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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 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
[Journal article]

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Abstract

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.

Authors/Creators:Capo, Eric and Spong, Göran and Norman, Sven and Königsson, Helena and Bartels, Pia and Bystrom, Par
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
Year of publishing :2019
Volume:14
Article number:e0226638
Number of Pages:19
Publisher:PLoS
ISSN:1932-6203
Language:English
Publication Type:Journal article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Fish and Aquacultural Science
URN:NBN:urn:nbn:se:slu:epsilon-p-106443
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-106443
Additional ID:
Type of IDID
DOI10.1371/journal.pone.0226638
Web of Science (WoS)000534242500053
ID Code:17186
Faculty:S - Faculty of Forest Sciences
Department:(S) > Dept. of Wildlife, Fish and Environmental Studies
Deposited By: SLUpub Connector
Deposited On:08 Jul 2020 07:18
Metadata Last Modified:08 Jul 2020 07:18

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