Interoperable vocabulary for marine microbial flow cytometry

Type Article
Date 2022-11-18
Language English
Author(s) Thyssen Melilotus1, Grégori Gérald1, Créach Véronique2, Lahbib Soumaya1, Dugenne Mathilde3, Aardema Hedy M.4, Artigas Luis-Felipe5, Huang Bangqin6, Barani Aude1, Beaugeard Laureen7, Bellaaj-Zouari Amel8, Beran Alfred9, Casotti Raffaella10, Del Amo Yolanda11, Denis Michel1, Dubelaar George B.J.12, Endres Sonja13, Haraguchi Lumi14, Karlson Bengt15, Lambert Christophe16, Louchart ArnaudORCID5, Marie Dominique17, Moncoiffé Gwenaëlle18, Pecqueur David19, Ribalet François20, Rijkeboer Machteld21, Silovic Tina22, Silva Ricardo23, Marro Sophie3, Sosik Heidi M.24, Sourisseau Marc25, Tarran Glen26, Van Oostende Nicolas27, Zhao Li28, Zheng Shan28
Affiliation(s) 1 : Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
2 : Centre for Environment, Fisheries and Aquaculture, Lowestoft, United Kingdom
3 : Sorbonne Université, CNRS, UMR 7093, Laboratoire d’Océanographie de Villefranche-sur-Mer (LOV), Villefranche-sur-Mer, France
4 : Department of Climate Geochemistry, Max Plank Institute for Chemistry, Mainz, Germany
5 : Université du Littoral Côte d’Opale, Université de Lille, IRD, CNRS, UMR 8187, LOG, Laboratoire d’Océanologie et de Géosciences, Wimereux, France
6 : National Observation and Research Station for the Taiwan Strait Marine Ecosystem, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
7 : Laboratoire LIENSs Littoral, Environnement et Sociétés, UMR 7266 Université de La Rochelle - CNRS, La Rochelle, France
8 : Institut National des Sciences et Technologies de la Mer, INSTM, Salammbô, Tunisia
9 : Physical Oceanography Group, National Institute of Oceanography and Applied Geophysics – OGS, Trieste, Italy
10 : Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Napoli, Italy
11 : Université de Bordeaux-CNRS, UMR 5805, Environnement"s et Paléoenvironnements Océaniques et Continentaux (EPOC), Arcachon, France
12 : Cytobuoy b.v., Woerden, Netherlands
13 : Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Project Polarstern II, Bremerhaven, Germany
14 : Marine Research Centre, Finnish Environment Institute, Helsinki, Finland
15 : Swedish Meteorological and Hydrological Institute, Oceanographic Research, Västra Frölunda, Sweden
16 : CNRS, Univ Brest, IRD, Ifremer, LEMAR, Plouzane, France
17 : Sorbonne University, UPMC Univ Paris 06, CNRS, UMR 7144, Roscoff, France
18 : National Oceanography Centre, British Oceanographic Data Centre, Liverpool, United Kingdom
19 : Sorbonne Université, CNRS, Observatoire Océanologique de Banyuls s/mer, Banyuls sur Mer, France
20 : School of Oceanography, University of Washington, Seattle, WA, United States
21 : Laboratory for Hydrobiological Analysis, Rijkswaterstaat (RWS), Lelystad, Netherlands
22 : Mercator Ocean International, Ramonville Saint - Agne, France
23 : Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP), Buenos Aires, Argentina
24 : Biology Department, Woods Hole Oceanographic Institution, Biology Department, Woods Hole, MA, United States
25 : IFREMER, DYNECO, Pelagos Laboratory, Plouzané, France
26 : Plymouth Marine Laboratory, Plymouth, United Kingdom
27 : Department of Geosciences, Princeton University, Princeton, NJ, United States
28 : Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
Source Frontiers in Marine Science (2296-7745) (Frontiers Media SA), 2022-11-18 , Vol. 9 , P. 975877. doi: 10.3389
DOI 10.3389/fmars.2022.975877
Keyword(s) flow cytometry, marine microorganisms, standardization, vocabulary, FAIR principle interoperable vocabulary for marine flow cytometry
Abstract

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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Thyssen Melilotus, Grégori Gérald, Créach Véronique, Lahbib Soumaya, Dugenne Mathilde, Aardema Hedy M., Artigas Luis-Felipe, 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 (2022). Interoperable vocabulary for marine microbial flow cytometry. Frontiers in Marine Science, 9, 975877. doi: 10.3389. Publisher's official version : https://doi.org/10.3389/fmars.2022.975877 , Open Access version : https://archimer.ifremer.fr/doc/00806/91756/