Robustness, sensitivity and reproducibility of eDNA metabarcoding as an environmental biomonitoring tool in coastal salmon aquaculture – An inter-laboratory study

Environmental DNA metabarcoding of benthic bacterial communities emerged as a very powerful technology to assess environmental disturbance effects of coastal salmon aquaculture. A prerequisite for the implementation of this approach into compliance monitoring regulations is its robustness and reprod...

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Autores principales:	Verena Dully, Heinrich Balliet, Larissa Frühe, Martin Däumer, Alexander Thielen, Sheena Gallie, Iain Berrill, Thorsten Stoeck
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Benthic bacterial communities eDNA metabarcoding Environmental compliance monitoring Infaunal Quality Index Macroinvertebrates Salmon aquaculture Ecology QH540-549.5
Acceso en línea:	https://doaj.org/article/e9da4ef92cda4c0f86d05f41f1570c1c
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spelling	oai:doaj.org-article:e9da4ef92cda4c0f86d05f41f1570c1c2021-12-01T04:33:28ZRobustness, sensitivity and reproducibility of eDNA metabarcoding as an environmental biomonitoring tool in coastal salmon aquaculture – An inter-laboratory study1470-160X10.1016/j.ecolind.2020.107049https://doaj.org/article/e9da4ef92cda4c0f86d05f41f1570c1c2021-02-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S1470160X20309882https://doaj.org/toc/1470-160XEnvironmental DNA metabarcoding of benthic bacterial communities emerged as a very powerful technology to assess environmental disturbance effects of coastal salmon aquaculture. A prerequisite for the implementation of this approach into compliance monitoring regulations is its robustness and reproducibility of obtained results. In the framework of regular compliance monitoring of a Scottish salmon farm, we therefore collected sediment samples along a transect from the salmon cages to reference sites in duplicates (biological replicates). Aliquots of both biological replicate samples were then processed by two different laboratories using independently the same eDNA metabarcoding protocol (technical replicates). Measures of alpha diversity and beta diversity, as well as taxonomic profiles of benthic bacterial communities were highly congruent among technical replicates, which even showed less variations then the biological replicates that were processed within each laboratory. Both technical replicate datasets identified the same bacterial indicator taxon groups and ASVs that are characteristic for the environmental quality (EQ) categories to which each of the samples was assigned based on traditional macroinvertebrate biomonitoring of the same samples. In a supervised machine learning (SML) approach, we could classify all individual samples from one technical replicate dataset into the correct EQ category using all samples of the other technical replicate dataset as a training dataset for the SML algorithm. We conclude that eDNA metabarcoding is sufficiently robust that different laboratories come to the same conclusions regarding officially regulated action criteria for environmental impact assessments in salmon aquaculture.Verena DullyHeinrich BallietLarissa FrüheMartin DäumerAlexander ThielenSheena GallieIain BerrillThorsten StoeckElsevierarticleBenthic bacterial communitieseDNA metabarcodingEnvironmental compliance monitoringInfaunal Quality IndexMacroinvertebratesSalmon aquacultureEcologyQH540-549.5ENEcological Indicators, Vol 121, Iss , Pp 107049- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Benthic bacterial communities eDNA metabarcoding Environmental compliance monitoring Infaunal Quality Index Macroinvertebrates Salmon aquaculture Ecology QH540-549.5
spellingShingle	Benthic bacterial communities eDNA metabarcoding Environmental compliance monitoring Infaunal Quality Index Macroinvertebrates Salmon aquaculture Ecology QH540-549.5 Verena Dully Heinrich Balliet Larissa Frühe Martin Däumer Alexander Thielen Sheena Gallie Iain Berrill Thorsten Stoeck Robustness, sensitivity and reproducibility of eDNA metabarcoding as an environmental biomonitoring tool in coastal salmon aquaculture – An inter-laboratory study
description	Environmental DNA metabarcoding of benthic bacterial communities emerged as a very powerful technology to assess environmental disturbance effects of coastal salmon aquaculture. A prerequisite for the implementation of this approach into compliance monitoring regulations is its robustness and reproducibility of obtained results. In the framework of regular compliance monitoring of a Scottish salmon farm, we therefore collected sediment samples along a transect from the salmon cages to reference sites in duplicates (biological replicates). Aliquots of both biological replicate samples were then processed by two different laboratories using independently the same eDNA metabarcoding protocol (technical replicates). Measures of alpha diversity and beta diversity, as well as taxonomic profiles of benthic bacterial communities were highly congruent among technical replicates, which even showed less variations then the biological replicates that were processed within each laboratory. Both technical replicate datasets identified the same bacterial indicator taxon groups and ASVs that are characteristic for the environmental quality (EQ) categories to which each of the samples was assigned based on traditional macroinvertebrate biomonitoring of the same samples. In a supervised machine learning (SML) approach, we could classify all individual samples from one technical replicate dataset into the correct EQ category using all samples of the other technical replicate dataset as a training dataset for the SML algorithm. We conclude that eDNA metabarcoding is sufficiently robust that different laboratories come to the same conclusions regarding officially regulated action criteria for environmental impact assessments in salmon aquaculture.
format	article
author	Verena Dully Heinrich Balliet Larissa Frühe Martin Däumer Alexander Thielen Sheena Gallie Iain Berrill Thorsten Stoeck
author_facet	Verena Dully Heinrich Balliet Larissa Frühe Martin Däumer Alexander Thielen Sheena Gallie Iain Berrill Thorsten Stoeck
author_sort	Verena Dully
title	Robustness, sensitivity and reproducibility of eDNA metabarcoding as an environmental biomonitoring tool in coastal salmon aquaculture – An inter-laboratory study
title_short	Robustness, sensitivity and reproducibility of eDNA metabarcoding as an environmental biomonitoring tool in coastal salmon aquaculture – An inter-laboratory study
title_full	Robustness, sensitivity and reproducibility of eDNA metabarcoding as an environmental biomonitoring tool in coastal salmon aquaculture – An inter-laboratory study
title_fullStr	Robustness, sensitivity and reproducibility of eDNA metabarcoding as an environmental biomonitoring tool in coastal salmon aquaculture – An inter-laboratory study
title_full_unstemmed	Robustness, sensitivity and reproducibility of eDNA metabarcoding as an environmental biomonitoring tool in coastal salmon aquaculture – An inter-laboratory study
title_sort	robustness, sensitivity and reproducibility of edna metabarcoding as an environmental biomonitoring tool in coastal salmon aquaculture – an inter-laboratory study
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/e9da4ef92cda4c0f86d05f41f1570c1c
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Robustness, sensitivity and reproducibility of eDNA metabarcoding as an environmental biomonitoring tool in coastal salmon aquaculture – An inter-laboratory study

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