Publication Abstract

The use of flow cytometry to collect datasets on phytoplankton functional groups is rapidly expanding worldwide, with deployments on scientific vessels, ships of opportunity, buoys, and autonomous environmental monitoring platforms. Automated flow cytometry for aquatic photosynthetic microbes offers precise quantification across the full size range of phytoplankton, combined with enhanced autonomy. Sharing these datasets with the scientific community—whether to improve global phytoplankton distribution resolution or facilitate the intercomparison of environmental indicators among monitoring laboratories—depends on quality-controlled instruments and standardised data acquisition and analysis. These flow cytometry instruments share a common principle of recording optical pulse shapes of particles as they pass through a laser beam, despite variations in configurations such as laser wavelength and power, sheath fluid management, sample inlet, and dataset output format. The characterisation of phytoplankton communities and their optical representation on cytograms has been standardised by experts, with resolution depending on the optimal configuration of the instrument in use. Here, we present best practices for optimising the settings of autonomous pulse shape-recording flow cytometers, such as those developed by CytoBuoy. We address key aspects such as particle counting limits, coincidence phenomenon, trigger threshold optimisation, and regular quality control procedures, illustrating these with datasets from two types of instruments. The primary goal of this study is to establish a framework that guides and supports the exploration and application of this type of flow cytometer, ultimately achieving a reliable and optimal resolution of sample acquisition.

Clémentine Gallot, Zéline Hubert, Lumi Haraguchi, Hedy Aardema, Luis Felipe Artigas, Amel Bellaaj Zouari, Arnaud Cauvin, Raffaella Casotti, Véronique Créach *, Georges Dubelaar, Alexandre Epinoux, Gérald Grégori, Oliver Grosso, Joanna Kolasinki, Harrie Kools,  Rob Lievaart, Arnaud P. Louchart, Glaucia Moreira Fragoso, Machteld Rijkeboer, Kévin Robache, Joseph Rolland, Thomas Rutten,  and Melilotus Thyssen.