Best Practices for Optimization of Phytoplankton Analysis in Natural Waters Using <scp>CytoSense</scp> Flow Cytometers

The use of flow cytometry to investigate phytoplankton functional groups is rapidly expanding worldwide, using lab- or ship-based instruments or autonomous environmental monitoring platforms. Automation, coupled with greater autonomy, allows for higher spatial and temporal resolution of phytoplankton groups, enhancing understanding of their dynamics and patterns, generating large datasets. The level of resolution is determined by both instrumental capabilities and optimization of its acquisition settings. Sharing these datasets with the scientific community, whether to improve global phytoplankton distribution resolution or facilitate the intercomparison of environmental indicators among monitoring laboratories, strongly relies on quality-controlled instruments and standardized data acquisition and analysis. This article focuses on CytoSense-type (CytoBuoy, NL) flow cytometers, which operate by recording the optical pulse shapes of particles as they pass through a laser beam. Different configurations such as laser wavelength and power, sheath fluid management, sample inlet design, and dataset output format were not considered, in order to focus on optimization and protocol standardization to resolve the whole phytoplankton size spectrum, from the smallest autofluorescing prokaryotes to colonies and chain-forming species. In this study, coincidence, PMT voltage, trigger threshold optimization, and regular quality control procedures are considered and discussed, using datasets from three types of instruments and two contrasted marine coastal waters as case studies. The primary goal of this study is to establish a framework to guide and support the exploration and application of this type of flow cytometer, ultimately achieving a reliable and optimal resolution for sample acquisition of natural waters.

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Journal
Cytometry Part A
Published
2025-10-16
DOI
https://doi.org/10.1002/cyto.a.24964
Citations
1
Primary Topic
Marine and coastal ecosystems
Type
article
Field-Weighted Citation Impact
1.79

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article

Best Practices for Optimization of Phytoplankton Analysis in Natural Waters Using CytoSense Flow Cytometers

Thomas Rütten, Amel Bellaaj Zouari, Oliver Grosso, Hedy M. Aardema et al.
1 citations
Cytometry Part A
Marine and coastal ecosystems
1.79
article

Best Practices for Optimization of Phytoplankton Analysis in Natural Waters Using CytoSense Flow Cytometers

Thomas Rütten, Amel Bellaaj Zouari, Oliver Grosso, Hedy M. Aardema, Glaucia M. Fragoso, Mélilotus Thyssen, Arnaud Louchart, Julien Yves Rolland, G. B. J. Dubelaar, Kévin Robache, Harrie J. Kools, Luis Felipe Artigas, Arnaud Cauvin, Machteld Rijkeboer, Clémentine Gallot, Raffaella Casotti, Alexandre Epinoux, Véronique Créach, Gérald Grégori, Zéline Hubert, Lumi Haraguchi, Joanna Kolasinki, Rob Lievaart, Maialen Palazot
article en
1 citations

Abstract

The use of flow cytometry to investigate phytoplankton functional groups is rapidly expanding worldwide, using lab- or ship-based instruments or autonomous environmental monitoring platforms. Automation, coupled with greater autonomy, allows for higher spatial and temporal resolution of phytoplankton groups, enhancing understanding of their dynamics and patterns, generating large datasets. The level of resolution is determined by both instrumental capabilities and optimization of its acquisition settings. Sharing these datasets with the scientific community, whether to improve global phytoplankton distribution resolution or facilitate the intercomparison of environmental indicators among monitoring laboratories, strongly relies on quality-controlled instruments and standardized data acquisition and analysis. This article focuses on CytoSense-type (CytoBuoy, NL) flow cytometers, which operate by recording the optical pulse shapes of particles as they pass through a laser beam. Different configurations such as laser wavelength and power, sheath fluid management, sample inlet design, and dataset output format were not considered, in order to focus on optimization and protocol standardization to resolve the whole phytoplankton size spectrum, from the smallest autofluorescing prokaryotes to colonies and chain-forming species. In this study, coincidence, PMT voltage, trigger threshold optimization, and regular quality control procedures are considered and discussed, using datasets from three types of instruments and two contrasted marine coastal waters as case studies. The primary goal of this study is to establish a framework to guide and support the exploration and application of this type of flow cytometer, ultimately achieving a reliable and optimal resolution for sample acquisition of natural waters.

Cytometry Part AVol. 107(11)
Centre National de la Recherche Scientifique (FR), Centre for Environment, Fisheries and Aquaculture Science (GB), Université de Toulon (FR), Ifremer (FR), Aix-Marseille Université (FR), Roosevelt Institute for American Studies (NL), Finnish Environment Institute (FI), Stazione Zoologica Anton Dohrn (IT), ETH Zurich (CH), Middelbaar Beroeps Onderwijs (NL), Trondheim Kommune (NO), Netherlands Institute of Ecology (NL), Max Planck Institute for Chemistry (DE), Hydrobiological Institute (MK), Institut National des Sciences et Technologies de la Mer (TN), Institut Méditerranéen d’Océanologie (FR), International Commission for the Hydrology of the Rhine Basin (NL), Écologie Marine Tropicale des Océans Pacifique et Indien (RE), Laboratoire d’Océanologie et de Géosciences (FR), NTNU Samfunnsforskning (NO), Institut de Recherche pour le Développement (FR)
Aix-Marseille Université, Institut Français de Recherche pour l'Exploitation de la Mer, Université du Littoral Côte d'Opale, Flotte Océanographique Française, European Commission, Agence Nationale de la Recherche, Centre National de la Recherche Scientifique, Horizon 2020 Framework Programme
Openalex Percentile: Top 13%
Marine and coastal ecosystems
1.79
DOIOpen Access PDFOpenAlex
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