Interoperable vocabulary for marine microbial flow cytometry - ARTICLE À COMITÉ DE LECTURE EN CYTOMÉTRIE EN FLUX APPLIQUÉE À L'OCÉANOGRAPHIE ET LA MICROBIOLOGIE
Journal Articles Frontiers in Marine Science Year : 2022

Interoperable vocabulary for marine microbial flow cytometry

Soumaya Lahbib
  • Function : Author
Hedy M Aardema
  • Function : Author
Bangqin Huang
  • Function : Author
Laureen Beaugeard
  • Function : Author
Alfred Beran
  • Function : Author
George B J Dubelaar
  • Function : Author
Sonja Endres
  • Function : Author
Christophe Lambert
Arnaud Louchart
  • Function : Author
Dominique Marie
  • Function : Author
  • PersonId : 965551
  • IdRef : 279090749
Gwenaëlle Moncoiffé
  • Function : Author
François Ribalet
  • Function : Author
Machteld Rijkeboer
  • Function : Author
Tina Silovic
  • Function : Author
Ricardo Silva
  • Function : Author
Sophie Marro
  • Function : Author
Heidi M Sosik
  • Function : Author
Marc Sourisseau
  • Function : Author
Glen Tarran
  • Function : Author
Nicolas van Oostende
  • Function : Author
Li Zhao
  • Function : Author
Shan Zheng
  • Function : Author

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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hal-04296915 , version 1 (22-11-2023)

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Melilotus Thyssen, Gérald Grégori, Véronique Créach, Soumaya Lahbib, Mathilde Dugenne, et al.. Interoperable vocabulary for marine microbial flow cytometry. Frontiers in Marine Science, 2022, 9 (5), ⟨10.3389/fmars.2022.975877⟩. ⟨hal-04296915⟩

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