Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles

10 pages, 3 figures, 2 tables, supplementary material https://www.frontiersin.org/articles/10.3389/fmicb.2020.01645/full#supplementary-material.-- Data Availability Statement. The raw sequence data have been deposited in the Figshare data repository, together with the non-rarefied OTU table, the tax...

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Autores: Puigcorbé, Viena, Ruiz-González, Clara, Masqué, Pere, Gasol, Josep M.
Tipo de documento: artigo
Estado:Versão publicada
Data de publicação:2020
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositório:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/217552
Acesso em linha:http://hdl.handle.net/10261/217552
Access Level:Acceso aberto
Palavra-chave:Prokaryotic communities
Marine particles
Size-fractionation
In situ pumps
Oceanographic bottles
Polynyas
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spelling Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic BottlesPuigcorbé, VienaRuiz-González, ClaraMasqué, PereGasol, Josep M.Prokaryotic communitiesMarine particlesSize-fractionationIn situ pumpsOceanographic bottlesPolynyas10 pages, 3 figures, 2 tables, supplementary material https://www.frontiersin.org/articles/10.3389/fmicb.2020.01645/full#supplementary-material.-- Data Availability Statement. The raw sequence data have been deposited in the Figshare data repository, together with the non-rarefied OTU table, the taxonomy table and the environmental data used in this study, 10.6084/m9.figshare.12333107Microbes associated with sinking marine particles play key roles in carbon sequestration in the ocean. The sampling of particle-attached microorganisms is often done with sediment traps or by filtration of water collected with oceanographic bottles, both involving a certain time lapse between collection and processing of samples that may result in changes in particle-attached microbial communities. Conversely, in situ water filtration through submersible pumps allows a faster storage of sampled particles, but it has rarely been used to study the associated microbial communities and has never been compared to other particle-sampling methods in terms of the recovery of particle microbial diversity. Here we compared the prokaryotic communities attached to small (1–53 μm) and large (>53 μm) particles collected from the mesopelagic zone (100–300 m) of two Antarctic polynyas using in situ pumps (ISP) and oceanographic bottles (BTL). Each sampling method retrieved largely different particle-attached communities, suggesting that they capture different kinds of particles. These device-driven differences were greater for large particles than for small particles. Overall, the ISP recovered 1.5- to 3-fold more particle-attached bacterial taxa than the BTL, and different taxonomic groups were preferentially recovered by each method. In particular, typical particle-attached groups such as Planctomycetes and Deltaproteobacteria recovered with ISP were nearly absent from BTL samples. Our results suggest that the method used to sample marine particles has a strong influence in our view of their associated microbial communitiesVP received funding from Edith Cowan University (G1003456) and from the School of Science at Edith Cowan University (G1003362) to support this work. CR-G and JG were supported by the grants CTM2015-70340-R and RTI2018-101025-B-I00 of the Spanish Ministry of Science, Innovation and Universities and by the Generalitat de Catalunya Consolidated Research Group 2017SGR/1568. PM acknowledges the support of the Generalitat de Catalunya (MERS 2017 SGR – 1588)With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)Peer reviewedFrontiers MediaEdith Cowan UniversityMinisterio de Economía y Competitividad (España)Ministerio de Ciencia, Innovación y Universidades (España)Generalitat de CatalunyaAgencia Estatal de Investigación (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202020202020info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/217552reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/CTM2015-70340-Rinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-101025-B-I00https://doi.org/10.3389/fmicb.2020.01645Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2175522026-05-22T06:33:51Z
dc.title.none.fl_str_mv Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles
title Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles
spellingShingle Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles
Puigcorbé, Viena
Prokaryotic communities
Marine particles
Size-fractionation
In situ pumps
Oceanographic bottles
Polynyas
title_short Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles
title_full Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles
title_fullStr Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles
title_full_unstemmed Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles
title_sort Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles
dc.creator.none.fl_str_mv Puigcorbé, Viena
Ruiz-González, Clara
Masqué, Pere
Gasol, Josep M.
author Puigcorbé, Viena
author_facet Puigcorbé, Viena
Ruiz-González, Clara
Masqué, Pere
Gasol, Josep M.
author_role author
author2 Ruiz-González, Clara
Masqué, Pere
Gasol, Josep M.
author2_role author
author
author
dc.contributor.none.fl_str_mv Edith Cowan University
Ministerio de Economía y Competitividad (España)
Ministerio de Ciencia, Innovación y Universidades (España)
Generalitat de Catalunya
Agencia Estatal de Investigación (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Prokaryotic communities
Marine particles
Size-fractionation
In situ pumps
Oceanographic bottles
Polynyas
topic Prokaryotic communities
Marine particles
Size-fractionation
In situ pumps
Oceanographic bottles
Polynyas
description 10 pages, 3 figures, 2 tables, supplementary material https://www.frontiersin.org/articles/10.3389/fmicb.2020.01645/full#supplementary-material.-- Data Availability Statement. The raw sequence data have been deposited in the Figshare data repository, together with the non-rarefied OTU table, the taxonomy table and the environmental data used in this study, 10.6084/m9.figshare.12333107
publishDate 2020
dc.date.none.fl_str_mv 2020
2020
2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/217552
url http://hdl.handle.net/10261/217552
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/CTM2015-70340-R
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-101025-B-I00
https://doi.org/10.3389/fmicb.2020.01645
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
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