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Interoperable vocabulary for marine microbial flow cytometry

Authors :
Melilotus Thyssen
Gérald Grégori
Véronique Créach
Soumaya Lahbib
Mathilde Dugenne
Hedy M. Aardema
Luis-Felipe Artigas
Bangqin Huang
Aude Barani
Laureen Beaugeard
Amel Bellaaj-Zouari
Alfred Beran
Raffaella Casotti
Yolanda Del Amo
Michel Denis
George B.J. Dubelaar
Sonja Endres
Lumi Haraguchi
Bengt Karlson
Christophe Lambert
Arnaud Louchart
Dominique Marie
Gwenaëlle Moncoiffé
David Pecqueur
François Ribalet
Machteld Rijkeboer
Tina Silovic
Ricardo Silva
Sophie Marro
Heidi M. Sosik
Marc Sourisseau
Glen Tarran
Nicolas Van Oostende
Li Zhao
Shan Zheng
Source :
Frontiers in Marine Science, Vol 9 (2022)
Publication Year :
2022
Publisher :
Frontiers Media S.A., 2022.

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.

Details

Language :
English
ISSN :
22967745
Volume :
9
Database :
Directory of Open Access Journals
Journal :
Frontiers in Marine Science
Publication Type :
Academic Journal
Accession number :
edsdoj.3068751a7b6a4dc8984fc30ebaadad6b
Document Type :
article
Full Text :
https://doi.org/10.3389/fmars.2022.975877