Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

Abstract Despite representing one of the largest biomes on earth, biodiversity of the deep seafloor is still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories and surveys, yet requires standardized sampling approaches and careful choice of environmental substrate. H...

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Autores principales:	Miriam I. Brandt, Florence Pradillon, Blandine Trouche, Nicolas Henry, Cathy Liautard-Haag, Marie-Anne Cambon-Bonavita, Valérie Cueff-Gauchard, Patrick Wincker, Caroline Belser, Julie Poulain, Sophie Arnaud-Haond, Daniela Zeppilli
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0bf9ae68010641a095d570d706532d9f
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spelling	oai:doaj.org-article:0bf9ae68010641a095d570d706532d9f2021-12-02T14:26:25ZEvaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA10.1038/s41598-021-86396-82045-2322https://doaj.org/article/0bf9ae68010641a095d570d706532d9f2021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86396-8https://doaj.org/toc/2045-2322Abstract Despite representing one of the largest biomes on earth, biodiversity of the deep seafloor is still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories and surveys, yet requires standardized sampling approaches and careful choice of environmental substrate. Here, we aimed to optimize the genetic assessment of prokaryote (16S), protistan (18S V4), and metazoan (18S V1–V2, COI) communities, by evaluating sampling strategies for sediment and aboveground water, deployed simultaneously at one deep-sea site. For sediment, while size-class sorting through sieving had no significant effect on total detected alpha diversity and resolved similar taxonomic compositions at the phylum level for all markers studied, it effectively increased the detection of meiofauna phyla. For water, large volumes obtained from an in situ pump (~ 6000 L) detected significantly more metazoan diversity than 7.5 L collected in sampling boxes. However, the pump being limited by larger mesh sizes (> 20 µm), only captured a fraction of microbial diversity, while sampling boxes allowed access to the pico- and nanoplankton. More importantly, communities characterized by aboveground water samples significantly differed from those characterized by sediment, whatever volume used, and both sample types only shared between 3 and 8% of molecular units. Together, these results underline that sediment sieving may be recommended when targeting metazoans, and aboveground water does not represent an alternative to sediment sampling for inventories of benthic diversity.Miriam I. BrandtFlorence PradillonBlandine TroucheNicolas HenryCathy Liautard-HaagMarie-Anne Cambon-BonavitaValérie Cueff-GauchardPatrick WinckerCaroline BelserJulie PoulainSophie Arnaud-HaondDaniela ZeppilliNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Miriam I. Brandt Florence Pradillon Blandine Trouche Nicolas Henry Cathy Liautard-Haag Marie-Anne Cambon-Bonavita Valérie Cueff-Gauchard Patrick Wincker Caroline Belser Julie Poulain Sophie Arnaud-Haond Daniela Zeppilli Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
description	Abstract Despite representing one of the largest biomes on earth, biodiversity of the deep seafloor is still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories and surveys, yet requires standardized sampling approaches and careful choice of environmental substrate. Here, we aimed to optimize the genetic assessment of prokaryote (16S), protistan (18S V4), and metazoan (18S V1–V2, COI) communities, by evaluating sampling strategies for sediment and aboveground water, deployed simultaneously at one deep-sea site. For sediment, while size-class sorting through sieving had no significant effect on total detected alpha diversity and resolved similar taxonomic compositions at the phylum level for all markers studied, it effectively increased the detection of meiofauna phyla. For water, large volumes obtained from an in situ pump (~ 6000 L) detected significantly more metazoan diversity than 7.5 L collected in sampling boxes. However, the pump being limited by larger mesh sizes (> 20 µm), only captured a fraction of microbial diversity, while sampling boxes allowed access to the pico- and nanoplankton. More importantly, communities characterized by aboveground water samples significantly differed from those characterized by sediment, whatever volume used, and both sample types only shared between 3 and 8% of molecular units. Together, these results underline that sediment sieving may be recommended when targeting metazoans, and aboveground water does not represent an alternative to sediment sampling for inventories of benthic diversity.
format	article
author	Miriam I. Brandt Florence Pradillon Blandine Trouche Nicolas Henry Cathy Liautard-Haag Marie-Anne Cambon-Bonavita Valérie Cueff-Gauchard Patrick Wincker Caroline Belser Julie Poulain Sophie Arnaud-Haond Daniela Zeppilli
author_facet	Miriam I. Brandt Florence Pradillon Blandine Trouche Nicolas Henry Cathy Liautard-Haag Marie-Anne Cambon-Bonavita Valérie Cueff-Gauchard Patrick Wincker Caroline Belser Julie Poulain Sophie Arnaud-Haond Daniela Zeppilli
author_sort	Miriam I. Brandt
title	Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
title_short	Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
title_full	Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
title_fullStr	Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
title_full_unstemmed	Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
title_sort	evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental dna
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/0bf9ae68010641a095d570d706532d9f
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Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

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