Interoperable vocabulary for marine microbial flow cytometry
In: ISSN: 2296-7745 ; Frontiers in Marine Science ; https://hal.science/hal-04296915 ; Frontiers in Marine Science, 2022, 2022
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academicJournal
Zugriff:
This article is part of the Research Topic Best Practices in Ocean Observing ; International audience ; The recent development of biological sensors has extended marine plankton studies from conducting laboratory bench work to in vivo and real-time observations. Flow cytometry (FCM) has shed new light on marine microorganisms since the 1980s through its single-cell approach and robust detection of the smallest cells. FCM records valuable optical properties of light scattering and fluorescence from cells passing in a single file in front of a narrow-collimated light source, recording tens of thousands of cells within a few minutes. Depending on the instrument settings, the sampling strategy, and the automation level, it resolves the spatial and temporal distribution of microbial marine prokaryotes and eukaryotes. Cells are usually classified and grouped on cytograms by experts and are still lacking standards, reducing data sharing capacities. Therefore, the need to make FCM data sets FAIR (Findability, Accessibility, Interoperability, and Reusability of digital assets) is becoming critical. In this paper, we present a consensus vocabulary for the 13 most common marine microbial groups observed with FCM using blue and red-light excitation. The authors designed a common layout on two-dimensional log-transformed cytograms reinforced by a decision tree that facilitates the characterization of groups. The proposed vocabulary aims at standardising data analysis and definitions, to promote harmonisation and comparison of data between users and instruments. This represents a much-needed step towards FAIRification of flow cytometric data collected in various marine environments.
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Interoperable vocabulary for marine microbial flow cytometry
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Autor/in / Beteiligte Person: | Thyssen, Melilotus ; Grégori, Gérald ; Créach, Véronique ; Lahbib, Soumaya ; Dugenne, Mathilde ; Aardema, Hedy, M ; Huang, Bangqin ; Barani, Aude ; Beaugeard, Laureen ; Bellaaj-Zouari, Amel ; Beran, Alfred ; Casotti, Raffaella ; del Amo, Yolanda ; Denis, Michel ; Dubelaar, George, B J ; Endres, Sonja ; Haraguchi, Lumi ; Karlson, Bengt ; Lambert, Christophe ; Louchart, Arnaud ; Marie, Dominique ; Moncoiffé, Gwenaëlle ; Pecqueur, David ; Ribalet, François ; Rijkeboer, Machteld ; Silovic, Tina ; Silva, Ricardo ; Marro, Sophie ; Sosik, Heidi, M ; Sourisseau, Marc ; Tarran, Glen ; van Oostende, Nicolas ; Zhao, Li ; Zheng, Shan ; Artigas, Luis Felipe ; Institut méditerranéen d'océanologie (MIO) ; Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS) ; Centre for Environment, Fisheries and Aquaculture Science Lowestoft (CEFAS) ; Laboratoire d'océanographie de Villefranche (LOV) ; Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV) ; Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS) ; Institut National des Sciences et Technologies de la Mer Salammbô (INSTM) ; Stazione Zoologica Anton Dohrn (SZN) ; Université de Bordeaux (UB) ; Finnish Environment Institute (SYKE) ; Swedish Meteorological and Hydrological Institute (SMHI) ; Observatoire océanologique de Banyuls (OOB) ; Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS) ; Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG) ; Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD France-Nord ) ; Université du Littoral Côte d'Opale (ULCO) ; European Project: 730960, SeaDataCloud(2016) ; European Project: 654410,H2020,H2020-INFRAIA-2014-2015,JERICO-NEXT(2015) ; European Project: 871153,H2020,H2020-INFRAIA-2018-2020, JERICO-S3(2020) |
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Zeitschrift: | ISSN: 2296-7745 ; Frontiers in Marine Science ; https://hal.science/hal-04296915 ; Frontiers in Marine Science, 2022, 2022 |
Veröffentlichung: | HAL CCSD ; Frontiers Media, 2022 |
Medientyp: | academicJournal |
DOI: | 10.3389/fmars.2022.975877 |
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