Abstract
Abstract The autofluorescence of algal pigments allows for non-invasive, high-throughput characterization of microalgae at a single-cell resolution. We applied full-spectrum cytometry, imaging flow cytometry, and cell sorting to analyze the spectral and morphological diversity among major microalgal groups and 102 Chlorophyta strains. The distinct spectral signatures from chlorophylls, carotenoids, and phycobiliproteins enabled us to achieve taxonomic resolution with clear separation of phycobiliprotein-containing taxa. Furthermore, principal component analysis of Volvocales revealed three spectral clusters supported by corresponding differences in cell size and shape. Additionally, in Gonium cultures, we observed that spectral signatures in the yellow-green region were altered by bacterial presence, suggesting that interactions between algal host and bacteria affect pigment-related fluorescence. Spectral heterogeneity observed within monocultures was linked to pigment accumulation, cell size, and morphological variability. These findings establish full-spectrum cytometry as a powerful method for profiling pigment composition, physiology, and structural diversity in microalgae, with broad applications in microbial ecology, environmental monitoring, and biotechnology.