Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds

The sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the increasing number of eDNA metabarcoding approaches, the ability to quantify species bi...

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Autores principales:	Cristina Di Muri, Lori Lawson Handley, Colin W. Bean, Jianlong Li, Graeme Peirson, Graham S. Sellers, Kerry Walsh, Hayley V. Watson, Ian J. Winfield, Bernd Hänfling
Formato:	article
Lenguaje:	EN
Publicado:	Pensoft Publishers 2020
Materias:	Ecology QH540-549.5
Acceso en línea:	https://doaj.org/article/df05e8017adb497c88475145e0eb8d94
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spelling	oai:doaj.org-article:df05e8017adb497c88475145e0eb8d942021-12-02T11:04:30ZRead counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds10.3897/mbmg.4.569592534-9708https://doaj.org/article/df05e8017adb497c88475145e0eb8d942020-10-01T00:00:00Zhttps://mbmg.pensoft.net/article/56959/download/pdf/https://mbmg.pensoft.net/article/56959/download/xml/https://mbmg.pensoft.net/article/56959/https://doaj.org/toc/2534-9708 The sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the increasing number of eDNA metabarcoding approaches, the ability to quantify species biomass and abundance in natural systems is still not fully understood. Previous studies have shown positive but sometimes weak correlations between abundance estimates from eDNA metabarcoding data and from conventional capture methods. As both methods have independent biases a lack of concordance is difficult to interpret. Here we tested whether read counts from eDNA metabarcoding provide accurate quantitative estimates of the absolute abundance of fish in holding ponds with known fish biomass and number of individuals. Environmental DNA samples were collected from two fishery ponds with high fish density and broad species diversity. In one pond, two different DNA capture strategies (on-site filtration with enclosed filters and three different preservation buffers versus lab filtration using open filters) were used to evaluate their performance in relation to fish community composition and biomass/abundance estimates. Fish species read counts were significantly correlated with both biomass and abundance, and this result, together with information on fish diversity, was repeatable when open or enclosed filters with different preservation buffers were used. This research demonstrates that eDNA metabarcoding provides accurate qualitative and quantitative information on fish communities in small ponds, and results are consistent between different methods of DNA capture. This method flexibility will be beneficial for future eDNA-based fish monitoring and their integration into fisheries management. Cristina Di MuriLori Lawson HandleyColin W. BeanJianlong LiGraeme PeirsonGraham S. SellersKerry WalshHayley V. WatsonIan J. WinfieldBernd HänflingPensoft PublishersarticleEcologyQH540-549.5ENMetabarcoding and Metagenomics, Vol 4, Iss , Pp 97-112 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Ecology QH540-549.5
spellingShingle	Ecology QH540-549.5 Cristina Di Muri Lori Lawson Handley Colin W. Bean Jianlong Li Graeme Peirson Graham S. Sellers Kerry Walsh Hayley V. Watson Ian J. Winfield Bernd Hänfling Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds
description	The sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the increasing number of eDNA metabarcoding approaches, the ability to quantify species biomass and abundance in natural systems is still not fully understood. Previous studies have shown positive but sometimes weak correlations between abundance estimates from eDNA metabarcoding data and from conventional capture methods. As both methods have independent biases a lack of concordance is difficult to interpret. Here we tested whether read counts from eDNA metabarcoding provide accurate quantitative estimates of the absolute abundance of fish in holding ponds with known fish biomass and number of individuals. Environmental DNA samples were collected from two fishery ponds with high fish density and broad species diversity. In one pond, two different DNA capture strategies (on-site filtration with enclosed filters and three different preservation buffers versus lab filtration using open filters) were used to evaluate their performance in relation to fish community composition and biomass/abundance estimates. Fish species read counts were significantly correlated with both biomass and abundance, and this result, together with information on fish diversity, was repeatable when open or enclosed filters with different preservation buffers were used. This research demonstrates that eDNA metabarcoding provides accurate qualitative and quantitative information on fish communities in small ponds, and results are consistent between different methods of DNA capture. This method flexibility will be beneficial for future eDNA-based fish monitoring and their integration into fisheries management.
format	article
author	Cristina Di Muri Lori Lawson Handley Colin W. Bean Jianlong Li Graeme Peirson Graham S. Sellers Kerry Walsh Hayley V. Watson Ian J. Winfield Bernd Hänfling
author_facet	Cristina Di Muri Lori Lawson Handley Colin W. Bean Jianlong Li Graeme Peirson Graham S. Sellers Kerry Walsh Hayley V. Watson Ian J. Winfield Bernd Hänfling
author_sort	Cristina Di Muri
title	Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds
title_short	Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds
title_full	Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds
title_fullStr	Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds
title_full_unstemmed	Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds
title_sort	read counts from environmental dna (edna) metabarcoding reflect fish abundance and biomass in drained ponds
publisher	Pensoft Publishers
publishDate	2020
url	https://doaj.org/article/df05e8017adb497c88475145e0eb8d94
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Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds

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