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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ftpubmed:oai:pubmedcentral.nih.gov:6919618 2023-05-15T14:55:53+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 Capo, Eric Spong, Göran Norman, Sven Königsson, Helena Bartels, Pia Byström, Pär 2019-12-18 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6919618/ http://www.ncbi.nlm.nih.gov/pubmed/31851707 https://doi.org/10.1371/journal.pone.0226638 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6919618/ http://www.ncbi.nlm.nih.gov/pubmed/31851707 http://dx.doi.org/10.1371/journal.pone.0226638 © 2019 Capo et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. CC-BY Research Article Text 2019 ftpubmed https://doi.org/10.1371/journal.pone.0226638 2020-01-12T01:15:44Z 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. Text Arctic Salvelinus alpinus PubMed Central (PMC) Arctic PLOS ONE 14 12 e0226638 |
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Research Article Capo, Eric Spong, Göran Norman, Sven Königsson, Helena Bartels, Pia Byström, Pär 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 |
Research Article |
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 |
Text |
author |
Capo, Eric Spong, Göran Norman, Sven Königsson, Helena Bartels, Pia Byström, Pär |
author_facet |
Capo, Eric Spong, Göran Norman, Sven Königsson, Helena Bartels, Pia Byström, Pär |
author_sort |
Capo, Eric |
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 |
publishDate |
2019 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6919618/ http://www.ncbi.nlm.nih.gov/pubmed/31851707 https://doi.org/10.1371/journal.pone.0226638 |
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Arctic |
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Arctic |
genre |
Arctic Salvelinus alpinus |
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Arctic Salvelinus alpinus |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6919618/ http://www.ncbi.nlm.nih.gov/pubmed/31851707 http://dx.doi.org/10.1371/journal.pone.0226638 |
op_rights |
© 2019 Capo et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0226638 |
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PLOS ONE |
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14 |
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12 |
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e0226638 |
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