Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise

Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise

12 pages, 6 figures, 1 table, supplementary material https://www.frontiersin.org/articles/10.3389/fmicb.2022.1064112/full#supplementary-material.-- Data availability statement: The datasets presented in this study can be found in online repositories. The name of the repository and accession link can be found at: SEANOE; https://doi.org/10.17882/90671

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Bibliographic Details
Main Authors: Pernice, Massimo, Gasol, Josep M.
Other Authors: Ministerio de Ciencia, Innovación y Universidades (España)
Format: artículo biblioteca
Language:English
Published: Frontiers Media 2023-01
Subjects:Flow cytometry, Marine prokaryotes, DNA stain, Automatization, Online cytometry, Conserve and sustainably use the oceans, seas and marine resources for sustainable development,
Online Access:http://hdl.handle.net/10261/289030
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id dig-icm-es-10261-289030
record_format koha
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 Flow cytometry
Marine prokaryotes
DNA stain
Automatization
Online cytometry
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
Flow cytometry
Marine prokaryotes
DNA stain
Automatization
Online cytometry
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
spellingShingle Flow cytometry
Marine prokaryotes
DNA stain
Automatization
Online cytometry
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
Flow cytometry
Marine prokaryotes
DNA stain
Automatization
Online cytometry
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
Pernice, Massimo
Gasol, Josep M.
Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise
description 12 pages, 6 figures, 1 table, supplementary material https://www.frontiersin.org/articles/10.3389/fmicb.2022.1064112/full#supplementary-material.-- Data availability statement: The datasets presented in this study can be found in online repositories. The name of the repository and accession link can be found at: SEANOE; https://doi.org/10.17882/90671
author2 Ministerio de Ciencia, Innovación y Universidades (España)
author_facet Ministerio de Ciencia, Innovación y Universidades (España)
Pernice, Massimo
Gasol, Josep M.
format artículo
topic_facet Flow cytometry
Marine prokaryotes
DNA stain
Automatization
Online cytometry
Conserve and sustainably use the oceans, seas and marine resources for sustainable development
author Pernice, Massimo
Gasol, Josep M.
author_sort Pernice, Massimo
title Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise
title_short Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise
title_full Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise
title_fullStr Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise
title_full_unstemmed Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise
title_sort automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise
publisher Frontiers Media
publishDate 2023-01
url http://hdl.handle.net/10261/289030
work_keys_str_mv AT pernicemassimo automatedflowcytometryasatooltoobtainafinegrainpictureofmarineprokaryotecommunitystructurealonganentireoceanographiccruise
AT gasoljosepm automatedflowcytometryasatooltoobtainafinegrainpictureofmarineprokaryotecommunitystructurealonganentireoceanographiccruise
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spelling dig-icm-es-10261-2890302023-02-14T08:57:46Z Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise Pernice, Massimo Gasol, Josep M. Ministerio de Ciencia, Innovación y Universidades (España) Agencia Estatal de Investigación (España) Flow cytometry Marine prokaryotes DNA stain Automatization Online cytometry Conserve and sustainably use the oceans, seas and marine resources for sustainable development 12 pages, 6 figures, 1 table, supplementary material https://www.frontiersin.org/articles/10.3389/fmicb.2022.1064112/full#supplementary-material.-- Data availability statement: The datasets presented in this study can be found in online repositories. The name of the repository and accession link can be found at: SEANOE; https://doi.org/10.17882/90671 On a standard oceanographic cruise, flow cytometry data are usually collected sparsely through a bottle-based sampling and with stations separated by kilometers leading to a fragmented view of the ecosystem; to improve the resolution of the datasets produced by this technique here it is proposed the application of an automatic method of sampling and staining. The system used consists of a flow-cytometer (Accuri-C6) connected to an automated continuous sampler (OC-300) that collects samples of marine surface waters every 15 min. We tested this system for five days during a brief Mediterranean cruise with the aim of estimating the abundance, relative size and phenotypic diversity of prokaryotes. Seawater was taken by a faucet linked to an inlet pump (ca. 5 m depth). Once the sample was taken, the Oncyt-300 stained it and sent it to the flow cytometer. A total of 366 samples were collected, effectively achieving a fine-grained scale view of microbial community composition both through space and time. A significative positive relationship was found comparing data obtained with the automatic method and 10 samples collected from the faucet but processed with the standard protocol. Abundance values retrieved varied from 3.56·105 cell mL−1 in the coastal area till 6.87 105 cell mL−1 in open waters, exceptional values were reached in the harbor area where abundances peaked to 1.28 106 cell mL−1. The measured features (abundance and size) were associated with metadata (temperature, salinity, conductivity) also taken in continuous, of which conductivity was the one that better explained the variability of abundance. A full 24 h measurement cycle was performed resulting in slightly higher median bacterial abundances values during daylight hours compared to night. Alpha diversity, calculated using computational cytometry techniques, showed a higher value in the coastal area above 41° of latitude and had a strong inverse relationship with both salinity and conductivity. This is the first time to our knowledge that the OC-300 is directly applied to the marine environment during an oceanographic cruise; due to its high-resolution, this set-up shows great potential both to cover large sampling areas, and to monitor day-night cycles in situ. The OC-300 and the cruise were funded by project MIAU (RTI2018-101025-B-I00) from the Spanish Ministry of Science and Innovation. We acknowledge project PID2021-125469NB-C31 form the same Ministry, and the generic support by the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S) Peer reviewed 2023-02-14T08:57:37Z 2023-02-14T08:57:37Z 2023-01 artículo Frontiers in Microbiology 13: 1064112 (2023) CEX2019-000928-S http://hdl.handle.net/10261/289030 10.3389/fmicb.2022.1064112 1664-302X en #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-101025-B-I00/ES/FORMACION Y CAMBIO EN LA ESTRUCTURA DE LAS COMUNIDADES MICROBIANAS MARINAS A ESCALAS TEMPORALES Y ESPACIALES CORTAS: EL PAPEL DE LAS ESPECIES DE CRECIMIENTO EXPLOSIVO/ info:eu-repo/grantAgreement/MICIUN//PID2021-125469NB-C31 Publisher's version https://doi.org/10.3389/fmicb.2022.1064112 Sí open Frontiers Media

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