Quantification of Environmental DNA (eDNA) shedding and decay rates for three commercially harvested fish species and comparison between eDNA detection and trawl catches

Abstract Stock assessments are critical to inform decisions for sustainable fisheries management. Environmental DNA (eDNA) analysis is a potential tool for assessing fish biomass and populations to aid in stock assessments. To facilitate modeling of biomass based on eDNA data, shedding and decay rat...

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Autores principales:	Anish Kirtane, Daniel Wieczorek, Thomas Noji, Liza Baskin, Claire Ober, Riley Plosica, Ashley Chenoweth, Katie Lynch, Lauren Sassoubre
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	black sea bass qPCR assay eDNA decay eDNA shedding eDNA–trawl comparison winter and summer flounder qPCR assays Environmental sciences GE1-350 Microbial ecology QR100-130
Acceso en línea:	https://doaj.org/article/7c2d160944374c7ea18b62377cf4e8c6
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spelling	oai:doaj.org-article:7c2d160944374c7ea18b62377cf4e8c62021-11-23T16:15:24ZQuantification of Environmental DNA (eDNA) shedding and decay rates for three commercially harvested fish species and comparison between eDNA detection and trawl catches2637-494310.1002/edn3.236https://doaj.org/article/7c2d160944374c7ea18b62377cf4e8c62021-11-01T00:00:00Zhttps://doi.org/10.1002/edn3.236https://doaj.org/toc/2637-4943Abstract Stock assessments are critical to inform decisions for sustainable fisheries management. Environmental DNA (eDNA) analysis is a potential tool for assessing fish biomass and populations to aid in stock assessments. To facilitate modeling of biomass based on eDNA data, shedding and decay rates are needed. We designed species‐specific, probe‐based qPCR assays for three economically important fish species: black sea bass (Centropristis striata), winter flounder (Pseudopleuronectes americanus), and summer flounder (Paralichthys dentatus). Winter flounder eDNA was measured using two qPCR assays (135 and 292 bp). We report the eDNA shedding and decay rates and the associated variability from two replicate experimental systems. The eDNA decay rates were not significantly different between all species. The eDNA shedding rates between the two replicate systems were significantly different for winter flounder (135 bp assay) and summer flounder. qPCR amplicon length did not affect the eDNA decay rates for winter flounder. The three new qPCR assays were tested in environmental waters alongside traditional trawl surveys. No eDNA from BSB, WF, or SF was detected by eDNA methods, and out of 13 bottom trawls over 6 days only 1 WF, 1 SF, and 2 BSB were caught. This research presents three new, efficient qPCR assays and shows agreement between eDNA methods and trawl surveys suggesting low abundance or absence of target fish.Anish KirtaneDaniel WieczorekThomas NojiLiza BaskinClaire OberRiley PlosicaAshley ChenowethKatie LynchLauren SassoubreWileyarticleblack sea bass qPCR assayeDNA decayeDNA sheddingeDNA–trawl comparisonwinter and summer flounder qPCR assaysEnvironmental sciencesGE1-350Microbial ecologyQR100-130ENEnvironmental DNA, Vol 3, Iss 6, Pp 1142-1155 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	black sea bass qPCR assay eDNA decay eDNA shedding eDNA–trawl comparison winter and summer flounder qPCR assays Environmental sciences GE1-350 Microbial ecology QR100-130
spellingShingle	black sea bass qPCR assay eDNA decay eDNA shedding eDNA–trawl comparison winter and summer flounder qPCR assays Environmental sciences GE1-350 Microbial ecology QR100-130 Anish Kirtane Daniel Wieczorek Thomas Noji Liza Baskin Claire Ober Riley Plosica Ashley Chenoweth Katie Lynch Lauren Sassoubre Quantification of Environmental DNA (eDNA) shedding and decay rates for three commercially harvested fish species and comparison between eDNA detection and trawl catches
description	Abstract Stock assessments are critical to inform decisions for sustainable fisheries management. Environmental DNA (eDNA) analysis is a potential tool for assessing fish biomass and populations to aid in stock assessments. To facilitate modeling of biomass based on eDNA data, shedding and decay rates are needed. We designed species‐specific, probe‐based qPCR assays for three economically important fish species: black sea bass (Centropristis striata), winter flounder (Pseudopleuronectes americanus), and summer flounder (Paralichthys dentatus). Winter flounder eDNA was measured using two qPCR assays (135 and 292 bp). We report the eDNA shedding and decay rates and the associated variability from two replicate experimental systems. The eDNA decay rates were not significantly different between all species. The eDNA shedding rates between the two replicate systems were significantly different for winter flounder (135 bp assay) and summer flounder. qPCR amplicon length did not affect the eDNA decay rates for winter flounder. The three new qPCR assays were tested in environmental waters alongside traditional trawl surveys. No eDNA from BSB, WF, or SF was detected by eDNA methods, and out of 13 bottom trawls over 6 days only 1 WF, 1 SF, and 2 BSB were caught. This research presents three new, efficient qPCR assays and shows agreement between eDNA methods and trawl surveys suggesting low abundance or absence of target fish.
format	article
author	Anish Kirtane Daniel Wieczorek Thomas Noji Liza Baskin Claire Ober Riley Plosica Ashley Chenoweth Katie Lynch Lauren Sassoubre
author_facet	Anish Kirtane Daniel Wieczorek Thomas Noji Liza Baskin Claire Ober Riley Plosica Ashley Chenoweth Katie Lynch Lauren Sassoubre
author_sort	Anish Kirtane
title	Quantification of Environmental DNA (eDNA) shedding and decay rates for three commercially harvested fish species and comparison between eDNA detection and trawl catches
title_short	Quantification of Environmental DNA (eDNA) shedding and decay rates for three commercially harvested fish species and comparison between eDNA detection and trawl catches
title_full	Quantification of Environmental DNA (eDNA) shedding and decay rates for three commercially harvested fish species and comparison between eDNA detection and trawl catches
title_fullStr	Quantification of Environmental DNA (eDNA) shedding and decay rates for three commercially harvested fish species and comparison between eDNA detection and trawl catches
title_full_unstemmed	Quantification of Environmental DNA (eDNA) shedding and decay rates for three commercially harvested fish species and comparison between eDNA detection and trawl catches
title_sort	quantification of environmental dna (edna) shedding and decay rates for three commercially harvested fish species and comparison between edna detection and trawl catches
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/7c2d160944374c7ea18b62377cf4e8c6
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Quantification of Environmental DNA (eDNA) shedding and decay rates for three commercially harvested fish species and comparison between eDNA detection and trawl catches

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