A1 Journal article (refereed)
Comparison of epifluorescence microscopy and flow cytometry in counting freshwater picophytoplankton (2021)

Salmi, P., Mäki, A., Mikkonen, A., Pupponen, V.-M., Vuorio, K., & Tiirola, M. (2021). Comparison of epifluorescence microscopy and flow cytometry in counting freshwater picophytoplankton. Boreal Environment Research, 26, 17-27. http://www.borenv.net/BER/archive/pdfs/ber26/ber26-017-027.pdf

JYU authors or editors

Publication details

All authors or editors: Salmi, Pauliina; Mäki, Anita; Mikkonen, Anu; Pupponen, Veli-Mikko; Vuorio, Kristiina; Tiirola, Marja

Journal or series: Boreal Environment Research

ISSN: 1239-6095

eISSN: 1797-2469

Publication year: 2021

Volume: 26

Pages range: 17-27

Publisher: Suomen ympäristökeskus

Publication country: Finland

Publication language: English

Persistent website address: http://www.borenv.net/BER/archive/pdfs/ber26/ber26-017-027.pdf

Research data link: http://urn.fi/URN:NBN:fi:jyu-201911084794

Publication open access: Openly available

Publication channel open access: Open Access channel

Publication is parallel published (JYX): https://jyx.jyu.fi/handle/123456789/76018


The smaller the phytoplankton, the greater effort is required to distinguish individual cells by optics-based methods. Flow cytometry is widely applied in marine picophytoplankton research, but in freshwater research its role has remained minor. We compared epifluorescence microscopy and flow cytometry in assessing the composition, abundance and cell sizes of autofluorescent picophytoplankton in epilimnia of 46 Finnish lakes. Phycocyaninrich picocyanobacteria were the most dominant. The two methods yielded comparable total picophytoplankton abundances, but the determination of cell sizes, and thus total biomasses, were on average an order of magnitude higher in the microscopy results. However, flow cytometry yielded higher cell sizes when applied on small-celled cultured algae. Our study demonstrated that both epifluorescence microscopy and flow cytometry are useful methods in assessing abundances of phycocyanin-rich and phycoerythrin-rich picocyanobacteria and eukaryotic picophytoplankton in lakes. However, accurate determination of cell size and biomass remain challenges for microscopy and especially for flow cytometry.

Keywords: plankton; cyanobacteria; microalgae; microscopy; fluorescence microscopy; biomass (ecology); calculation models

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Ministry reporting: Yes

Reporting Year: 2021

JUFO rating: 1

Last updated on 2023-03-10 at 15:16