Droplet digital PCR assays for the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) from environmental DNA collected in the water of mountain lakes.
Classical methods for estimating the abundance of fish populations are often both expensive, time-consuming and destructive. Analyses of the environmental DNA (eDNA) present in water samples could alleviate such constraints. Here, we developed protocols to detect and quantify brown trout (Salmo trut...
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ftdoajarticles:oai:doaj.org/article:e53fb3bc9b394ec2b3fc501cdf95eb13 2023-05-15T14:55:35+02:00 Droplet digital PCR assays for the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) from environmental DNA collected in the water of mountain lakes. Eric Capo Göran Spong Sven Norman Helena Königsson Pia Bartels Pär Byström 2019-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0226638 https://doaj.org/article/e53fb3bc9b394ec2b3fc501cdf95eb13 EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pone.0226638 https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0226638 https://doaj.org/article/e53fb3bc9b394ec2b3fc501cdf95eb13 PLoS ONE, Vol 14, Iss 12, p e0226638 (2019) Medicine R Science Q article 2019 ftdoajarticles https://doi.org/10.1371/journal.pone.0226638 2022-12-31T11:25:48Z Classical methods for estimating the abundance of fish populations are often both expensive, time-consuming and destructive. Analyses of the environmental DNA (eDNA) present in water samples could alleviate such constraints. Here, we developed protocols to detect and quantify brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) populations by applying the droplet digital PCR (ddPCR) method to eDNA molecules extracted from water samples collected in 28 Swedish mountain lakes. Overall, contemporary fish CPUE (catch per unit effort) estimates from standardized survey gill nettings were not correlated to eDNA concentrations for either of the species. In addition, the measured environmental variables (e.g. dissolved organic carbon concentrations, temperature, and pH) appear to not influence water eDNA concentrations of the studied fish species. Detection probabilities via eDNA analysis showed moderate success (less than 70% for both species) while the presence of eDNA from Arctic char (in six lakes) and brown trout (in one lake) was also indicated in lakes where the species were not detected with the gillnetting method. Such findings highlight the limits of one or both methods to reliably detect fish species presence in natural systems. Additional analysis showed that the filtration of water samples through 1.2 μm glass fiber filters and 0.45 μm mixed cellulose ester filters was more efficient in recovering DNA than using 0.22 μm enclosed polyethersulfone filters, probably due to differential efficiencies of DNA extraction. Altogether, this work showed the potentials and limits of the approach for the detection and the quantification of fish abundance in natural systems while providing new insights in the application of the ddPCR method applied to environmental DNA. Article in Journal/Newspaper Arctic Salvelinus alpinus Directory of Open Access Journals: DOAJ Articles Arctic PLOS ONE 14 12 e0226638 |
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English |
topic |
Medicine R Science Q |
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Medicine R Science Q Eric Capo Göran Spong Sven Norman Helena Königsson Pia Bartels Pär Byström Droplet digital PCR assays for the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) from environmental DNA collected in the water of mountain lakes. |
topic_facet |
Medicine R Science Q |
description |
Classical methods for estimating the abundance of fish populations are often both expensive, time-consuming and destructive. Analyses of the environmental DNA (eDNA) present in water samples could alleviate such constraints. Here, we developed protocols to detect and quantify brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) populations by applying the droplet digital PCR (ddPCR) method to eDNA molecules extracted from water samples collected in 28 Swedish mountain lakes. Overall, contemporary fish CPUE (catch per unit effort) estimates from standardized survey gill nettings were not correlated to eDNA concentrations for either of the species. In addition, the measured environmental variables (e.g. dissolved organic carbon concentrations, temperature, and pH) appear to not influence water eDNA concentrations of the studied fish species. Detection probabilities via eDNA analysis showed moderate success (less than 70% for both species) while the presence of eDNA from Arctic char (in six lakes) and brown trout (in one lake) was also indicated in lakes where the species were not detected with the gillnetting method. Such findings highlight the limits of one or both methods to reliably detect fish species presence in natural systems. Additional analysis showed that the filtration of water samples through 1.2 μm glass fiber filters and 0.45 μm mixed cellulose ester filters was more efficient in recovering DNA than using 0.22 μm enclosed polyethersulfone filters, probably due to differential efficiencies of DNA extraction. Altogether, this work showed the potentials and limits of the approach for the detection and the quantification of fish abundance in natural systems while providing new insights in the application of the ddPCR method applied to environmental DNA. |
format |
Article in Journal/Newspaper |
author |
Eric Capo Göran Spong Sven Norman Helena Königsson Pia Bartels Pär Byström |
author_facet |
Eric Capo Göran Spong Sven Norman Helena Königsson Pia Bartels Pär Byström |
author_sort |
Eric Capo |
title |
Droplet digital PCR assays for the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) from environmental DNA collected in the water of mountain lakes. |
title_short |
Droplet digital PCR assays for the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) from environmental DNA collected in the water of mountain lakes. |
title_full |
Droplet digital PCR assays for the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) from environmental DNA collected in the water of mountain lakes. |
title_fullStr |
Droplet digital PCR assays for the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) from environmental DNA collected in the water of mountain lakes. |
title_full_unstemmed |
Droplet digital PCR assays for the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) from environmental DNA collected in the water of mountain lakes. |
title_sort |
droplet digital pcr assays for the quantification of brown trout (salmo trutta) and arctic char (salvelinus alpinus) from environmental dna collected in the water of mountain lakes. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2019 |
url |
https://doi.org/10.1371/journal.pone.0226638 https://doaj.org/article/e53fb3bc9b394ec2b3fc501cdf95eb13 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Salvelinus alpinus |
genre_facet |
Arctic Salvelinus alpinus |
op_source |
PLoS ONE, Vol 14, Iss 12, p e0226638 (2019) |
op_relation |
https://doi.org/10.1371/journal.pone.0226638 https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0226638 https://doaj.org/article/e53fb3bc9b394ec2b3fc501cdf95eb13 |
op_doi |
https://doi.org/10.1371/journal.pone.0226638 |
container_title |
PLOS ONE |
container_volume |
14 |
container_issue |
12 |
container_start_page |
e0226638 |
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