Chemotaxonomic and Molecular Insights into Phytoplankton Communities in Tropical Aquatic Ecosystems via MALDI FT-ICR Mass Spectrometry

Accurate identification of phytoplankton communities is essential for understanding the ecological dynamics of aquatic ecosystems. Conventional optical microscopy, while widely used, is labor-intensive and limited in its ability to resolve small-sized taxa or organisms present at low cell densities. Here, we present a rapid, one-step chemotaxonomic approach based on ultrahigh-resolution Matrix-Assisted Laser Desorption/Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (MALDI FT-ICR MS) performed on a 21 T instrument for the molecular characterization of phytoplankton assemblages. Phytoplankton samples were collected from two contrasting sites in the Ciénaga Grande de Santa Marta (CGSM)─Ciénaga La Luna and Boca de La Barra─during the dry (June) and rainy (August) seasons of 2022. The 21 T MALDI FT-ICR MS platform enabled the simultaneous detection of chlorophylls, carotenoids, and cyanobacterial secondary metabolites directly from crude solvent extracts, generating reproducible molecular fingerprints without prior chromatographic separation. Clear spatial and seasonal differences in molecular composition were observed between sampling sites and seasons, as evidenced by distinct pigment and metabolite profiles and supported by a multivariate analysis. Specific biomarkers, including chlorophyll derivatives, diagnostic carotenoids (e.g., fucoxanthin- and zeaxanthin-related compounds), and cyanobacterial metabolites, showed qualitative agreement with phytoplankton taxa identified by optical microscopy. These results demonstrate that 21 T MALDI FT-ICR MS provides a robust and time-efficient platform for resolving chemically driven differences among phytoplankton communities and for complementing traditional taxonomic identification in complex estuarine systems.