eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters

Abstract Zooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; however, the visual identification of early-stage larvae (the “missing biomass”) is difficult and laborious. Here, eDNA metabarcoding was employed to detect zooplankton specie...

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Autores principales:	Eva Garcia-Vazquez, Oriane Georges, Sara Fernandez, Alba Ardura
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b1dc8df0f2e44303b89292bc6e891a18
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spelling	oai:doaj.org-article:b1dc8df0f2e44303b89292bc6e891a182021-12-02T18:17:53ZeDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters10.1038/s41598-021-86731-z2045-2322https://doaj.org/article/b1dc8df0f2e44303b89292bc6e891a182021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86731-zhttps://doaj.org/toc/2045-2322Abstract Zooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; however, the visual identification of early-stage larvae (the “missing biomass”) is difficult and laborious. Here, eDNA metabarcoding was employed to detect zooplankton species of interest for fisheries from open and coastal waters. High-Throughput sequencing (HTS) from environmental samples using small water volumes has been proposed to detect species of interest whose DNA is the most abundant. We analyzed 6-L water samples taken from subtropical and tropical waters using Cytochrome oxidase I (COI) gene as metabarcode. In the open ocean, several commercial fish larvae and invertebrate species important in fish diet were found from metabarcodes and confirmed from individual barcoding. Comparing Atlantic, Mediterranean, Red Sea, and Pacific samples we found a lower taxonomic depth of OTU assignments in samples from tropical waters than in those from temperate ones, suggesting large gaps in reference databases for those areas; thus a higher effort of zooplankton barcoding in tropical oceans is highly recommended. This and similar simplified sampling protocols could be applied in early detection of species important for fisheries.Eva Garcia-VazquezOriane GeorgesSara FernandezAlba ArduraNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Eva Garcia-Vazquez Oriane Georges Sara Fernandez Alba Ardura eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters
description	Abstract Zooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; however, the visual identification of early-stage larvae (the “missing biomass”) is difficult and laborious. Here, eDNA metabarcoding was employed to detect zooplankton species of interest for fisheries from open and coastal waters. High-Throughput sequencing (HTS) from environmental samples using small water volumes has been proposed to detect species of interest whose DNA is the most abundant. We analyzed 6-L water samples taken from subtropical and tropical waters using Cytochrome oxidase I (COI) gene as metabarcode. In the open ocean, several commercial fish larvae and invertebrate species important in fish diet were found from metabarcodes and confirmed from individual barcoding. Comparing Atlantic, Mediterranean, Red Sea, and Pacific samples we found a lower taxonomic depth of OTU assignments in samples from tropical waters than in those from temperate ones, suggesting large gaps in reference databases for those areas; thus a higher effort of zooplankton barcoding in tropical oceans is highly recommended. This and similar simplified sampling protocols could be applied in early detection of species important for fisheries.
format	article
author	Eva Garcia-Vazquez Oriane Georges Sara Fernandez Alba Ardura
author_facet	Eva Garcia-Vazquez Oriane Georges Sara Fernandez Alba Ardura
author_sort	Eva Garcia-Vazquez
title	eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters
title_short	eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters
title_full	eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters
title_fullStr	eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters
title_full_unstemmed	eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters
title_sort	edna metabarcoding of small plankton samples to detect fish larvae and their preys from atlantic and pacific waters
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/b1dc8df0f2e44303b89292bc6e891a18
work_keys_str_mv	AT evagarciavazquez ednametabarcodingofsmallplanktonsamplestodetectfishlarvaeandtheirpreysfromatlanticandpacificwaters AT orianegeorges ednametabarcodingofsmallplanktonsamplestodetectfishlarvaeandtheirpreysfromatlanticandpacificwaters AT sarafernandez ednametabarcodingofsmallplanktonsamplestodetectfishlarvaeandtheirpreysfromatlanticandpacificwaters AT albaardura ednametabarcodingofsmallplanktonsamplestodetectfishlarvaeandtheirpreysfromatlanticandpacificwaters
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eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters

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