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...
Main Authors: | , , , , , |
---|---|
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
2019
|
Subjects: | |
Online Access: | https://pub.epsilon.slu.se/17186/ https://pub.epsilon.slu.se/17186/1/e_capo_et_al_200617.pdf |
id |
ftslunivuppsala:oai:pub.epsilon.slu.se:17186 |
---|---|
record_format |
openpolar |
spelling |
ftslunivuppsala:oai:pub.epsilon.slu.se:17186 2023-05-15T14:26:26+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 Bystrom, Par 2019 application/pdf https://pub.epsilon.slu.se/17186/ https://pub.epsilon.slu.se/17186/1/e_capo_et_al_200617.pdf en eng eng https://pub.epsilon.slu.se/17186/1/e_capo_et_al_200617.pdf Capo, Eric and Spong, Göran and Norman, Sven and Königsson, Helena and Bartels, Pia and Bystrom, Par (2019). 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. PLoS ONE. 14 , e0226638 , 1-19 [Research article] Fish and Aquacultural Science Research article NonPeerReviewed 2019 ftslunivuppsala 2022-01-09T19:15:14Z 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 Arctic Salvelinus alpinus Swedish University of Agricultural Sciences (SLU): Epsilon Open Archive Arctic |
institution |
Open Polar |
collection |
Swedish University of Agricultural Sciences (SLU): Epsilon Open Archive |
op_collection_id |
ftslunivuppsala |
language |
English |
topic |
Fish and Aquacultural Science |
spellingShingle |
Fish and Aquacultural Science Capo, Eric Spong, Göran Norman, Sven Königsson, Helena Bartels, Pia Bystrom, Par 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 |
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, Göran Norman, Sven Königsson, Helena Bartels, Pia Bystrom, Par |
author_facet |
Capo, Eric Spong, Göran Norman, Sven Königsson, Helena Bartels, Pia Bystrom, Par |
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 |
publishDate |
2019 |
url |
https://pub.epsilon.slu.se/17186/ https://pub.epsilon.slu.se/17186/1/e_capo_et_al_200617.pdf |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Arctic Salvelinus alpinus |
genre_facet |
Arctic Arctic Salvelinus alpinus |
op_relation |
https://pub.epsilon.slu.se/17186/1/e_capo_et_al_200617.pdf Capo, Eric and Spong, Göran and Norman, Sven and Königsson, Helena and Bartels, Pia and Bystrom, Par (2019). 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. PLoS ONE. 14 , e0226638 , 1-19 [Research article] |
_version_ |
1766298998532997120 |