Ayagoz Meirkhanova, Damir Ussibaliyev, Aizada Bexeitova, Ivan A. Vorobjev and Natasha S. Barteneva of Nazarbayev University, Sabina Marks of the University of Duisburg-Essen, Stella A. Berger of the Leibniz Institute of Freshwater Ecology and Inland Fisheries, and Michael Melkonian of the Max Planck Institute for Plant Breeding Research show that full-spectrum cytometry can distinguish and monitor microalgae and bacteria through their natural autofluorescence.

A new study demonstrates that full-spectrum cytometry can provide rapid, non-invasive, single-cell analysis of microalgae and pigmented bacteria by capturing detailed autofluorescence signatures from chlorophylls, carotenoids, and phycobiliproteins. The researchers showed that this approach can separate major microalgal groups, identify heterogeneity within individual cultures, and detect physiological and pigment-related changes linked to cell state and microbial interactions. The work positions spectral cytometry as a powerful tool for microbial ecology, environmental monitoring, and biotechnology.

Key findings

• Full-spectrum cytometry clearly distinguished major microalgal groups based on their pigment-related autofluorescence, especially separating taxa with and without phycobiliproteins.
• Analysis of 102 Volvocales strains revealed three distinct spectral clusters, supported by differences in cell size and shape.
• Even within monocultures, the method identified multiple autofluorescent subpopulations linked to cell division, morphology, stress, and metabolic state.
• In Gonium cultures, spectral differences between axenic and non-axenic strains suggested that bacterial associations can alter algal pigment-related fluorescence.
• In stressed Haematococcus cultures, the approach detected autofluorescence shifts consistent with carotenoid accumulation.
• Time-resolved measurements of Serratia marcescens captured fluorescence changes associated with the accumulation of the red pigment prodigiosin, showing the method’s relevance beyond algae.

Why it matters
Traditional pigment-analysis methods often rely on bulk measurements and can miss important variation between individual cells. This study shows that full-spectrum cytometry can reveal microbial diversity, physiological heterogeneity, and stress responses at single-cell resolution, making it valuable for algal biotechnology, microbial ecology, and environmental surveillance. The method could help researchers and industry monitor culture health, optimize pigment production, and better understand interactions between microorganisms in complex systems.