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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Frontiers Media
2023-01
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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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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 |
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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 |
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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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Ministerio de Ciencia, Innovación y Universidades (España) |
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Ministerio de Ciencia, Innovación y Universidades (España) Pernice, Massimo Gasol, Josep M. |
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Flow cytometry Marine prokaryotes DNA stain Automatization Online cytometry Conserve and sustainably use the oceans, seas and marine resources for sustainable development |
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Pernice, Massimo Gasol, Josep M. |
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Pernice, Massimo |
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Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise |
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Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise |
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Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise |
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Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise |
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Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise |
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automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise |
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Frontiers Media |
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2023-01 |
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http://hdl.handle.net/10261/289030 |
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AT pernicemassimo automatedflowcytometryasatooltoobtainafinegrainpictureofmarineprokaryotecommunitystructurealonganentireoceanographiccruise AT gasoljosepm automatedflowcytometryasatooltoobtainafinegrainpictureofmarineprokaryotecommunitystructurealonganentireoceanographiccruise |
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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 |