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

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 taxonomy table and the environmental data used in this study, 10.6084/m9.figshare.12333107

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Main Authors: Puigcorbé, Viena, Ruiz-González, Clara, Masqué, Pere, Gasol, Josep M.
Other Authors: Edith Cowan University
Format: artículo biblioteca
Language:English
Published: Frontiers Media 2020-07
Subjects:Prokaryotic communities, Marine particles, Size-fractionation, In situ pumps, Oceanographic bottles, Polynyas,
Online Access:http://hdl.handle.net/10261/217552
http://dx.doi.org/10.13039/501100001798
http://dx.doi.org/10.13039/501100002809
http://dx.doi.org/10.13039/501100003329
http://dx.doi.org/10.13039/501100011033
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spelling dig-icm-es-10261-2175522021-12-28T15:36:11Z Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles Puigcorbé, Viena Ruiz-González, Clara Masqué, Pere Gasol, Josep M. Edith Cowan University Ministerio de Economía y Competitividad (España) Ministerio de Ciencia, Innovación y Universidades (España) Generalitat de Catalunya Agencia Estatal de Investigación (España) Prokaryotic communities Marine particles Size-fractionation In situ pumps Oceanographic bottles Polynyas 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 Microbes 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 communities VP 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 reviewed 2020-08-07T07:38:33Z 2020-08-07T07:38:33Z 2020-07 artículo http://purl.org/coar/resource_type/c_6501 Frontiers in Microbiology 11: 1645 (2020) CEX2019-000928-S http://hdl.handle.net/10261/217552 10.3389/fmicb.2020.01645 1664-302X http://dx.doi.org/10.13039/501100001798 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100003329 http://dx.doi.org/10.13039/501100011033 32760385 en #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 Publisher's version https://doi.org/10.3389/fmicb.2020.01645 Sí open Frontiers Media
institution ICM ES
collection DSpace
country España
countrycode ES
component Bibliográfico
access En linea
databasecode dig-icm-es
tag biblioteca
region Europa del Sur
libraryname Biblioteca del ICM España
language English
topic Prokaryotic communities
Marine particles
Size-fractionation
In situ pumps
Oceanographic bottles
Polynyas
Prokaryotic communities
Marine particles
Size-fractionation
In situ pumps
Oceanographic bottles
Polynyas
spellingShingle Prokaryotic communities
Marine particles
Size-fractionation
In situ pumps
Oceanographic bottles
Polynyas
Prokaryotic communities
Marine particles
Size-fractionation
In situ pumps
Oceanographic bottles
Polynyas
Puigcorbé, Viena
Ruiz-González, Clara
Masqué, Pere
Gasol, Josep M.
Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles
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
author2 Edith Cowan University
author_facet Edith Cowan University
Puigcorbé, Viena
Ruiz-González, Clara
Masqué, Pere
Gasol, Josep M.
format artículo
topic_facet Prokaryotic communities
Marine particles
Size-fractionation
In situ pumps
Oceanographic bottles
Polynyas
author Puigcorbé, Viena
Ruiz-González, Clara
Masqué, Pere
Gasol, Josep M.
author_sort Puigcorbé, Viena
title Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles
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
publisher Frontiers Media
publishDate 2020-07
url http://hdl.handle.net/10261/217552
http://dx.doi.org/10.13039/501100001798
http://dx.doi.org/10.13039/501100002809
http://dx.doi.org/10.13039/501100003329
http://dx.doi.org/10.13039/501100011033
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