek P, Bammer V, Dejean T, Erős T, Jean P, Lenhardt M, Nagel C, Pekarik L, Schabuss M, Stoeckle BC, Stoica E, Zornig H, Weigand A, Valentini A. Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR.. in Molecular Ecology Resources. 2022;.
doi:10.1111/1755-0998.13715 .

Pont, Didier, Meulenbroek, Paul, Bammer, Vincenz, Dejean, Tony, Erős, Tibor, Jean, Pauline, Lenhardt, Mirjana, Nagel, Christoffer, Pekarik, Ladislav, Schabuss, Michael, Stoeckle, Bernhard C, Stoica, Elena, Zornig, Horst, Weigand, Alexander, Valentini, Alice, "Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR." in Molecular Ecology Resources (2022),
https://doi.org/10.1111/1755-0998.13715 . .

TY  - JOUR
AU  - Meulenbroek, Paul
AU  - Hein, Thomas
AU  - Friedrich, Thomas
AU  - Valentini, Alice
AU  - Erős, Tibor
AU  - Schabuss, Michael
AU  - Zornig, Horst
AU  - Lenhardt, Mirjana
AU  - Pekarik, Ladislav
AU  - Jean, Pauline
AU  - Dejean, Tony
AU  - Pont, Didier
PY  - 2022
UR  - https://link.springer.com/10.1007/s10531-022-02459-w
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5083
AB  - Sturgeon populations are declining worldwide and are the target of extensive conservation efforts. Addressed in several pieces of legislation, sturgeons have received considerable attention as flagship or umbrella species. Despite the need for a better understanding of the distribution and population status, the use of traditional sampling methods failed in the past, thereby hampering reliable assessments, a prerequisite for conservation. Here, we describe the development and application of an environmental DNA (eDNA) metabarcoding approach for detecting rare sturgeons in large rivers. Exemplarily, we developed a reference database for five native Danube sturgeons ( Acipenser stellatus , Acipenser gueldenstaedtii , Acipenser ruthenus, Acipenser nudiventris, and Huso huso ) and two non-native species ( Acipenser baerii and Acipenser transmontanus ), assessed these ex situ, and used eDNA as a detection tool along the entire length of the Danube (Europe, ~ 2850 km) and major tributaries. In ex situ analyses, all assays yielded positive amplifications for the assessed sturgeon species. In the Danube, the presence of A. ruthenus was confirmed at 14 of 29 sites (48.3%), and in 2 of 18 tributary sites (11.1%), providing the first comprehensive large-scale biogeographical snapshot of this species. Relative number of reads assigned to A. ruthenus varied between 0 and 2.5%, with sites registering positive detections being clustered in 3 sections of the Danube. Our findings enabled us to confirm the advantages of eDNA monitoring over traditional sampling methods for comprehensive whole-river snapshot studies of sturgeons conducted on a large geographical scale, and therefore we consider it to be a promising approach for application in conservation measures, fisheries management, scientific studies, and adaptive management plans for sturgeons on a global scale.
PB  - Dordrecht: Springer
T2  - Biodiversity and Conservation
T1  - Sturgeons in large rivers: detecting the near-extinct needles in a haystack via eDNA metabarcoding from water samples
IS  - 11
VL  - 31
DO  - 10.1007/s10531-022-02459-w
SP  - 2817
EP  - 2832
ER  - 

@article{
author = "Meulenbroek, Paul and Hein, Thomas and Friedrich, Thomas and Valentini, Alice and Erős, Tibor and Schabuss, Michael and Zornig, Horst and Lenhardt, Mirjana and Pekarik, Ladislav and Jean, Pauline and Dejean, Tony and Pont, Didier",
year = "2022",
abstract = "Sturgeon populations are declining worldwide and are the target of extensive conservation efforts. Addressed in several pieces of legislation, sturgeons have received considerable attention as flagship or umbrella species. Despite the need for a better understanding of the distribution and population status, the use of traditional sampling methods failed in the past, thereby hampering reliable assessments, a prerequisite for conservation. Here, we describe the development and application of an environmental DNA (eDNA) metabarcoding approach for detecting rare sturgeons in large rivers. Exemplarily, we developed a reference database for five native Danube sturgeons ( Acipenser stellatus , Acipenser gueldenstaedtii , Acipenser ruthenus, Acipenser nudiventris, and Huso huso ) and two non-native species ( Acipenser baerii and Acipenser transmontanus ), assessed these ex situ, and used eDNA as a detection tool along the entire length of the Danube (Europe, ~ 2850 km) and major tributaries. In ex situ analyses, all assays yielded positive amplifications for the assessed sturgeon species. In the Danube, the presence of A. ruthenus was confirmed at 14 of 29 sites (48.3%), and in 2 of 18 tributary sites (11.1%), providing the first comprehensive large-scale biogeographical snapshot of this species. Relative number of reads assigned to A. ruthenus varied between 0 and 2.5%, with sites registering positive detections being clustered in 3 sections of the Danube. Our findings enabled us to confirm the advantages of eDNA monitoring over traditional sampling methods for comprehensive whole-river snapshot studies of sturgeons conducted on a large geographical scale, and therefore we consider it to be a promising approach for application in conservation measures, fisheries management, scientific studies, and adaptive management plans for sturgeons on a global scale.",
publisher = "Dordrecht: Springer",
journal = "Biodiversity and Conservation",
title = "Sturgeons in large rivers: detecting the near-extinct needles in a haystack via eDNA metabarcoding from water samples",
number = "11",
volume = "31",
doi = "10.1007/s10531-022-02459-w",
pages = "2817-2832"
}

Meulenbroek, P., Hein, T., Friedrich, T., Valentini, A., Erős, T., Schabuss, M., Zornig, H., Lenhardt, M., Pekarik, L., Jean, P., Dejean, T.,& Pont, D.. (2022). Sturgeons in large rivers: detecting the near-extinct needles in a haystack via eDNA metabarcoding from water samples. in Biodiversity and Conservation
Dordrecht: Springer., 31(11), 2817-2832.
https://doi.org/10.1007/s10531-022-02459-w

Meulenbroek P, Hein T, Friedrich T, Valentini A, Erős T, Schabuss M, Zornig H, Lenhardt M, Pekarik L, Jean P, Dejean T, Pont D. Sturgeons in large rivers: detecting the near-extinct needles in a haystack via eDNA metabarcoding from water samples. in Biodiversity and Conservation. 2022;31(11):2817-2832.
doi:10.1007/s10531-022-02459-w .

Meulenbroek, Paul, Hein, Thomas, Friedrich, Thomas, Valentini, Alice, Erős, Tibor, Schabuss, Michael, Zornig, Horst, Lenhardt, Mirjana, Pekarik, Ladislav, Jean, Pauline, Dejean, Tony, Pont, Didier, "Sturgeons in large rivers: detecting the near-extinct needles in a haystack via eDNA metabarcoding from water samples" in Biodiversity and Conservation, 31, no. 11 (2022):2817-2832,
https://doi.org/10.1007/s10531-022-02459-w . .