Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons

Marine sediments are home to one of the richest species pools on Earth, but logistics and a dearth of taxonomic work-force hinders the knowledge of their biodiversity. We characterized α- and β-diversity of deep-sea assemblages from submarine canyons in the western Mediterranean using an environment...

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Autores: Guardiola, Magdalena, Uriz, María Jesús, Taberlet, Pierre, Coissac, Eric, Wangensteen Fuentes, Owen S. (Simon), Turon Barrera, Xavier
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2015
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:2445/191484
Acceso en línea:https://hdl.handle.net/2445/191484
Access Level:acceso abierto
Palabra clave:Sediments marins
ADN
Marine sediments
DNA
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spelling Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyonsGuardiola, MagdalenaUriz, María JesúsTaberlet, PierreCoissac, EricWangensteen Fuentes, Owen S. (Simon)Turon Barrera, XavierSediments marinsADNMarine sedimentsDNAMarine sediments are home to one of the richest species pools on Earth, but logistics and a dearth of taxonomic work-force hinders the knowledge of their biodiversity. We characterized α- and β-diversity of deep-sea assemblages from submarine canyons in the western Mediterranean using an environmental DNA metabarcoding. We used a new primer set targeting a short eukaryotic 18S sequence (ca. 110 bp). We applied a protocol designed to obtain extractions enriched in extracellular DNA from replicated sediment corers. With this strategy we captured information from DNA (local or deposited from the water column) that persists adsorbed to inorganic particles and buffered short-term spatial and temporal heterogeneity. We analysed replicated samples from 20 localities including 2 deep-sea canyons, 1 shallower canal, and two open slopes (depth range 100-2,250 m). We identified 1,629 MOTUs, among which the dominant groups were Metazoa (with representatives of 19 phyla), Alveolata, Stramenopiles, and Rhizaria. There was a marked small-scale heterogeneity as shown by differences in replicates within corers and within localities. The spatial variability between canyons was significant, as was the depth component in one of the canyons where it was tested. Likewise, the composition of the first layer (1 cm) of sediment was significantly different from deeper layers. We found that qualitative (presence-absence) and quantitative (relative number of reads) data showed consistent trends of differentiation between samples and geographic areas. The subset of exclusively benthic MOTUs showed similar patterns of β-diversity and community structure as the whole dataset. Separate analyses of the main metazoan phyla (in number of MOTUs) showed some differences in distribution attributable to different lifestyles. Our results highlight the differentiation that can be found even between geographically close assemblages, and sets the ground for future monitoring and conservation efforts on these bottoms of ecological and economic importance.Public Library of Science (PLoS)2022202220152022info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion26 p.application/pdfhttps://hdl.handle.net/2445/191484Articles publicats en revistes (Biologia Evolutiva, Ecologia i Ciències Ambientals)reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésReproducció del document publicat a: https://doi.org/10.1371/journal.pone.0139633PLoS One, 2015, vol. 11, num. 4, p. e0153836https://doi.org/10.1371/journal.pone.0139633cc-by (c) Guardiola, Magdalena et al., 2015https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:2445/1914842026-05-29T05:05:01Z
dc.title.none.fl_str_mv Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons
title Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons
spellingShingle Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons
Guardiola, Magdalena
Sediments marins
ADN
Marine sediments
DNA
title_short Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons
title_full Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons
title_fullStr Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons
title_full_unstemmed Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons
title_sort Deep-sea, deep-sequencing: metabarcoding extracellular DNA from sediments of marine canyons
dc.creator.none.fl_str_mv Guardiola, Magdalena
Uriz, María Jesús
Taberlet, Pierre
Coissac, Eric
Wangensteen Fuentes, Owen S. (Simon)
Turon Barrera, Xavier
author Guardiola, Magdalena
author_facet Guardiola, Magdalena
Uriz, María Jesús
Taberlet, Pierre
Coissac, Eric
Wangensteen Fuentes, Owen S. (Simon)
Turon Barrera, Xavier
author_role author
author2 Uriz, María Jesús
Taberlet, Pierre
Coissac, Eric
Wangensteen Fuentes, Owen S. (Simon)
Turon Barrera, Xavier
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Sediments marins
ADN
Marine sediments
DNA
topic Sediments marins
ADN
Marine sediments
DNA
description Marine sediments are home to one of the richest species pools on Earth, but logistics and a dearth of taxonomic work-force hinders the knowledge of their biodiversity. We characterized α- and β-diversity of deep-sea assemblages from submarine canyons in the western Mediterranean using an environmental DNA metabarcoding. We used a new primer set targeting a short eukaryotic 18S sequence (ca. 110 bp). We applied a protocol designed to obtain extractions enriched in extracellular DNA from replicated sediment corers. With this strategy we captured information from DNA (local or deposited from the water column) that persists adsorbed to inorganic particles and buffered short-term spatial and temporal heterogeneity. We analysed replicated samples from 20 localities including 2 deep-sea canyons, 1 shallower canal, and two open slopes (depth range 100-2,250 m). We identified 1,629 MOTUs, among which the dominant groups were Metazoa (with representatives of 19 phyla), Alveolata, Stramenopiles, and Rhizaria. There was a marked small-scale heterogeneity as shown by differences in replicates within corers and within localities. The spatial variability between canyons was significant, as was the depth component in one of the canyons where it was tested. Likewise, the composition of the first layer (1 cm) of sediment was significantly different from deeper layers. We found that qualitative (presence-absence) and quantitative (relative number of reads) data showed consistent trends of differentiation between samples and geographic areas. The subset of exclusively benthic MOTUs showed similar patterns of β-diversity and community structure as the whole dataset. Separate analyses of the main metazoan phyla (in number of MOTUs) showed some differences in distribution attributable to different lifestyles. Our results highlight the differentiation that can be found even between geographically close assemblages, and sets the ground for future monitoring and conservation efforts on these bottoms of ecological and economic importance.
publishDate 2015
dc.date.none.fl_str_mv 2015
2022
2022
2022
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/191484
url https://hdl.handle.net/2445/191484
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.1371/journal.pone.0139633
PLoS One, 2015, vol. 11, num. 4, p. e0153836
https://doi.org/10.1371/journal.pone.0139633
dc.rights.none.fl_str_mv cc-by (c) Guardiola, Magdalena et al., 2015
https://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc-by (c) Guardiola, Magdalena et al., 2015
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 26 p.
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science (PLoS)
publisher.none.fl_str_mv Public Library of Science (PLoS)
dc.source.none.fl_str_mv Articles publicats en revistes (Biologia Evolutiva, Ecologia i Ciències Ambientals)
reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812429

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