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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Umeå universitet, Institutionen för ekologi, miljö och geovetenskap
2019
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Online Access: | http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-173821 https://doi.org/10.1371/journal.pone.0226638 |
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ftumeauniv:oai:DiVA.org:umu-173821 2023-10-09T21:48:41+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, Goran Norman, Sven Königsson, Helena Bartels, Pia Byström, Pär 2019 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-173821 https://doi.org/10.1371/journal.pone.0226638 eng eng Umeå universitet, Institutionen för ekologi, miljö och geovetenskap Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, SLU, Umeå, Sweden Public Library of Science PLOS ONE, 2019, 14:12, orcid:0000-0001-9143-7061 http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-173821 doi:10.1371/journal.pone.0226638 PMID 31851707 ISI:000534242500053 Scopus 2-s2.0-85076717146 info:eu-repo/semantics/openAccess Fish and Aquacultural Science Fisk- och akvakulturforskning Article in journal info:eu-repo/semantics/article text 2019 ftumeauniv https://doi.org/10.1371/journal.pone.0226638 2023-09-22T13:59:11Z 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 mu m glass fiber filters and 0.45 mu m mixed cellulose ester filters was more efficient in recovering DNA than using 0.22 mu m 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 Umeå University: Publications (DiVA) Arctic PLOS ONE 14 12 e0226638 |
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collection |
Umeå University: Publications (DiVA) |
op_collection_id |
ftumeauniv |
language |
English |
topic |
Fish and Aquacultural Science Fisk- och akvakulturforskning |
spellingShingle |
Fish and Aquacultural Science Fisk- och akvakulturforskning Capo, Eric Spong, Goran 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 |
Fish and Aquacultural Science Fisk- och akvakulturforskning |
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 mu m glass fiber filters and 0.45 mu m mixed cellulose ester filters was more efficient in recovering DNA than using 0.22 mu m 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 |
Capo, Eric Spong, Goran Norman, Sven Königsson, Helena Bartels, Pia Byström, Pär |
author_facet |
Capo, Eric Spong, Goran 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 |
Umeå universitet, Institutionen för ekologi, miljö och geovetenskap |
publishDate |
2019 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-173821 https://doi.org/10.1371/journal.pone.0226638 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Salvelinus alpinus |
genre_facet |
Arctic Salvelinus alpinus |
op_relation |
PLOS ONE, 2019, 14:12, orcid:0000-0001-9143-7061 http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-173821 doi:10.1371/journal.pone.0226638 PMID 31851707 ISI:000534242500053 Scopus 2-s2.0-85076717146 |
op_rights |
info:eu-repo/semantics/openAccess |
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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