Community eDNA metabarcoding as a detection tool for documenting freshwater mussel (Unionidae) species assemblages

Abstract Documenting species occurrences and habitat occupancy of unionid mussels can often be challenging. Environmental DNA (eDNA) has been shown to be a reliable tool for detecting unionids with comparable or greater sensitivity than conventional sampling and has the added advantages of not distu...

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Autores principales:	Stephanie A. Coghlan, Charise A. Currier, Joanna Freeland, Todd J. Morris, Chris C. Wilson
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	eDNA metabarcoding species assemblages species diversity unionid mussels Environmental sciences GE1-350 Microbial ecology QR100-130
Acceso en línea:	https://doaj.org/article/c37dd1d080b24a7ab4def9b559f7e58f
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spelling	oai:doaj.org-article:c37dd1d080b24a7ab4def9b559f7e58f2021-11-23T16:15:25ZCommunity eDNA metabarcoding as a detection tool for documenting freshwater mussel (Unionidae) species assemblages2637-494310.1002/edn3.239https://doaj.org/article/c37dd1d080b24a7ab4def9b559f7e58f2021-11-01T00:00:00Zhttps://doi.org/10.1002/edn3.239https://doaj.org/toc/2637-4943Abstract Documenting species occurrences and habitat occupancy of unionid mussels can often be challenging. Environmental DNA (eDNA) has been shown to be a reliable tool for detecting unionids with comparable or greater sensitivity than conventional sampling and has the added advantages of not disturbing individuals or occupied habitats. However, single‐species eDNA assays are limited to targeting individual species of interest and are functionally blind to the presence of other species. Community eDNA assays have the potential to characterize local species assemblages simultaneously but are currently less extensively developed and implemented than single‐species eDNA testing. We tested the effectiveness of community eDNA markers to identify unionid species assemblages, using two overlapping conserved primers that target the maternal mitochondrial 16S rDNA region. Both primer sets were optimized using three mock communities and successfully amplified 62.5%–81.6% of species with largely consistent results between the primer sets. Following optimization, eDNA from water samples from 24 reference sites with known mussel communities was amplified and sequenced to quantify species richness and diversity within and among sites. Metabarcoding results from the monitoring sites largely mirrored those from the mock communities, with >80% of species detections identified by both assays. The results were broadly consistent with species data from quadrat‐based manual field surveys, although both community eDNA and conventional sampling detected some species that the other method did not. These results demonstrate that community eDNA assays using conserved primers and next‐generation sequencing have the potential to simultaneously target eDNA from multiple unionid species and provide a powerful tool for complementing or augmenting conventional field surveys to characterize and monitor unionid species assemblages.Stephanie A. CoghlanCharise A. CurrierJoanna FreelandTodd J. MorrisChris C. WilsonWileyarticleeDNA metabarcodingspecies assemblagesspecies diversityunionid musselsEnvironmental sciencesGE1-350Microbial ecologyQR100-130ENEnvironmental DNA, Vol 3, Iss 6, Pp 1172-1191 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	eDNA metabarcoding species assemblages species diversity unionid mussels Environmental sciences GE1-350 Microbial ecology QR100-130
spellingShingle	eDNA metabarcoding species assemblages species diversity unionid mussels Environmental sciences GE1-350 Microbial ecology QR100-130 Stephanie A. Coghlan Charise A. Currier Joanna Freeland Todd J. Morris Chris C. Wilson Community eDNA metabarcoding as a detection tool for documenting freshwater mussel (Unionidae) species assemblages
description	Abstract Documenting species occurrences and habitat occupancy of unionid mussels can often be challenging. Environmental DNA (eDNA) has been shown to be a reliable tool for detecting unionids with comparable or greater sensitivity than conventional sampling and has the added advantages of not disturbing individuals or occupied habitats. However, single‐species eDNA assays are limited to targeting individual species of interest and are functionally blind to the presence of other species. Community eDNA assays have the potential to characterize local species assemblages simultaneously but are currently less extensively developed and implemented than single‐species eDNA testing. We tested the effectiveness of community eDNA markers to identify unionid species assemblages, using two overlapping conserved primers that target the maternal mitochondrial 16S rDNA region. Both primer sets were optimized using three mock communities and successfully amplified 62.5%–81.6% of species with largely consistent results between the primer sets. Following optimization, eDNA from water samples from 24 reference sites with known mussel communities was amplified and sequenced to quantify species richness and diversity within and among sites. Metabarcoding results from the monitoring sites largely mirrored those from the mock communities, with >80% of species detections identified by both assays. The results were broadly consistent with species data from quadrat‐based manual field surveys, although both community eDNA and conventional sampling detected some species that the other method did not. These results demonstrate that community eDNA assays using conserved primers and next‐generation sequencing have the potential to simultaneously target eDNA from multiple unionid species and provide a powerful tool for complementing or augmenting conventional field surveys to characterize and monitor unionid species assemblages.
format	article
author	Stephanie A. Coghlan Charise A. Currier Joanna Freeland Todd J. Morris Chris C. Wilson
author_facet	Stephanie A. Coghlan Charise A. Currier Joanna Freeland Todd J. Morris Chris C. Wilson
author_sort	Stephanie A. Coghlan
title	Community eDNA metabarcoding as a detection tool for documenting freshwater mussel (Unionidae) species assemblages
title_short	Community eDNA metabarcoding as a detection tool for documenting freshwater mussel (Unionidae) species assemblages
title_full	Community eDNA metabarcoding as a detection tool for documenting freshwater mussel (Unionidae) species assemblages
title_fullStr	Community eDNA metabarcoding as a detection tool for documenting freshwater mussel (Unionidae) species assemblages
title_full_unstemmed	Community eDNA metabarcoding as a detection tool for documenting freshwater mussel (Unionidae) species assemblages
title_sort	community edna metabarcoding as a detection tool for documenting freshwater mussel (unionidae) species assemblages
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/c37dd1d080b24a7ab4def9b559f7e58f
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Community eDNA metabarcoding as a detection tool for documenting freshwater mussel (Unionidae) species assemblages

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